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Bioinformatics advances, 2024

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Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.

Nishijima S, Stankevic E, Aasmets O, Schmidt TSB, Nagata N, Keller MI, Ferretti P, Juel HB, Fullam A, Robbani SM, Schudoma C, Hansen JK, Holm LA, Israelsen M, Schierwagen R, Torp N, Telzerow A, Hercog R, Kandels S, Hazenbrink DHM, Arumugam M, Bendtsen F, Brøns C, Fonvig CE, Holm JC, Nielsen T, Pedersen JS, Thiele MS, Trebicka J, Org E, Krag A, Hansen T, Kuhn M, Bork P, GALAXY and MicrobLiver Consortia

Cell, 2024

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Correction: Pancreatic cancer-initiating cell exosome message transfer into noncancer-initiating cells: the importance of CD44v6 in reprogramming.

Wang Z, Sun H, Provaznik J, Hackert T, Zöller M

Journal of experimental & clinical cancer research : CR, 2024

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Callegari A, Kueblbeck M, Morero NR, Serrano-Solano B, Ellenberg J

Nature protocols, 2024

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Höps W, Rausch T, Jendrusch M, Human Genome Structural Variation Consortium (HGSVC), Korbel JO, Sedlazeck FJ

Nature communications, 2024

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Nature communications, 2024

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bioRxiv, 2024

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Mitoferrin2 is a synthetic lethal target for chromosome 8p deleted cancers.

Krieg S, Rohde T, Rausch T, Butthof L, Wendler-Link L, Eckert C, Breuhahn K, Galy B, Korbel J, Billmann M, Breinig M, Tschaharganeh DF

Genome medicine, 2024

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Data in brief, 2024

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RNA (New York, N.Y.), 2024

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Grimes K, Jeong H, Amoah A, Xu N, Niemann J, Raeder B, Hasenfeld P, Stober C, Rausch T, Benito E, Jann JC, Nowak D, Emini R, Hoenicka M, Liebold A, Ho A, Shuai S, Geiger H, Sanders AD, Korbel JO

Nature genetics, 2024

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Foxo3 regulates cortical and medullary thymic epithelial cell homeostasis with implications in T cell development.

Ribeiro C, Ferreirinha P, Landry JJM, Macedo F, Sousa LG, Pinto R, Benes V, Alves NL

Cell death & disease, 2024

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van den Berg NI, Tramontano M, Guan R, Andrejev S, Blasche S, Kim Y, Klünemann M, Brochado AR, Kalmar L, Telzerow A, Bork P, Sevin DC, Typas A, Patil KR

bioRxiv, 2024

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Molecular profiling of axial spondyloarthritis patients reveals an association between innate and adaptive cell populations and therapeutic response to tumor necrosis factor inhibitors.

Sobral D, Fernandes AF, Bernardes M, Pinto P, Santos H, Lagoas-Gomes J, Tavares-Costa J, Silva JAP, Dias JM, Bernardo A, Gaillard JC, Armengaud J, Benes V, Domingues L, Maia S, Branco JC, Coelho AV, Pimentel-Santos FM

Biomolecules, 2024

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Ferritin heavy chain supports stability and function of the regulatory T cell lineage.

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The EMBO journal, 2024

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Escape from X inactivation is directly modulated by levels of Xist non-coding RNA.

Hauth A, Panten J, Kneuss E, Picard C, Servant N, Rall I, Pérez-Rico YA, Clerquin L, Servaas N, Villacorta L, Jung F, Luong C, Chang HY, Zaugg JB, Stegle O, Odom DT, Loda A, Heard E

bioRxiv, 2024

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Development of non-alcoholic steatohepatitis is associated with gut microbiota but not with oxysterol enzymes CH25H, EBI2, or CYP7B1 in mice.

Wyss J, Raselli T, Wyss A, Telzerow A, Rogler G, Krupka N, Yilmaz B, Schmidt TSB, Misselwitz B

BMC microbiology, 2024

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Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 - 07/2023.

Bundschuh C, Weidner N, Klein J, Rausch T, Azevedo N, Telzerow A, Mallm JP, Kim H, Steiger S, Seufert I, Börner K, Bauer K, Hübschmann D, Jost KL, Parthé S, Schnitzler P, Boutros M, Rippe K, Müller B, Bartenschlager R, Kräusslich HG, Benes V

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2024

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Stability of gut microbiome after COVID-19 vaccination in healthy and immuno-compromised individuals.

Boston RH, Guan R, Kalmar L, Beier S, Horner EC, Beristain-Covarrubias N, Yam-Puc JC, Pereyra Gerber P, Faria L, Kuroshchenkova A, Lindell AE, Blasche S, Correa-Noguera A, Elmer A, Saunders C, Bermperi A, Jose S, Kingston N, CITIID-NIHR COVID-19 BioResource Collaboration, Grigoriadou S, Staples E, Buckland MS, Lear S, Matheson NJ, Benes V, Parkinson C, Thaventhiran JE, Patil KR

Life science alliance, 2024

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Varying conjunctival immune response adaptations of house finch populations to a rapidly evolving bacterial pathogen.

Kuttiyarthu Veetil N, Henschen AE, Hawley DM, Melepat B, Dalloul RA, Beneš V, Adelman JS, Vinkler M

Frontiers in immunology, 2024

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Non-apoptotic FAS signaling controls mTOR activation and extrafollicular maturation in human B cells.

Staniek J, Kalina T, Andrieux G, Boerries M, Janowska I, Fuentes M, Díez P, Bakardjieva M, Stancikova J, Raabe J, Neumann J, Schwenk S, Arpesella L, Stuchly J, Benes V, García Valiente R, Fernández García J, Carsetti R, Piano Mortari E, Catala A, de la Calle O, Sogkas G, Neven B, Rieux-Laucat F, Magerus A, Neth O, Olbrich P, Voll RE, Alsina L, Allende LM, Gonzalez-Granado LI, Böhler C, Thiel J, Venhoff N, Lorenzetti R, Warnatz K, Unger S, Seidl M, Mielenz D, Schneider P, Ehl S, Rensing-Ehl A, Smulski CR, Rizzi M

Science immunology, 2024

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Metabolic control of germ layer proportions through regulation of Nodal and Wnt signalling.

Stapornwongkul KS, Hahn E, Palau LS, Arato K, Gritti N, Anlas K, Poliński P, Lopez OM, Eibisuya M, Trivedi V

bioRxiv, 2023

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Peripheral inflammation-induced changes in songbird brain gene expression: 3' mRNA transcriptomic approach.

Veetil NK, de Oliveira HC, Samblas MG, Divín D, Melepat B, Voukali E, Świderská Z, Krajzingrová T, Těšický M, Jung F, Beneš V, Madsen O, Vinkler M

Developmental and comparative immunology, 2023

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Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti.

Treitli SC, Hanousková P, Beneš V, Brune A, Čepička I, Hampl V

The ISME journal, 2023

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Assembly of 43 human Y chromosomes reveals extensive complexity and variation.

Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K, Human Genome Structural Variation Consortium (HGSVC), O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C

Nature, 2023

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Consistency across multi-omics layers in a drug-perturbed gut microbial community.

Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P

Molecular systems biology, 2023

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Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation.

Pikkupeura LM, Bressan RB, Guiu J, Chen Y, Maimets M, Mayer D, Schweiger PJ, Hansen SL, Maciag GJ, Larsen HL, Lõhmussaar K, Pedersen MT, Teves JMY, Bornholdt J, Benes V, Sandelin A, Jensen KB

Science advances, 2023

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Co-translational binding of importins to nascent proteins.

Seidel M, Romanov N, Obarska-Kosinska A, Becker A, Trevisan Doimo de Azevedo N, Provaznik J, Nagaraja SR, Landry JJM, Benes V, Beck M

Nature communications, 2023

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The role of repetitive sequences in repatterning of major ribosomal DNA clusters in Lepidoptera.

Dalíková M, Provazníková I, Provazník J, Grof-Tisza P, Pepi A, Nguyen P

Genome biology and evolution, 2023

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High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD.

Schwartz U, Llamazares Prada M, Pohl ST, Richter M, Tamas R, Schuler M, Keller C, Mijosek V, Muley T, Schneider MA, Quast K, Hey J, Heußel CP, Warth A, Winter H, Serçin Ö, Karmouty-Quintana H, Jyothula SS, Patel MK, Herth F, Koch I, Petrosino G, Titimeaua A, Mardin BR, Weichenhan D, Jurkowski TP, Imbusch CD, Brors B, Benes V, Jung B, Wyatt D, Stahl HF, Plass C, Jurkowska RZ

The EMBO journal, 2023

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Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia.

Beneyto-Calabuig S, Merbach AK, Kniffka JA, Antes M, Szu-Tu C, Rohde C, Waclawiczek A, Stelmach P, Gräßle S, Pervan P, Janssen M, Landry JJM, Benes V, Jauch A, Brough M, Bauer M, Besenbeck B, Felden J, Bäumer S, Hundemer M, Sauer T, Pabst C, Wickenhauser C, Angenendt L, Schliemann C, Trumpp A, Haas S, Scherer M, Raffel S, Müller-Tidow C, Velten L

Cell stem cell, 2023

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Hormone-regulated expansins: expression, localization, and cell wall biomechanics in Arabidopsis root growth.

Samalova M, Melnikava A, Elsayad K, Peaucelle A, Gahurova E, Gumulec J, Spyroglou I, Zemlyanskaya EV, Ubogoeva EV, Balkova D, Demko M, Blavet N, Alexiou P, Benes V, Mouille G, Hejatko J

Plant physiology, 2023

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Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.

Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E, Bonder MJ, Ernst A, Korbel JO

Cell genomics, 2023

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Disclosing quantitative RT-PCR raw data during manuscript submission:a call for action.

Untergasser A, Hellemans J, Pfaffl MW, Ruijter JM, van den Hoff MJB, Dragomir MP, Adamoski D, Dias SMG, Reis RM, Ferracin M, Dias-Neto E, Marsh I, Kubista M, Fabbri M, Goel A, Slabý O, Knutsen E, Chen B, Negrini M, Mimori K, Pichler M, Papatriantafyllou M, Anfossi S, Schmittgen TD, Huggett J, Bustin S, Vandesompele J, Calin GA, HEROIC (tHe initiativE gRoup On qRT dIsClosure) Consortium

Molecular oncology, 2023

doi:10.1002/1878-0261.13418.

Author correction: the NSL complex maintains nuclear architecture stability via lamin A/C acetylation.

Karoutas A, Szymanski W, Rausch T, Guhathakurta S, Rog-Zielinska EA, Peyronnet R, Seyfferth J, Chen HR, de Leeuw R, Herquel B, Kimura H, Mittler G, Kohl P, Medalia O, Korbel JO, Akhtar A

Nature cell biology, 2023

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Microbe-mediated intestinal NOD2 stimulation improves linear growth of undernourished infant mice.

Schwarzer M, Gautam UK, Makki K, Lambert A, Brabec T, Joly A, Šrůtková D, Poinsot P, Novotná T, Geoffroy S, Courtin P, Hermanová PP, Matos RC, Landry JJM, Gérard C, Bulteau AL, Hudcovic T, Kozáková H, Filipp D, Chapot-Chartier MP, Šinkora M, Peretti N, Boneca IG, Chamaillard M, Vidal H, De Vadder F, Leulier F

Science (New York, N.Y.), 2023

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LAMP2 regulates autophagy in the thymic epithelium and thymic stroma-dependent CD4 T cell development.

Rodrigues PM, Sousa LG, Perrod C, Maceiras AR, Ferreirinha P, Pombinho R, Romera-Cárdenas G, Gomez-Lazaro M, Senkara M, Pistolic J, Cabanes D, Klein L, Saftig P, Alves NL

Autophagy, 2022

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Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in C. elegans.

Fragoso-Luna A, Romero-Bueno R, Eibl M, Ayuso C, Muñoz-Jiménez C, Benes V, Cases I, Askjaer P

Genetics, 2022

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The Maleth program: Malta's first space mission discoveries on the microbiome of diabetic foot ulcers.

Gatt C, Tierney BT, Madrigal P, Mason CE, Beheshti A, Telzerow A, Benes V, Zahra G, Bonett J, Cassar K, Borg J

Heliyon, 2022

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Impact of high platelet turnover on the platelet transcriptome: results from platelet RNA-sequencing in patients with sepsis.

Nührenberg TG, Stöckle J, Marini F, Zurek M, Grüning BA, Benes V, Hein L, Neumann FJ, Stratz C, Cederqvist M, Hochholzer W

PloS one, 2022

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Small non-coding RNA Interactome Capture reveals pervasive, carbon source-dependent tRNA engagement of yeast glycolytic enzymes.

Asencio C, Schwarzl T, Sahadevan S, Hentze MW

RNA (New York, N.Y.), 2022

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DNA damage independent inhibition of NF-kB transcription by anthracyclines.

Chora AF, Pedroso D, Kyriakou E, Pejanovic N, Colaço H, Gozzelino R, Barros A, Willmann K, Velho TR, Moita C, Santos I, Pereira P, Carvalho S, Martins FB, Ferreira JA, de Almeida SF, Benes V, Anrather J, Weis S, Soares MP, Geerlof A, Neefjes J, Sattler M, Messias AC, Neves Costa A, Moita LF

eLife, 2022

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Cannabinoid receptor 2 evolutionary gene loss makes parrots more susceptible to neuroinflammation.

Divín D, Goméz Samblas M, Kuttiyarthu Veetil N, Voukali E, Świderská Z, Krajzingrová T, Těšický M, Beneš V, Elleder D, Bartoš O, Vinkler M

Proceedings. Biological sciences, 2022

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Functional analysis of structural variants in single cells using Strand-seq.

Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO

Nature biotechnology, 2022

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Interferon-driven immune dysregulation in common variable immunodeficiency-associated villous atrophy and norovirus infection.

Strohmeier V, Andrieux G, Unger S, Pascual-Reguant A, Klocperk A, Seidl M, Marques OC, Eckert M, Gräwe K, Shabani M, von Spee-Mayer C, Friedmann D, Harder I, Gutenberger S, Keller B, Proietti M, Bulashevska A, Grimbacher B, Provaznik J, Benes V, Goldacker S, Schell C, Hauser AE, Boerries M, Hasselblatt P, Warnatz K

Journal of clinical immunology, 2022

doi:10.1007/s10875-022-01379-2.

Deciphering high-resolution 3D chromatin organization via Capture Hi-C.

Hauth A, Galupa R, Servant N, Villacorta L, Hauschulz K, van Bemmel JG, Loda A, Heard E

Journal of visualized experiments : JoVE, 2022

doi:10.3791/64166.

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data.

Eliášová K, Lucas Lledó JI, Grau JH, Loudová M, Bannikova AA, Zolotareva KI, Beneš V, Hulva P, Černá Bolfíková B

Heredity, 2022

doi:10.1038/s41437-022-00567-5.

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants.

Ferretti P, Wirbel J,Maistrenko OM, Van Rossum T, Alves R, Fullam A, Akanni W, Schudoma C, Schwarz A, Thielemann R, Thomas L, Kandels S, Hercog R, Telzerow A, Letunic I, Kuhn M, Zeller G, Schmidt SBT, Bork P

bioRxiv, 2022

doi:10.1101/2022.02.16.480740.

Drivers and determinants of strain dynamics following fecal microbiota transplantation.

Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P

Nature medicine, 2022

doi:10.1038/s41591-022-01913-0.

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.

Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Human Genome Structural Variation Consortium, Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC

Cell, 2022

doi:10.1016/j.cell.2022.08.004.

Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.

Mathur L, Szalai B, Du NH, Utharala R, Ballinger M, Landry JJM, Ryckelynck M, Benes V, Saez-Rodriguez J, Merten CA

Nature communications, 2022

doi:10.1038/s41467-022-32197-0.

Targeted parallel DNA sequencing detects circulating tumor-associated variants of the mitochondrial and nuclear genomes in patients with neuroblastoma.

Riehl L, Mulaw M, Kneer K, Beer M, Beer A, Barth TF, Benes V, Schulte J, Fischer M, Debatin KM, Beltinger C

Cancer reports (Hoboken, N.J.), 2022

doi:10.1002/cnr2.1687.

Dissolved iron released from nanoscale zero-valent iron (nZVI) activates the defense system in bacterium Pseudomonas putida, leading to high tolerance to oxidative stress.

Yeap CSY, Nguyen NHA, Spanek R, Too CC, Benes V, Provaznik J, Cernik M, Sevcu A

Journal of hazardous materials, 2022

doi:10.1016/j.jhazmat.2022.129627.

Regulation of the COPII secretory machinery via focal adhesions and extracellular matrix signaling.

Jung J, Khan MM, Landry J, Halavatyi A, Machado P, Reiss M, Pepperkok R

The Journal of cell biology, 2022

doi:10.1083/jcb.202110081.

MicroRNAs and other small RNAs in Aedes aegypti saliva and salivary glands following chikungunya virus infection.

Fiorillo C, Yen PS, Colantoni A, Mariconti M, Azevedo N, Lombardo F, Failloux AB, Arcà B

Scientific reports, 2022

doi:10.1038/s41598-022-13780-3.

Neuropathic pain caused by miswiring and abnormal end organ targeting.

Gangadharan V, Zheng H, Taberner FJ, Landry J, Nees TA, Pistolic J, Agarwal N, Männich D, Benes V, Helmstaedter M, Ommer B, Lechner SG, Kuner T, Kuner R

Nature, 2022

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Identification of fibroblast progenitors in the developing thymus.

Ferreirinha P, Pinheiro R, Landry JJM, Alves NL

Development (Cambridge, England), 2022

doi:10.1242/dev.200513.

Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain.

Petrosino G, Ponte G, Volpe M, Zarrella I, Ansaloni F, Langella C, Di Cristina G, Finaurini S, Russo MT, Basu S, Musacchia F, Ristoratore F, Pavlinic D, Benes V, Ferrante MI, Albertin C, Simakov O, Gustincich S, Fiorito G, Sanges R

BMC biology, 2022

doi:10.1186/s12915-022-01303-5.

Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution.

Richter-Pechańska P, Kunz JB, Rausch T, Erarslan-Uysal B, Bornhauser B, Frismantas V, Assenov Y, Zimmermann M, Happich M, von Knebel-Doeberitz C, von Neuhoff N, Köhler R, Stanulla M, Schrappe M, Cario G, Escherich G, Kirschner-Schwabe R, Eckert C, Avigad S, Pfister SM, Muckenthaler MU, Bourquin JP, Korbel JO, Kulozik AE

Leukemia, 2022

doi:10.1038/s41375-022-01587-0.

Double-stranded RNA viruses are released from Trichomonas vaginalis inside small extracellular vesicles and modulate the exosomal cargo.

Rada P, Hrdý I, Zdrha A, Narayanasamy RK, Smutná T, Horáčková J, Harant K, Beneš V, Ong SC, Tsai CY, Luo HW, Chiu CH, Tang P, Tachezy J

Frontiers in microbiology, 2022

doi:10.3389/fmicb.2022.893692.

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.

Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T

Nature genetics, 2022

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Neutralizing antibody response against the B.1.617.2 (delta) and the B.1.1.529 (omicron) variant after a third mRNA SARS-CoV-2 vaccine dose in kidney transplant recipients.

Benning L, Morath C, Bartenschlager M, Kim H, Reineke M, Beimler J, Buylaert M, Nusshag C, Kälble F, Reichel P, Töllner M, Schaier M, Klein K, Benes V, Rausch T, Rieger S, Stich M, Tönshoff B, Weidner N, Schnitzler P, Zeier M, Süsal C, Tran TH, Bartenschlager R, Speer C

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 2022

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Structural snapshots of La Crosse virus polymerase reveal the mechanisms underlying Peribunyaviridae replication and transcription.

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Nature communications, 2022

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Glucose metabolism and aging of hematopoietic stem and progenitor cells.

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International journal of molecular sciences, 2022

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Seidel M, Becker A, Pereira F, Landry JJM, de Azevedo NTD, Fusco CM, Kaindl E, Romanov N, Baumbach J, Langer JD, Schuman EM, Patil KR, Hummer G, Benes V, Beck M

Nature communications, 2022

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A faecal microbiota signature with high specificity for pancreatic cancer.

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Gut, 2022

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gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues.

Duarte I, Carraco G, de Azevedo NTD, Benes V, Andrade RP

Scientific data, 2022

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Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.

Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA

Cell reports methods, 2022

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Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development.

Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R

Journal of experimental botany, 2022

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P23 acts as functional RBP in the macrophage inflammation response.

de Vries S, Benes V, Naarmann-de Vries IS, Rücklé C, Zarnack K, Marx G, Ostareck DH, Ostareck-Lederer A

Frontiers in molecular biosciences, 2021

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Siglec-H-deficient mice show enhanced type I IFN responses, but do not develop autoimmunity after influenza or LCMV infections.

Szumilas N, Corneth OBJ, Lehmann CHK, Schmitt H, Cunz S, Cullen JG, Chu T, Marosan A, Mócsai A, Benes V, Zehn D, Dudziak D, Hendriks RW, Nitschke L

Frontiers in immunology, 2021

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Rewired glycosylation activity promotes scarless regeneration and functional recovery in spiny mice after complete spinal cord transection.

Nogueira-Rodrigues J, Leite SC, Pinto-Costa R, Sousa SC, Luz LL, Sintra MA, Oliveira R, Monteiro AC, Pinheiro GG, Vitorino M, Silva JA, Simão S, Fernandes VE, Provazník J, Benes V, Cruz CD, Safronov BV, Magalhães A, Reis CA, Vieira J, Vieira CP, Tiscórnia G, Araújo IM, Sousa MM

Developmental cell, 2021

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Patient-derived gene and protein expression signatures of NGLY1 deficiency.

Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, Benes V, Drewes G, Snyder M, Steinmetz LM

Journal of biochemistry, 2021

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Evidence for the Association between the Intronic Haplotypes of Ionotropic Glutamate Receptors and First-Episode Schizophrenia.

Hirschfeldova K, Cerny J, Bozikova P, Kuchtiak V, Rausch T, Benes V, Spaniel F, Gregus D, Horacek J, Vyklicky L, Balik A

Journal of personalized medicine, 2021

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Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.

Triana S, Vonficht D, Jopp-Saile L, Raffel S, Lutz R, Leonce D, Antes M, Hernández-Malmierca P, Ordoñez-Rueda D, Ramasz B, Boch T, Jann JC, Nowak D, Hofmann WK, Müller-Tidow C, Hübschmann D, Alexandrov T, Benes V, Trumpp A, Paulsen M, Velten L, Haas S

Nature immunology, 2021

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Trophectoderm cell failure leads to peri-implantation lethality in Trpm7-deficient mouse embryos.

Schütz A, Richter C, Weissgerber P, Tsvilovskyy V, Hesse M, Ottenheijm R, Zimmermann F, Buchholz S, Medert R, Dlugosz S, Kuryshev V, Benes V, Flockerzi V, Fleischmann BK, Cavalié A, Freichel M

Cell reports, 2021

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The expansion of human T-bethighCD21low B cells is T cell dependent.

Keller B, Strohmeier V, Harder I, Unger S, Payne KJ, Andrieux G, Boerries M, Felixberger PT, Landry JJM, Nieters A, Rensing-Ehl A, Salzer U, Frede N, Usadel S, Elling R, Speckmann C, Hainmann I, Ralph E, Gilmour K, Wentink MWJ, van der Burg M, Kuehn HS, Rosenzweig SD, Kölsch U, von Bernuth H, Kaiser-Labusch P, Gothe F, Hambleton S, Vlagea AD, Garcia Garcia A, Alsina L, Markelj G, Avcin T, Vasconcelos J, Guedes M, Ding JY, Ku CL, Shadur B, Avery DT, Venhoff N, Thiel J, Becker H, Erazo-Borrás L, Trujillo-Vargas CM, Franco JL, Fieschi C, Okada S, Gray PE, Uzel G, Casanova JL, Fliegauf M, Grimbacher B, Eibel H, Ehl S, Voll RE, Rizzi M, Stepensky P, Benes V, Ma CS, Bossen C, Tangye SG, Warnatz K

Science immunology, 2021

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Combi-Seq: multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.

Mathur L, Szalai B, Utharala R, Ballinger M, Landry JJM, Ryckelynck M, Benes V, Saez-Rodriguez J, Merten CA

bioRxiv, 2021

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Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data.

Untergasser A, Ruijter JM, Benes V, van den Hoff MJB

BMC bioinformatics, 2021

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Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors.

Marongiu L, Landry JJM, Rausch T, Abba ML, Delecluse S, Delecluse HJ, Allgayer H

Molecular oncology, 2021

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Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.

Triana S, Stanifer ML, Metz-Zumaran C, Shahraz M, Mukenhirn M, Kee C, Serger C, Koschny R, Ordonez-Rueda D, Paulsen M, Benes V, Boulant S, Alexandrov T

Molecular Systems Biology , 2021

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3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex.

Sabinina VJ, Hossain MJ, Hériché JK, Hoess P, Nijmeijer B, Mosalaganti S, Kueblbeck M, Callegari A, Szymborska A, Beck M, Ries J, Ellenberg J

Molecular biology of the cell, 2021

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AXL inhibition in macrophages stimulates host-versus-leukemia immunity and eradicates naive and treatment resistant leukemia.

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Cancer discovery, 2021

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Genomic insights into the pathogenesis of Epstein-Barr virus-associated diffuse large B-cell lymphoma by whole-genome and targeted amplicon sequencing.

Gebauer N, Künstner A, Ketzer J, Witte HM, Rausch T, Benes V, Zimmermann J, Gebauer J, Merz H, Bernard V, Harder L, Ratjen K, Gesk S, Peter W, Busch Y, Trojok P, von Bubnoff N, Biersack H, Busch H, Feller AC

Blood cancer journal, 2021

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Lack of conserved miRNA deregulation in HPV-induced squamous cell carcinomas.

Nunvar J, Pagacova L, Vojtechova Z, Azevedo NTD, Smahelova J, Salakova M, Tachezy R

Biomolecules, 2021

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Glucocorticoids exacerbate TGFß1 mediated fibrotic signalling in lung fibroblasts by inhibition of metalloproteinase expression and activity.

Khan MM, Zukowska-Kasprzyk J, Neumann B, Halavatyi A, Tischer C, Haberkant P, Stein F, Jung F, Landry J, Lewis J, Pepperkok R

ERJ open research, 2021

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Comprehensive microRNA and transcriptomic profiling of rheumatoid arthritis monocytes: role of microRNA-146b in proinflammatory progression.

Ciechomska M, Wojtas B, Bonek K, Roszkowski L, Gluszko P, Benes V, Maslinski W

Rheumatology (Oxford, England), 2021

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USP42 protects ZNRF3/RNF43 from R-spondin-dependent clearance and inhibits Wnt signalling.

Giebel N, de Jaime-Soguero A, García Del Arco A, Landry JJM, Tietje M, Villacorta L, Benes V, Fernández-Sáiz V, Acebrón SP

EMBO reports, 2021

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FoxO1-GAB1 axis regulates homing capacity and tonic AKT activity in chronic lymphocytic leukemia.

Seda V, Vojackova E, Ondrisova L, Kostalova L, Sharma S, Loja T, Pavlasova G, Zicha D, Peskova MK, Krivanek J, Liskova K, Kren L, Benes V, Litzmanova K, Borsky M, Oppelt J, Verner J, Pospisilova S, Brychtova Y, Panovska A, Tan Z, Zhang S, Doubek M, Cerna K, Mayer J, Mraz M

Blood, 2021

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Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE

Science (New York, N.Y.), 2021

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Versatile workflow for cell-type resolved transcriptional and epigenetic profiles from cryopreserved human lung.

Llamazares Prada M, Espinet E, Mijošek V, Schwartz U, Lutsik P, Tamas R, Richter M, Behrendt A, Pohl ST, Benz NP, Muley T, Warth A, Heußel CP, Winter H, Landry JJM, Herth FJ, Mertens TC, Karmouty-Quintana H, Koch I, Benes V, Korbel JO, Waszak SM, Trumpp A, Wyatt DM, Stahl HF, Plass C, Jurkowska RZ

JCI insight, 2021

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BipA exerts temperature-dependent translational control of biofilm-associated colony morphology in Vibrio cholerae.

Del Peso Santos T, Alvarez L, Sit B, Irazoki O, Blake J, Warner BR, Warr AR, Bala A, Benes V, Waldor MK, Fredrick K, Cava F

eLife, 2021

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The Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba.

Žárský V, Klimeš V, Pačes J, Vlček Č, Hradilová M, Beneš V, Nývltová E, Hrdý I, Pyrih J, Mach J, Barlow L, Stairs CW, Eme L, Hall N, Eliáš M, Dacks JB, Roger A, Tachezy J

Molecular biology and evolution, 2021

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Molecular co-occupancy identifies transcription factor binding cooperativity in vivo.

Sönmezer C, Kleinendorst R, Imanci D, Barzaghi G, Villacorta L, Schübeler D, Benes V, Molina N, Krebs AR

Molecular cell, 2020

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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.

Blasche S, Kim Y, Mars RAT, Machado D, Maansson M, Kafkia E, Milanese A, Zeller G, Teusink B, Nielsen J, Benes V, Neves R, Sauer U, Patil KR

Nature microbiology, 2021

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Extensive OMICS resource for Sf21 and Tni cell lines.

Galik B, Landry JM, Kirkpatrick J, Fritz M, Baying B, Blake J, Haase B, Collier PG, Hercog R, Pavlinic D, Stolt-Bergner P, Besir H, Remans K, Gyenesei A, Benes V

2021

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A high throughput SEC23 functional interaction screen reveals a role for focal adhesion and extracellular matrix signalling in the regulation of COPII subunit SEC23A

Jung J, Khan MM, Landry J, Halavatyi A, Machado P, Reiss M, Pepperkok R

2021

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A mutation upstream of the rplN-rpsD ribosomal operon downregulates Bordetella pertussis virulence factor production without compromising bacterial survival within human macrophages.

Novák J, Jurnečka D, Linhartová I, Holubová J, Staněk O, Štipl D, Dienstbier A, Večerek B, Azevedo N, Provazník J, Beneš V, Šebo P

mSystems, 2020

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Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast.

Zhang Y, Kuster D, Schmidt T, Kirrmaier D, Nübel G, Ibberson D, Benes V, Hombauer H, Knop M, Jäschke A

Nature communications, 2020

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Tetracycline antibiotics induce host-dependent disease tolerance to infection.

Colaço HG, Barros A, Neves-Costa A, Seixas E, Pedroso D, Velho T, Willmann KL, Faisca P, Grabmann G, Yi HS, Shong M, Benes V, Weis S, Köcher T, Moita LF

Immunity, 2020

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TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data.

Bolognini D, Magi A, Benes V, Korbel JO, Rausch T

GigaScience, 2020

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Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae).

Těšický M, Velová H, Novotný M, Kreisinger J, Beneš V, Vinkler M

Molecular ecology, 2020

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Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods.

Courtine D, Provaznik J, Reboul J, Blanc G, Benes V, Ewbank JJ

GigaScience, 2020

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Cautionary note on contamination of reagents used for molecular detection of SARS-CoV-2.

Huggett JF, Benes V, Bustin SA, Garson JA, Harris K, Kammel M, Kubista M, McHugh TD, Moran-Gilad J, Nolan T, Pfaffl MW, Salit M, Shipley G, Vallone PM, Vandesompele J, Wittwer C, Zeichhardt H

Clinical chemistry, 2020

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M2-like macrophages dictate clinically relevant immunosuppression in metastatic ovarian cancer.

Hensler M, Kasikova L, Fiser K, Rakova J, Skapa P, Laco J, Lanickova T, Pecen L, Truxova I, Vosahlikova S, Moserova I, Praznovec I, Drochytek V, Rehackova M, Brtnicky T, Rob L, Benes V, Pistolic J, Sojka L, Ryska A, Sautes-Fridman C, Fridman WH, Galluzzi L, Spisek R, Fucikova J

Journal for ImmunoTherapy of Cancer, 2020

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A novel method to identify post-aire stages of medullary thymic epithelial cell differentiation.

Ferreirinha P, Ribeiro C, Morimoto J, Landry JJM, Matsumoto M, Meireles C, White AJ, Ohigashi I, Araújo L, Benes V, Takahama Y, Anderson G, Matsumoto M, Alves N

European journal of immunology, 2020

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In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.

Turoňová B, Sikora M, Schürmann C, Hagen WJH, Welsch S, Blanc FEC, von Bülow S, Gecht M, Bagola K, Hörner C, van Zandbergen G, Landry J, de Azevedo NTD, Mosalaganti S, Schwarz A, Covino R, Mühlebach MD, Hummer G, Krijnse Locker J, Beck M

Science (New York, N.Y.), 2020

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Trebonia kvetii gen. nov., sp. nov., an acidophilic actinobacterium, and proposal of the new actinobacterial family Treboniaceae fam. nov.

Rapoport D, Sagova-Mareckova M, Sedláček I, Provaznik J, Králová S, Pavlinic D, Benes V, Kopecky J

International Journal of Systematic and Evolutionary Microbiology, 2020

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Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors.

Erarslan-Uysal B, Kunz JB, Rausch T, Richter-Pechańska P, van Belzen IA, Frismantas V, Bornhauser B, Ordoñez-Rueada D, Paulsen M, Benes V, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Loukanov T, Gorenflo M, Waszak SM, Bourquin JP, Muckenthaler MU, Korbel JO, Kulozik AE

EMBO molecular medicine, 2020

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The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020.

dMIQE Group, Huggett JF

Clinical chemistry, 2020

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Deciphering patterns of adaptation and acclimation in the transcriptome of Phaeocystis Antarctica to changing iron conditions 1.

Rizkallah MR, Frickenhaus S, Trimborn S, Harms L, Moustafa A, Benes V, Gäbler-Schwarz S, Beszteri S

Journal of phycology, 2020

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Pseudo-RNA-binding domains mediate RNA structure specificity in Upstream of N-Ras.

Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Moojiman D, Benes V, Savitski MM, Gebauer F, Hennig J

2020

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Catalogue of stage-specific transcripts in Ixodes ricinus and their potential functions during the tick life-cycle.

Vechtova P, Fussy Z, Cegan R, Sterba J, Erhart J, Benes V, Grubhoffer L

Parasites & vectors, 2020

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Germline Elongator mutations in Sonic Hedgehog medulloblastoma.

Waszak SM, Robinson GW, Gudenas BL, Smith KS, Forget A, Kojic M, Garcia-Lopez J, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Kerssemakers J, Jäger N, Sharma T, Rausch T, Kool M, Sturm D, Jones DTW, Vasilyeva A, Tatevossian RG, Neale G, Lombard B, Loew D, Nakitandwe J, Rusch M, Bowers DC, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Eggen T, Wesenberg F, Kjaerheim K, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM

Nature, 2020

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Toll-like receptor signaling in thymic epithelium controls monocyte-derived dendritic cell recruitment and Treg generation.

Vobořil M, Brabec T, Dobeš J, Šplíchalová I, Březina J, Čepková A, Dobešová M, Aidarova A, Kubovčiak J, Tsyklauri O, Štěpánek O, Beneš V, Sedláček R, Klein L, Kolář M, Filipp D

Nature communications, 2020

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A structure-based model for the complete transcription cycle of influenza polymerase.

Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S

Cell, 2020

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MorphoSeq: full single-cell transcriptome dynamics up to gastrulation in a chordate.

Sladitschek HL, Fiuza UM, Pavlinic D, Benes V, Hufnagel L, Neveu PA

Cell, 2020

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McQ – an open-source multiplexed SARS-CoV-2 quantification platform.

Vonesch SC, Bredikhin D, Dobrev N, Villacorta L, Kleinendorst R, Cacace E, Flock J, Frank M, Jung F, Kornienko J, Mitosch K, Osuna-Lopez M, Zimmermann J, Goettig S, Hamprecht A, Kraeusslich H, Knop M, Typas A, Steinmetz LM, Benes V, Remans K, Krebs AR

medRxiv, 2020

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Loss of N-glycanase 1 alters transcriptional and translational regulation in K562 cell lines.

Mueller WF, Jakob P, Sun H, Clauder-Münster S, Ghidelli-Disse S, Ordonez D, Boesche M, Bantscheff M, Collier P, Haase B, Benes V, Paulsen M, Sehr P, Lewis J, Drewes G, Steinmetz LM

G3 (Bethesda, Md.), 2020

doi:10.1534/g3.119.401031.

Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.

Rausch T, Fritz MH, Untergasser A, Benes V

BMC genomics, 2020

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Exhausted phenotype of follicular CD8 T cells in CVID.

Klocperk A, Unger S, Friedmann D, Seidl M, Zoldan K, Pfeiffer J, Hausmann O, Benes V, Andrieux G, Boettler T, Sediva A, Bengsch B, Warnatz K

The Journal of allergy and clinical immunology, 2020

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Complex evolution of insect insulin receptors and homologous decoy receptors, and functional significance of their multiplicity.

Smýkal V, Pivarči M, Provazník J, Bazalová O, Jedlička P, Lukšan O, Horák A, Vaněčková H, Beneš V, Fiala I, Hanus R, Doležel D

Molecular biology and evolution, 2020

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Global miRNA and mRNA expression profiles identify miRNA-26a-2-3p dependent repression of IFN signature in systemic sclerosis human monocytes.

Ciechomska M, Wojtas B, Swacha M, Olesinska M, Benes V, Maslinski W

European journal of immunology, 2020

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Heme oxygenase-1 deficiency triggers exhaustion of hematopoietic stem cells.

Szade K, Zukowska M, Szade A, Nowak W, Skulimowska I, Ciesla M, Bukowska-Strakova K, Gulati GS, Kachamakova-Trojanowska N, Kusienicka A, Einwallner E, Kijowski J, Czauderna S, Esterbauer H, Benes V, Dulak J, L Weissman I, Jozkowicz A

EMBO reports, 2019

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Nature biotechnology, 2019

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Nature, 2019

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International journal of cancer, 2019

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European journal of immunology, 2019

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Karoutas A, Szymanski W, Rausch T, Guhathakurta S, Rog-Zielinska EA, Peyronnet R, Seyfferth J, Chen HR, de Leeuw R, Herquel B, Kimura H, Mittler G, Kohl P, Medalia O, Korbel JO, Akhtar A

Nature cell biology, 2019

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Sande-Melón M, Marques IJ, Galardi-Castilla M, Langa X, Pérez-López M, Botos MA, Sánchez-Iranzo H, Guzmán-Martínez G, Ferreira Francisco DM, Pavlinic D, Benes V, Bruggmann R, Mercader N

Cell reports, 2019

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Expansion of imaginal disc growth factor gene family in Diptera reflects the evolution of novel functions.

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Insects, 2019

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Apoptotic cell exclusion and bias-free single-cell selection are important quality control requirements for successful single-cell sequencing applications.

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Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2019

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VISOR: a versatile haplotype-aware structural variant simulator for short and long read sequencing.

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Bioinformatics (Oxford, England), 2019

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Microorganisms, 2019

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Distinct origin of claudin7 in early tumor endosomes affects exosome assembly.

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International journal of biological sciences, 2019

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Isolation of open chromatin identifies regulators of systemic acquired resistance.

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Nuclear factor of activated T-cells, NFATC1, governs FLT3(ITD)-driven hematopoietic stem cell transformation and a poor prognosis in AML.

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Journal of hematology & oncology, 2019

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BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.

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Small-molecule-mediated chemical knock-down of MuRF1/MuRF2 and attenuation of diaphragm dysfunction in chronic heart failure.

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The legacy of sexual ancestors in phenotypic variability, gene expression and homoeolog regulation of asexual hybrids and polyploids.

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Nature cell biology, 2019

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GemC1 governs multiciliogenesis through direct interaction and transcriptional regulation of p73.

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Aire-expressing ILC3-like cells in the lymph node display potent APC features.

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The Journal of experimental medicine, 2019

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Pancreatic cancer-initiating cell exosome message transfer into noncancer-initiating cells: the importance of CD44v6 in reprogramming.

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Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology, 2019

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JUNB, DUSP2, SGK1, SOCS1 and CREBBP are frequently mutated in T-cell/histiocyte rich large B-cell lymphoma.

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Haematologica, 2018

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MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions.

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Fluctuating light interacts with time of day and leaf development stage to reprogram gene expression.

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Plant physiology, 2019

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Antibiotics-induced monodominance of a novel gut bacterial order.

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Virome analysis reveals no association of head and neck vascular anomalies with an active viral infection.

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Alfred: Interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.

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Bioinformatics (Oxford, England), 2018

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The Response of Three Southern Ocean Phytoplankton Species to Ocean Acidification and Light Availability: A Transcriptomic Study.

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Protist, 2018

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Domestic Fowl Breed Variation in Egg White Protein Expression: Application of Proteomics and Transcriptomics

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Development, function and clinical significance of plasmacytoid dendritic cells in chronic myeloid leukemia.

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Cancer research, 2018

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The molecular signature of AML with increased ALDH activity suggests a stem cell origin.

Blume R, Rempel E, Manta L, Saeed BR, Wang W, Raffel S, Ermakova O, Eckstein V, Benes V, Trumpp A, Ho AD, Lutz C

Leukemia & lymphoma, 2018

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MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells.

Cerna K, Oppelt J, Chochola V, Musilova K, Seda V, Pavlasova G, Radova L, Arigoni M, Calogero RA, Benes V, Trbusek M, Brychtova Y, Doubek M, Mayer J, Pospisilova S, Mraz M

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Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis.

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Metagenomic analysis of gut microbial communities from a Central Asian population.

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Nature, 2018

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Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development.

Oatley M, Vargel O, Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV, Milchevskaya V, Foteva VV, Natarajan KN, Baying B, Benes V, Patil KR, Teichmann SA, Lancrin C

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Immunoregulatory Effects of Myeloid-Derived Suppressor Cell Exosomes in Mouse Model of Autoimmune Alopecia Areata.

Zöller M, Zhao K, Kutlu N, Bauer N, Provaznik J, Hackert T, Schnölzer M

Frontiers in immunology, 2018

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RNA-Sequencing from Low-Input Material in Multiple Myeloma for Application in Clinical Routine.

Seckinger A, Bähr-Ivacevic T, Benes V, Hose D

Methods in molecular biology (Clifton, N.J.), 2018

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Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart.

Cerychova R, Bohuslavova R, Papousek F, Sedmera D, Abaffy P, Benes V, Kolar F, Pavlinkova G

Cardiovascular diabetology, 2018

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Whole-body single-cell sequencing reveals transcriptional domains in the annelid larval body

Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D

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Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano.

Viver T, Orellana L, González-Torres P, Díaz S, Urdiain M, Farías ME, Benes V, Kaempfer P, Shahinpei A, Ali Amoozegar M, Amann R, Antón J, Konstantinidis KT, Rosselló-Móra R

Systematic and applied microbiology, 2018

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ToTem: a tool for variant calling pipeline optimization.

Tom N, Tom O, Malcikova J, Pavlova S, Kubesova B, Rausch T, Kolarik M, Benes V, Bystry V, Pospisilova S

BMC bioinformatics, 2018

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Extensive impact of non-antibiotic drugs on human gut bacteria.

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A

Nature, 2018

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Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis.

Bergiers I, Andrews T, Vargel Bölükbaşı Ö, Buness A, Janosz E, Lopez-Anguita N, Ganter K, Kosim K, Celen C, Itır Perçin G, Collier P, Baying B, Benes V, Hemberg M, Lancrin C

eLife, 2018

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Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers.

Kikulska A, Rausch T, Krzywinska E, Pawlak M, Wilczynski B, Benes V, Rutkowski P, Wilanowski T

BMC cancer, 2018

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A miRNA181a/NFAT5 axis links impaired T cell tolerance induction with autoimmune type 1 diabetes.

Serr I, Scherm MG, Zahm AM, Schug J, Flynn VK, Hippich M, Kälin S, Becker M, Achenbach P, Nikolaev A, Gerlach K, Liebsch N, Loretz B, Lehr CM, Kirchner B, Spornraft M, Haase B, Segars J, Küper C, Palmisano R, Waisman A, Willis RA, Kim WU, Weigmann B, Kaestner KH, Ziegler AG, Daniel C

Science translational medicine, 2018

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Phenotype inference in an Escherichia coli strain panel.

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P

eLife, 2017

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Combined methylome and transcriptome analysis during rat hepatic stellate cell activation.

Schumacher E, Götze S, Kordes C, Benes V, Häussinger D

Stem cells and development, 2017

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A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression.

Goyal A, Fiškin E, Gutschner T, Polycarpou-Schwarz M, Groß M, Neugebauer J, Gandhi M, Caudron-Herger M, Benes V, Diederichs S

Nucleic acids research, 2017

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Towards standards for human fecal sample processing in metagenomic studies.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P

Nature biotechnology, 2017

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Genetic Labeling of Nuclei-Specific Thalamocortical Neurons Reveals Putative Sensory-Modality Specific Genes.

Gezelius H, Moreno-Juan V, Mezzera C, Thakurela S, Rodríguez-Malmierca LM, Pistolic J, Benes V, Tiwari VK, López-Bendito G

Cerebral cortex (New York, N.Y. : 1991), 2017

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Potential Protective Role of Grainyhead-like Genes in the Development of Clear Cell Renal Cell Carcinoma.

Pawlak M, Kikulska A, Wrzesinski T, Rausch T, Kwias Z, Wilczynski B, Benes V, Wesoly J, Wilanowski T

Molecular carcinogenesis, 2017

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Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation.

Kole K, Komuro Y, Provaznik J, Pistolic J, Benes V, Tiesinga P, Celikel T

GigaScience, 2017

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mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.

Morgan M, Much C, DiGiacomo M, Azzi C, Ivanova I, Vitsios DM, Pistolic J, Collier P, Moreira PN, Benes V, Enright AJ, O'Carroll D

Nature, 2017

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Distribution, community composition and potential metabolic activity of bacterioplankton in an urbanized Mediterranean Sea coastal zone.

Richa K, Balestra C, Piredda R, Benes V, Borra M, Passarelli A, Margiotta F, Saggiomo M, Biffali E, Sanges R, Scanlan DJ, Casotti R

Applied and environmental microbiology, 2017

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Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Pajer P, Dresler J, Kabíckova H, Písa L, Aganov P, Fucik K, Elleder D, Hron T, Kuzelka V, Velemínsky P, Klimentova J, Fucikova A, Pejchal J, Hrabakova R, Benes V, Rausch T, Dundr P, Pilin A, Cabala R, Hubalek M, Stríbrny J, Antwerpen MH, Meyer H

Viruses, 2017

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Thymic epithelial cells require p53 to support their long-term function in thymopoiesis in mice.

Rodrigues PM, Ribeiro AR, Perrod C, Landry JJM, Araújo L, Pereira-Castro I, Benes V, Moreira A, Xavier-Ferreira H, Meireles C, Alves NL

Blood, 2017

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Single-virus droplet microfluidics for high-throughput screening of neutralizing epitopes on HIV particles.

Chaipan C, Pryszlak A, Dean H, Poignard P, Benes V, Griffiths AD, Merten CA

CELL CHEMICAL BIOLOGY, 2017

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3'uridylation controls mature microRNA turnover during CD4 T cell activation.

Gutierrez-Vazquez C, Enright AJ, Rodríguez-Galán A, Perez-García A, Collier P, Jones MR, Benes V, Mizgerd JP, Mittelbrunn M, Ramiro AR, Sanchez-Madrid F

RNA (New York, N.Y.), 2017

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Vitamin A-retinoic acid signaling regulates hematopoietic stem cell dormancy.

Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A

Cell, 2017

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Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment.

Jaruskova M, Curik N, Hercog R, Polivkova V, Motlova E, Benes V, Klamova H, Pecherkova P, Belohlavkova P, Vrbacky F, Machova Polakova K

Journal of experimental & clinical cancer research : CR, 2017

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Identification of novel follicular dendritic cell sarcoma markers, FDCSP and SRGN, by whole transcriptome sequencing.

Lorenzi L, Döring C, Rausch T, Benes V, Lonardi S, Bugatti M, Campo E, Cabeçadas J, Simonitsch-Klupp I, Borges A, Mehta J, Agostinelli C, Pileri SA, Facchetti F, Hansmann ML, Hartmann S

Oncotarget, 2017

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Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia.

Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE

Blood Cancer Journal, 2017

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Identification of MiR-21-5p as a Functional Regulator of Mesothelin Expression Using MicroRNA Capture Affinity Coupled with Next Generation Sequencing.

De Santi C, Vencken S, Blake J, Haase B, Benes V, Gemignani F, Landi S, Greene CM

PloS one, 2017

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Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells.

Franzen J, Zirkel A, Blake J, Rath B, Benes V, Papantonis A, Wagner W

Aging cell, 2016

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miRNA92a targets KLF2 and the phosphatase PTEN signaling to promote human T follicular helper precursors in T1D islet autoimmunity.

Serr I, Fürst RW, Ott VB, Scherm MG, Nikolaev A, Gökmen F, Kälin S, Zillmer S, Bunk M, Weigmann B, Kunschke N, Loretz B, Lehr CM, Kirchner B, Haase B, Pfaffl M, Waisman A, Willis RA, Ziegler AG, Daniel C

Proceedings of the National Academy of Sciences of the United States of America, 2016

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Genetic code expansion for multiprotein complex engineering.

Koehler C, Sauter PF, Wawryszyn M, Girona GE, Gupta K, Landry JJ, Fritz MH, Radic K, Hoffmann JE, Chen ZA, Zou J, Tan PS, Galik B, Junttila S, Stolt-Bergner P, Pruneri G, Gyenesei A, Schultz C, Biskup MB, Besir H, Benes V, Rappsilber J, Jechlinger M, Korbel JO, Berger I, Braese S, Lemke EA

Nature methods, 2016

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The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion.

Hollerer I, Curk T, Haase B, Benes V, Hauer C, Neu-Yilik G, Bhuvanagiri M, Hentze MW, Kulozik AE

RNA (New York, N.Y.), 2016

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The Slicer Activity of ARGONAUTE1 is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis.

Arribas-Hernández L, Marchais A, Poulsen C, Haase B, Hauptmann J, Benes V, Meister G, Brodersen P

The Plant cell, 2016

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Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein.

Much C, Auchynnikava T, Pavlinic D, Buness A, Rappsilber J, Benes V, Allshire R, O'Carroll D

PLoS genetics, 2016

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Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R

PloS one, 2016

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Next-generation sequencing-based detection of germline L1-mediated transductions.

Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO

BMC genomics, 2016

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Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P

Science (New York, N.Y.), 2016

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Highly recurrent mutations of SGK1, DUSP2 and JUNB in nodular lymphocyte predominant Hodgkin lymphoma.

Hartmann S, Schuhmacher B, Rausch T, Fuller L, Döring C, Weniger M, Lollies A, Weiser C, Thurner L, Rengstl B, Brunnberg U, Vornanen M, Pfreundschuh M, Benes V, Küppers R, Newrzela S, Hansmann ML

Leukemia, 2016

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HnRNP K-mediated translational control links NMHC IIA to erythroid enucleation.

Naarmann-de Vries IS, Brendle A, Bähr-Ivacevic T, Benes V, Ostareck DH, Ostareck-Lederer A

Journal of cell science, 2016

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Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O

Nature, 2015

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miRNAs in multiple myeloma - a survival relevant complex regulator of gene expression.

Seckinger A, Meißner T, Moreaux J, Benes V, Hillengass J, Castoldi M, Zimmermann J, Ho AD, Jauch A, Goldschmidt H, Klein B, Hose D

Oncotarget, 2015

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Epigenetic program and transcription factor circuitry of dendritic cell development.

Lin Q, Chauvistré H, Costa IG, Gusmao EG, Mitzka S, Hänzelmann S, Baying B, Klisch T, Moriggl R, Hennuy B, Smeets H, Hoffmann K, Benes V, Seré K, Zenke M

Nucleic acids research, 2015

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A novel autosomal recessive TERT T1129P mutation in a dyskeratosis congenita family leads to cellular senescence and loss of CD34+ hematopoietic stem cells not reversible by mTOR-inhibition.

Stockklausner C, Raffel S, Klermund J, Bandapalli OR, Beier F, Brümmendorf TH, Bürger F, Sauer SW, Hoffmann GF, Lorenz H, Tagliaferri L, Nowak D, Hofmann WK, Buergermeister R, Kerber C, Rausch T, Korbel JO, Luke B, Trumpp A, Kulozik AE

Aging, 2015

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De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum.

Petrella V, Aceto S, Musacchia F, Colonna V, Robinson M, Benes V, Cicotti G, Bongiorno G, Gradoni L, Volf P, Salvemini M

BMC genomics, 2015

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An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO

Nature, 2015

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Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.

Poupardin R, Schöttner K, Korbelová J, Provazník J, Doležel D, Pavlinic D, Beneš V, Koštál V

BMC genomics, 2015

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Pediatric T-lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation.

Kunz JB, Rausch T, Bandapalli OR, Eilers J, Pechanska P, Schuessele S, Assenov Y, Stütz AM, Kirschner-Schwabe R, Hof J, Eckert C, von Stackelberg A, Schrappe M, Stanulla M, Koehler R, Avigad S, Elitzur S, Handgretinger R, Benes V, Weischenfeldt J, Korbel JO, Muckenthaler MU, Kulozik AE

Haematologica, 2015

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Genomic Analysis and Isolation of RNA Polymerase II Dependent Promoters from Spodoptera frugiperda

Bleckmann M, Fritz MHY, Bhuju S, Jarek M, Schurig M, Geffers R, Benes V, Besir H, van den Heuvel J

PLOS ONE, 2015

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Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing.

Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C

BMC medical genomics, 2015

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Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A

Nature methods, 2015

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RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish.

Frese KS, Meder B, Keller A, Just S, Haas J, Vogel B, Fischer S, Backes C, Matzas M, Köhler D, Benes V, Katus HA, Rottbauer W

Journal of cell science, 2015

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Identification of cytokine-induced modulation of microRNA expression and secretion as measured by a novel microRNA specific qPCR assay.

Benes V, Collier P, Kordes C, Stolte J, Rausch T, Muckentaler MU, Häussinger D, Castoldi M

Scientific reports, 2015

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RDML-Ninja and RDMLdb for standardized exchange of qPCR data.

Ruijter JM, Lefever S, Anckaert J, Hellemans J, Pfaffl MW, Benes V, Bustin SA, Vandesompele J, Untergasser A, RDML consortium

BMC bioinformatics, 2015

doi:10.1186/s12859-015-0637-6.

Intracellular microRNA profiles form in the Xenopus laevis oocyte that may contribute to asymmetric cell division.

Sidova M, Sindelka R, Castoldi M, Benes V, Kubista M

Scientific reports, 2015

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CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

Agarwal P, Collier P, Fritz MH, Benes V, Wiklund HJ, Westermark B, Singh U

BMC genomics, 2015

doi:10.1186/s12864-015-1593-2.

Lymphocyte Gene Expression Signatures from Patients and Mouse Models of Hereditary Hemochromatosis Reveal a Function of HFE as a Negative Regulator of CD8+ T-Lymphocyte Activation and Differentiation In Vivo.

Costa M, Cruz E, Oliveira S, Benes V, Ivacevic T, Silva MJ, Vieira I, Dias F, Fonseca S, Gonçalves M, Lima M, Leitão C, Muckenthaler MU, Pinto J, Porto G

PloS one, 2015

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Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites

Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W

Clinical epigenetics, 2015

doi:10.1186/s13148-015-0057-5.

Consequences of the loss of the Grainyhead-like 1 gene for renal gene expression, regulation of blood pressure and heart rate in a mouse model.

Pawlak M, Walkowska A, Mlącki M, Pistolic J, Wrzesiński T, Benes V, Jane SM, Wesoły J, Kompanowska-Jezierska E, Wilanowski T

Acta biochimica Polonica, 2015

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Reprogramming of the ERRα and ERα Target Gene Landscape Triggers Tamoxifen Resistance in Breast Cancer.

Thewes V, Simon R, Schroeter P, Schlotter M, Anzeneder T, Büttner R, Benes V, Sauter G, Burwinkel B, Nicholson RI, Sinn HP, Schneeweiss A, Deuschle U, Zapatka M, Heck S, Lichter P

Cancer research, 2015

doi:10.1158/0008-5472.CAN-14-0652.

Geminin deletion increases the number of fetal hematopoietic stem cells by affecting the expression of key transcription factors.

Karamitros D, Patmanidi AL, Kotantaki P, Potocnik AJ, Bähr-Ivacevic T, Benes V, Lygerou Z, Kioussis D, Taraviras S

Development (Cambridge, England), 2015

doi:10.1242/dev.109454.

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P

Molecular systems biology, 2014

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The landscape of human STR variation.

Willems T, Gymrek M, Highnam G, 1000 Genomes Project Consortium, Mittelman D, Erlich Y

Genome research, 2014

doi:10.1101/gr.177774.114.

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, Würch A, Bönisch U, Günther S, Backofen R, Fleischmann BK, Schübeler D, Hein L

Nature communications, 2014

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A cisplatin-resistant head and neck cancer cell line with cytoplasmic p53(mut) exhibits ATP-binding cassette transporter upregulation and high glutathione levels.

Tonigold M, Rossmann A, Meinold M, Bette M, Märken M, Henkenius K, Bretz AC, Giel G, Cai C, Rodepeter FR, Beneš V, Grénman R, Carey TE, Lage H, Stiewe T, Neubauer A, Werner JA, Brendel C, Mandic R

Journal of cancer research and clinical oncology, 2014

doi:10.1007/s00432-014-1727-y.

CBFB - MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia.

Hájková H, Fritz M, Haškovec C, Schwarz J, Šálek C, Marková J, Krejčík ZK, Dostálová Merkerová M, Kostečka AT, Vostrý M, Fuchs O, Michalová K, Cetkovský P, Beneš V

Journal of Hematology and Oncology, 2014

doi:10.1186/s13045-014-0066-4.

Optimization of Extraction of Circulating RNAs from Plasma - Enabling Small RNA Sequencing

Spornraft M, Kirchner B, Haase B, Benes V, Pfaffl MW, Riedmaier I

PloS one, 2014

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Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

Pougach K, Voet A, Kondrashov FA, Voordeckers K, Christiaens JF, Baying B, Benes V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen KJ

Nature communications, 2014

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On the current status of Phakopsora pachyrhizi genome sequencing

Loehrer M, Vogel A, Huettel B, Reinhardt R, Benes V, Duplessis S, Usadel B, Schaffrath U

Frontiers in plant science, 2014

doi:10.3389/fpls.2014.00377.

Telomerase stimulates ribosomal DNA transcription under hyperproliferative conditions

Gonzalez OG, Assfalg R, Koch S, Schelling A, Meena JK, Kraus J, Lechel A, Katz SF, Benes V, Scharffetter-Kochanek K, Kestler HA, Günes C, Iben S

Nature communications, 2014

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TGFβ pathway activation blocks the endothelial to hematopoietic transition.

Vargel O, Zhang Y, Collier P, Baying B, Benes V, Lancrin C

EXPERIMENTAL HEMATOLOGY, 2014

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Identification of novel sequence variations in microRNAs in chronic lymphocytic leukemia.

Kminkova J, Mraz M, Zaprazna K, Navrkalova V, Tichy B, Plevova K, Malcikova J, Cerna K, Rausch T, Benes V, Brychtova Y, Doubek M, Mayer J, Pospisilova S

Carcinogenesis, 2014

doi:10.1093/carcin/bgt396.

Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk loci by structural variation

Blake J, Riddell A, Theiss S, Gonzalez AP, Haase B, Jauch A, Janssen JW, Ibberson D, Pavlinic D, Moog U, Benes V, Runz H

PloS one, 2014

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Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM

Molecular systems biology, 2014

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SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor

Paakinaho V, Kaikkonen S, Makkonen H, Benes V, Palvimo JJ

Nucleic acids research, 2013

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Accounting for technical noise in single-cell RNA-seq experiments

Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG

Nature methods, 2013

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The need for transparency and good practices in the qPCR literature

Bustin SA, Benes V, Garson J, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley G, Wittwer CT, Schjerling P, Day PJ, Abreu M, Aguado B, Beaulieu JF, Beckers A, Bogaert S, Browne JA, Carrasco-Ramiro F, Ceelen L, Ciborowski K, Cornillie P, Coulon S, Cuypers A, De Brouwer S, De Ceuninck L, De Craene J, De Naeyer H, De Spiegelaere W, Deckers K, Dheedene A, Durinck K, Ferreira-Teixeira M, Fieuw A, Gallup JM, Gonzalo-Flores S, Goossens K, Heindryckx F, Herring E, Hoenicka H, Icardi L, Jaggi R, Javad F, Karampelias M, Kibenge F, Kibenge M, Kumps C, Lambertz I, Lammens T, Markey A, Messiaen P, Mets E, Morais S, Mudarra-Rubio A, Nakiwala J, Nelis H, Olsvik PA, Pérez-Novo C, Plusquin M, Remans T, Rihani A, Rodrigues-Santos P, Rondou P, Sanders R, Schmidt-Bleek K, Skovgaard K, Smeets K, Tabera L, Toegel S, Van Acker T, Van den Broeck W, Van der Meulen J, Van Gele M, Van Peer G, Van Poucke M, Van Roy N, Vergult S, Wauman J, Tshuikina-Wiklander M, Willems E, Zaccara S, Zeka F, Vandesompele J

Nature methods, 2013

doi:10.1038/nmeth.2697.

Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation

Frühmesser A, Blake J, Haberlandt E, Baying B, Raeder B, Runz H, Spreiz A, Fauth C, Benes V, Utermann G, Zschocke J, Kotzot D

European journal of human genetics : EJHG, 2013

doi:10.1038/ejhg.2013.18.

Primate genome architecture influences structural variation mechanisms and functional consequences

Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO

Proceedings of the National Academy of Sciences of the United States of America, 2013

doi:10.1073/pnas.1305904110.

An efficient method for genome-wide polyadenylation site mapping and RNA quantification (vol 41, pg e65, 2013)

Wilkening S, Pelechano V, Jarvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM

NUCLEIC ACIDS RESEARCH, 2013

doi:10.1093/nar/gkt364.

The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments

Huggett JF, Foy CA, Benes V, Emslie K, Garson JA, Haynes R, Hellemans J, Kubista M, Mueller RD, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT, Bustin SA

Clinical chemistry, 2013

doi:10.1373/clinchem.2013.206375.

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis

Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D

Molecular cell, 2013

doi:10.1016/j.molcel.2013.04.026.

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

Wilkening S, Pelechano V, Järvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM

Nucleic acids research, 2013

doi:10.1093/nar/gks1249.

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

Weischenfeldt J, Simon R, Feuerbach L, Schlangen K, Weichenhan D, Minner S, Wuttig D, Warnatz HJ, Stehr H, Rausch T, Jäger N, Gu L, Bogatyrova O, Stütz AM, Claus R, Eils J, Eils R, Gerhäuser C, Huang PH, Hutter B, Kabbe R, Lawerenz C, Radomski S, Bartholomae CC, Fälth M, Gade S, Schmidt M, Amschler N, Haß T, Galal R, Gjoni J, Kuner R, Baer C, Masser S, von Kalle C, Zichner T, Benes V, Raeder B, Mader M, Amstislavskiy V, Avci M, Lehrach H, Parkhomchuk D, Sultan M, Burkhardt L, Graefen M, Huland H, Kluth M, Krohn A, Sirma H, Stumm L, Steurer S, Grupp K, Sültmann H, Sauter G, Plass C, Brors B, Yaspo ML, Korbel JO, Schlomm T

Cancer cell, 2013

doi:10.1016/j.ccr.2013.01.002.

Actin-binding protein regulation by microRNAs as a novel microbial strategy to modulate phagocytosis by host cells: the case of N-Wasp and miR-142-3p

Bettencourt P, Marion S, Pires D, Santos LF, Lastrucci C, Carmo N, Blake J, Benes V, Griffiths G, Neyrolles O, Lugo-Villarino G, Anes E

Frontiers in cellular and infection microbiology, 2013

doi:10.3389/fcimb.2013.00019.

Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin

Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G

Molecular cell, 2012

doi:10.1016/j.molcel.2012.08.021.

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer

Paris O, Ferraro L, Grober OM, Ravo M, De Filippo MR, Giurato G, Nassa G, Tarallo R, Cantarella C, Rizzo F, Di Benedetto A, Mottolese M, Benes V, Ambrosino C, Nola E, Weisz A

Oncogene, 2012

doi:10.1038/onc.2011.583.

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO

Bioinformatics (Oxford, England), 2012

doi:10.1093/bioinformatics/bts378.

A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing

Xiol J, Cora E, Koglgruber R, Chuma S, Subramanian S, Hosokawa M, Reuter M, Yang Z, Berninger P, Palencia A, Benes V, Penninger J, Sachidanandam R, Pillai RS

Molecular cell, 2012

doi:10.1016/j.molcel.2012.07.019.

Dissecting the genomic complexity underlying medulloblastoma

Jones DT, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Hovestadt V, Stütz AM, Rausch T, Warnatz HJ, Ryzhova M, Bender S, Sturm D, Pleier S, Cin H, Pfaff E, Sieber L, Wittmann A, Remke M, Witt H, Hutter S, Tzaridis T, Weischenfeldt J, Raeder B, Avci M, Amstislavskiy V, Zapatka M, Weber UD, Wang Q, Lasitschka B, Bartholomae CC, Schmidt M, von Kalle C, Ast V, Lawerenz C, Eils J, Kabbe R, Benes V, van Sluis P, Koster J, Volckmann R, Shih D, Betts MJ, Russell RB, Coco S, Tonini GP, Schüller U, Hans V, Graf N, Kim YJ, Monoranu C, Roggendorf W, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, von Deimling A, Witt O, Maass E, Rössler J, Ebinger M, Schuhmann MU, Frühwald MC, Hasselblatt M, Jabado N, Rutkowski S, von Bueren AO, Williamson D, Clifford SC, McCabe MG, Collins VP, Wolf S, Wiemann S, Lehrach H, Brors B, Scheurlen W, Felsberg J, Reifenberger G, Northcott PA, Taylor MD, Meyerson M, Pomeroy SL, Yaspo ML, Korbel JO, Korshunov A, Eils R, Pfister SM, Lichter P

Nature, 2012

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RNA-sequencing as useful screening tool in the combat against the misuse of anabolic agents

Riedmaier I, Benes V, Blake J, Bretschneider N, Zinser C, Becker C, Meyer HH, Pfaffl MW

Analytical chemistry, 2012

doi:10.1021/ac301433d.

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

Preussner M, Schreiner S, Hung LH, Porstner M, Jäck HM, Benes V, Rätsch G, Bindereif A

Nucleic acids research, 2012

doi:10.1093/nar/gks221.

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway

Simpson JC, Joggerst B, Laketa V, Verissimo F, Cetin C, Erfle H, Bexiga MG, Singan VR, Hériché JK, Neumann B, Mateos A, Blake J, Bechtel S, Benes V, Wiemann S, Ellenberg J, Pepperkok R

Nature cell biology, 2012

doi:10.1038/ncb2510.

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma (vol 482, pg 226, 2012)

Schwartzentruber J, Korshunov A, Liu XY, Jones DTW, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DAK, Tonjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jager N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Fruhwald MC, Roggendorf W, Kramm C, Durken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong ZF, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N

NATURE, 2012

doi:10.1038/nature11026.

Role of CXCL13 in asthma: novel therapeutic target

Baay-Guzman GJ, Huerta-Yepez S, Vega MI, Aguilar-Leon D, Campillos M, Blake J, Benes V, Hernandez-Pando R, Teran LM

Chest, 2012

doi:10.1378/chest.11-0633.

Hfe deficiency impairs pulmonary neutrophil recruitment in response to inflammation

Benesova K, Vujić Spasić M, Schaefer SM, Stolte J, Baehr-Ivacevic T, Waldow K, Zhou Z, Klingmueller U, Benes V, Mall MA, Muckenthaler MU

PloS one, 2012

doi:10.1371/journal.pone.0039363.

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS

2012

doi:3:886 10.1038/ncomms1878.

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

Rausch T, Jones DT, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, von Deimling A, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, Zhang C, Porat R, Merino DM, Wasserman J, Jabado N, Fontebasso A, Bullinger L, Rücker FG, Döhner K, Döhner H, Koster J, Molenaar JJ, Versteeg R, Kool M, Tabori U, Malkin D, Korshunov A, Taylor MD, Lichter P, Pfister SM, Korbel JO

Cell, 2012

doi:10.1016/j.cell.2011.12.013.

Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis

Suffert G, Malterer G, Hausser J, Viiliäinen J, Fender A, Contrant M, Ivacevic T, Benes V, Gros F, Voinnet O, Zavolan M, Ojala PM, Haas JG, Pfeffer S

PLoS pathogens, 2011

doi:10.1371/journal.ppat.1002405.

Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy

Galmiche L, Serre V, Beinat M, Assouline Z, Lebre AS, Chretien D, Nietschke P, Benes V, Boddaert N, Sidi D, Brunelle F, Rio M, Munnich A, Rötig A

Human mutation, 2011

doi:10.1002/humu.21562.

Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy

Heikkinen S, Väisänen S, Pehkonen P, Seuter S, Benes V, Carlberg C

Nucleic acids research, 2011

doi:10.1093/nar/gkr654.

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins

Sanchez M, Galy B, Schwanhaeusser B, Blake J, Bähr-Ivacevic T, Benes V, Selbach M, Muckenthaler MU, Hentze MW

Blood, 2011

doi:10.1182/blood-2011-04-343541.

Mycobacteria-induced anaemia revisited: a molecular approach reveals the involvement of NRAMP1 and lipocalin-2, but not of hepcidin

Rodrigues PN, Gomes SS, Neves JV, Gomes-Pereira S, Correia-Neves M, Nunes-Alves C, Stolte J, Sanchez M, Appelberg R, Muckenthaler MU, Gomes MS

Immunobiology, 2011

doi:10.1016/j.imbio.2011.04.004.

Primer sequence disclosure: a clarification of the MIQE guidelines

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT

Clinical chemistry, 2011

doi:10.1373/clinchem.2011.162958.

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation

Rösel TD, Hung LH, Medenbach J, Donde K, Starke S, Benes V, Rätsch G, Bindereif A

The EMBO journal, 2011

doi:10.1038/emboj.2011.106.

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice

Castoldi M, Vujic Spasic M, Altamura S, Elmén J, Lindow M, Kiss J, Stolte J, Sparla R, D'Alessandro LA, Klingmüller U, Fleming RE, Longerich T, Gröne HJ, Benes V, Kauppinen S, Hentze MW, Muckenthaler MU

The Journal of clinical investigation, 2011

doi:10.1172/jci44883.

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM

Nucleic acids research, 2011

doi:10.1093/nar/gkq934.

Differentially expressed genes associated with human limbal epithelial phenotypes: new molecules that potentially facilitate selection of stem cell-enriched populations

Takács L, Tóth E, Losonczy G, Szanto A, Bähr-Ivacevic T, Benes V, Berta A, Vereb G

Investigative ophthalmology & visual science, 2011

doi:10.1167/iovs.10-5242.

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

Grober OM, Mutarelli M, Giurato G, Ravo M, Cicatiello L, De Filippo MR, Ferraro L, Nassa G, Papa MF, Paris O, Tarallo R, Luo S, Schroth GP, Benes V, Weisz A

BMC genomics, 2011

doi:10.1186/1471-2164-12-36.

Micro-RNA profiling reveals a role for miR-29 in human and murine liver fibrosis

Roderburg C, Urban GW, Bettermann K, Vucur M, Zimmermann H, Schmidt S, Janssen J, Koppe C, Knolle P, Castoldi M, Tacke F, Trautwein C, Luedde T

Hepatology (Baltimore, Md.), 2011

doi:10.1002/hep.23922.

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BH, Langmann T

Genome research, 2010

doi:10.1101/gr.109405.110.

Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available

Benes V, Castoldi M

Methods (San Diego, Calif.), 2010

doi:10.1016/j.ymeth.2010.01.026.

Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells

Gavriouchkina D, Fischer S, Ivacevic T, Stolte J, Benes V, Dekens MP

PloS one, 2010

doi:10.1371/journal.pone.0012542.

Genome-wide transcriptome profile of the human osteosarcoma Sa OS and U-2 OS cell lines

Trougakos IP, Chondrogianni N, Amarantos I, Blake J, Schwager C, Wirkner U, Ansorge W, Gonos ES

Cancer genetics and cytogenetics, 2010

doi:10.1016/j.cancergencyto.2009.09.012.

An assessment of air as a source of DNA contamination encountered when performing PCR

Witt N, Rodger G, Vandesompele J, Benes V, Zumla A, Rook GA, Huggett JF

Journal of biomolecular techniques : JBT, 2009

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Transcriptome complexity in a genome-reduced bacterium

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L

Science (New York, N.Y.), 2009

doi:10.1126/science.1176951.

Widespread estrogen-dependent repression of micrornas involved in breast tumor cell growth

Maillot G, Lacroix-Triki M, Pierredon S, Gratadou L, Schmidt S, Bénès V, Roché H, Dalenc F, Auboeuf D, Millevoi S, Vagner S

Cancer research, 2009

doi:10.1158/0008-5472.can-09-2206.

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT

Clinical chemistry, 2009

doi:10.1373/clinchem.2008.112797.

Inhibition of aurora kinases for tailored risk-adapted treatment of multiple myeloma

Hose D, Rème T, Meissner T, Moreaux J, Seckinger A, Lewis J, Benes V, Benner A, Hundemer M, Hielscher T, Shaughnessy JD Jr, Barlogie B, Neben K, Krämer A, Hillengass J, Bertsch U, Jauch A, De Vos J, Rossi JF, Möhler T, Blake J, Zimmermann J, Klein B, Goldschmidt H

Blood, 2009

doi:10.1182/blood-2008-09-178350.

Unreliable real-time PCR analysis of human endogenous retrovirus-W (HERV-W) RNA expression and DNA copy number in multiple sclerosis

Garson JA, Huggett JF, Bustin SA, Pfaffl MW, Benes V, Vandesompele J, Shipley GL

AIDS research and human retroviruses, 2009

doi:10.1089/aid.2008.0270.

Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs

Weinmann L, Höck J, Ivacevic T, Ohrt T, Mütze J, Schwille P, Kremmer E, Benes V, Urlaub H, Meister G

Cell, 2009

doi:10.1016/j.cell.2008.12.023.

Analysis of microribonucleic acid expression by quantitative real-time polymerase chain reaction

Benes V, Stolte J, Ibberson D, Castoldi M, Muckenthaler M

2009

doi:10.1017/cbo9780511818974.008.

RNA degradation compromises the reliability of microRNA expression profiling

Ibberson D, Benes V, Muckenthaler MU, Castoldi M

BMC biotechnology, 2009

doi:10.1186/1472-6750-9-102.

MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer

Lowery AJ, Miller N, Devaney A, McNeill RE, Davoren PA, Lemetre C, Benes V, Schmidt S, Blake J, Ball G, Kerin MJ

Breast cancer research : BCR, 2009

doi:10.1186/bcr2257.

Transient cyclical methylation of promoter DNA

Kangaspeska S, Stride B, Métivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, Benes V, Gannon F, Reid G

Nature, 2008

doi:10.1038/nature06640.

Cyclical DNA methylation of a transcriptionally active promoter

Métivier R, Gallais R, Tiffoche C, Le Péron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G

Nature, 2008

doi:10.1038/nature06544.

Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast-specific regulation of the insulin-like growth factor binding protein 4 gene

Denger S, Bähr-Ivacevic T, Brand H, Reid G, Blake J, Seifert M, Lin CY, May K, Benes V, Liu ET, Gannon F

Molecular endocrinology (Baltimore, Md.), 2008

doi:10.1210/me.2007-0292.

Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis

Hung LH, Heiner M, Hui J, Schreiner S, Benes V, Bindereif A

RNA (New York, N.Y.), 2008

doi:10.1261/rna.725208.

Hfe acts in hepatocytes to prevent hemochromatosis

Vujić Spasić M, Kiss J, Herrmann T, Galy B, Martinache S, Stolte J, Gröne HJ, Stremmel W, Hentze MW, Muckenthaler MU

Cell metabolism, 2008

doi:10.1016/j.cmet.2007.11.014.

Text mining for biology--the way forward: opinions from leading scientists

Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A

Genome biology, 2008

doi:10.1186/gb-2008-9-s2-s7.

miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes

Castoldi M, Schmidt S, Benes V, Hentze MW, Muckenthaler MU

Nature protocols, 2008

doi:10.1038/nprot.2008.4.

Replicative senescence of mesenchymal stem cells: a continuous and organized process

Wagner W, Horn P, Castoldi M, Diehlmann A, Bork S, Saffrich R, Benes V, Blake J, Pfister S, Eckstein V, Ho AD

PloS one, 2008

doi:10.1371/journal.pone.0002213.

miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes

Castoldi M, Benes V, Hentze MW, Muckenthaler MU

Methods (San Diego, Calif.), 2007

doi:10.1016/j.ymeth.2007.04.009.

Lack of haptoglobin affects iron transport across duodenum by modulating ferroportin expression

Marro S, Barisani D, Chiabrando D, Fagoonee S, Muckenthaler MU, Stolte J, Meneveri R, Haile D, Silengo L, Altruda F, Tolosano E

Gastroenterology, 2007

doi:10.1053/j.gastro.2007.07.004.

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Koutsos AC, Blass C, Meister S, Schmidt S, MacCallum RM, Soares MB, Collins FH, Benes V, Zdobnov E, Kafatos FC, Christophides GK

Proceedings of the National Academy of Sciences of the United States of America, 2007

doi:10.1073/pnas.0703988104.

Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but context specificity in vivo

Kozmik Z, Holland ND, Kreslova J, Oliveri D, Schubert M, Jonasova K, Holland LZ, Pestarino M, Benes V, Candiani S

Developmental biology, 2007

doi:10.1016/j.ydbio.2007.03.009.

Physiologic systemic iron metabolism in mice deficient for duodenal Hfe

Vujic Spasic M, Kiss J, Herrmann T, Kessler R, Stolte J, Galy B, Rathkolb B, Wolf E, Stremmel W, Hentze MW, Muckenthaler MU

Blood, 2007

doi:10.1182/blood-2006-07-036186.

Modular proteins from the Drosophila sallimus (sls) gene and their expression in muscles with different extensibility

Burkart C, Qiu F, Brendel S, Benes V, Hååg P, Labeit S, Leonard K, Bullard B

Journal of molecular biology, 2007

doi:10.1016/j.jmb.2007.01.059.

Adhesion of hematopoietic progenitor cells to human mesenchymal stem cells as a model for cell-cell interaction

Wagner W, Wein F, Roderburg C, Saffrich R, Faber A, Krause U, Schubert M, Benes V, Eckstein V, Maul H, Ho AD

Experimental hematology, 2007

doi:10.1016/j.exphem.2006.10.003.

STAT3 mediates hepatic hepcidin expression and its inflammatory stimulation

Verga Falzacappa MV, Vujic Spasic M, Kessler R, Stolte J, Hentze MW, Muckenthaler MU

Blood, 2007

doi:10.1182/blood-2006-07-033969.

Molecular composition of cell-cell contact between hematopoietic stem cells and mesenchymal stem cells

Wagner W, Wein F, Roderburg C, Benes V, Frankhauser M, Wuchter P, Eckstein V, Ho AD

Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation, 2007

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Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy

Sanchez M, Galy B, Dandekar T, Bengert P, Vainshtein Y, Stolte J, Muckenthaler MU, Hentze MW

The Journal of biological chemistry, 2006

doi:10.1074/jbc.m603876200.

A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)

Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU

RNA (New York, N.Y.), 2006

doi:10.1261/rna.2332406.

The heterogeneity of human mesenchymal stem cell preparations--evidence from simultaneous analysis of proteomes and transcriptomes

Wagner W, Feldmann RE Jr, Seckinger A, Maurer MH, Wein F, Blake J, Krause U, Kalenka A, Bürgers HF, Saffrich R, Wuchter P, Kuschinsky W, Ho AD

Experimental hematology, 2006

doi:10.1016/j.exphem.2006.01.002.

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression

Blake J, Schwager C, Kapushesky M, Brazma A

Bioinformatics (Oxford, England), 2006

doi:10.1093/bioinformatics/btk022.

The molecular elasticity of the insect flight muscle proteins projectin and kettin

Bullard B, Garcia T, Benes V, Leake MC, Linke WA, Oberhauser AF

Proceedings of the National Academy of Sciences of the United States of America, 2006

doi:10.1073/pnas.0509016103.

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D

Science (New York, N.Y.), 2005

doi:10.1126/science.1119089.

Comparative characteristics of mesenchymal stem cells from human bone marrow, adipose tissue, and umbilical cord blood

Wagner W, Wein F, Seckinger A, Frankhauser M, Wirkner U, Krause U, Blake J, Schwager C, Eckstein V, Ansorge W, Ho AD

Experimental hematology, 2005

doi:10.1016/j.exphem.2005.07.003.

Retroviral integration sites correlate with expressed genes in hematopoietic stem cells

Wagner W, Laufs S, Blake J, Schwager C, Wu X, Zeller JW, Ho AD, Fruehauf S

Stem cells (Dayton, Ohio), 2005

doi:10.1634/stemcells.2005-0006.

Hematopoietic progenitor cells and cellular microenvironment: behavioral and molecular changes upon interaction

Wagner W, Saffrich R, Wirkner U, Eckstein V, Blake J, Ansorge A, Schwager C, Wein F, Miesala K, Ansorge W, Ho AD

Stem cells (Dayton, Ohio), 2005

doi:10.1634/stemcells.2004-0361.

Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A

Reid G, Métivier R, Lin CY, Denger S, Ibberson D, Ivacevic T, Brand H, Benes V, Liu ET, Gannon F

Oncogene, 2005

doi:10.1038/sj.onc.1208662.

Quantitative real-time RT-PCR--a perspective

Bustin SA, Benes V, Nolan T, Pfaffl MW

Journal of molecular endocrinology, 2005

doi:10.1677/jme.1.01755.

Bloader--a batch loader application for MIAMExpress

Schwager C, Blake J

Bioinformatics (Oxford, England), 2005

doi:10.1093/bioinformatics/bti231.

Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells

Relógio A, Ben-Dov C, Baum M, Ruggiu M, Gemund C, Benes V, Darnell RB, Valcárcel J

The Journal of biological chemistry, 2005

doi:10.1074/jbc.m411976200.

Transcriptional complexes engaged by apo-estrogen receptor-alpha isoforms have divergent outcomes

Métivier R, Penot G, Carmouche RP, Hübner MR, Reid G, Denger S, Manu D, Brand H, Kos M, Benes V, Gannon F

The EMBO journal, 2004

doi:10.1038/sj.emboj.7600377.

Characterization of an Escherichia coli elaC deletion mutant

Schilling O, Rüggeberg S, Vogel A, Rittner N, Weichert S, Schmidt S, Doig S, Franz T, Benes V, Andrews SC, Baum M, Meyer-Klaucke W

Biochemical and biophysical research communications, 2004

doi:10.1016/j.bbrc.2004.05.227.

Molecular evidence for stem cell function of the slow-dividing fraction among human hematopoietic progenitor cells by genome-wide analysis

Wagner W, Ansorge A, Wirkner U, Eckstein V, Schwager C, Blake J, Miesala K, Selig J, Saffrich R, Ansorge W, Ho AD

Blood, 2004

doi:10.1182/blood-2003-10-3423.

Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling

Almstrup K, Hoei-Hansen CE, Wirkner U, Blake J, Schwager C, Ansorge W, Nielsen JE, Skakkebaek NE, Rajpert-De Meyts E, Leffers H

Cancer research, 2004

doi:10.1158/0008-5472.can-04-0679.

Targeted mutagenesis of the murine IRP1 and IRP2 genes reveals context-dependent RNA processing differences in vivo

Galy B, Ferring D, Benesova M, Benes V, Hentze MW

RNA (New York, N.Y.), 2004

doi:10.1261/rna.7220704.

Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS

Pacheco TR, Gomes AQ, Barbosa-Morais NL, Benes V, Ansorge W, Wollerton M, Smith CW, Valcárcel J, Carmo-Fonseca M

The Journal of biological chemistry, 2004

doi:10.1074/jbc.m402136200.

An Hfe-dependent pathway mediates hyposideremia in response to lipopolysaccharide-induced inflammation in mice

Roy CN, Custodio AO, de Graaf J, Schneider S, Akpan I, Montross LK, Sanchez M, Gaudino A, Hentze MW, Andrews NC, Muckenthaler MU

Nature genetics, 2004

doi:10.1038/ng1350.

Developmentally regulated switching of titin size alters myofibrillar stiffness in the perinatal heart

Opitz CA, Leake MC, Makarenko I, Benes V, Linke WA

Circulation research, 2004

doi:10.1161/01.res.0000124301.48193.e1.

Microcontact printing of DNA molecules

Lange SA, Benes V, Kern DP, Hörber JK, Bernard A

Analytical chemistry, 2004

doi:10.1021/ac035127w.

SMART 4.0: towards genomic data integration

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P

Nucleic acids research, 2004

doi:10.1093/nar/gkh088.

ET recombination: DNA engineering using homologous recombination in E. coli

Muyrers JP, Zhang Y, Benes V, Testa G, Rientjes JM, Stewart AF

Methods in molecular biology (Clifton, N.J.), 2004

doi:10.1385/1-59259-753-x:107.

BAC engineering for the generation of ES cell-targeting constructs and mouse transgenes

Testa G, Vintersten K, Zhang Y, Benes V, Muyrers JP, Stewart AF

Methods in molecular biology (Clifton, N.J.), 2004

doi:10.1385/1-59259-753-x:123.

Metabolites: a helping hand for pathway evolution?

Schmidt S, Sunyaev S, Bork P, Dandekar T

Trends in biochemical sciences, 2003

doi:10.1016/s0968-0004(03)00114-2.

Standardization of protocols in cDNA microarray analysis

Benes V, Muckenthaler M

Trends in biochemical sciences, 2003

doi:10.1016/s0968-0004(03)00068-9.

Regulatory defects in liver and intestine implicate abnormal hepcidin and Cybrd1 expression in mouse hemochromatosis

Muckenthaler M, Roy CN, Custodio AO, Miñana B, deGraaf J, Montross LK, Andrews NC, Hentze MW

Nature genetics, 2003

doi:10.1038/ng1152.

Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles

Testa G, Zhang Y, Vintersten K, Benes V, Pijnappel WW, Chambers I, Smith AJ, Smith AG, Stewart AF

Nature biotechnology, 2003

doi:10.1038/nbt804.

Cloning and developmental expression of amphioxus Dachschund

Candiani S, Kreslova J, Benes V, Oliveri D, Castagnola P, Pestarino M, Kozmik Z

Gene expression patterns : GEP, 2003

doi:10.1016/s1567-133x(02)00070-4.

STRING: a database of predicted functional associations between proteins

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B

Nucleic acids research, 2003

doi:10.1093/nar/gkg034.

Two (betaalpha)(8)-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates

Henn-Sax M, Thoma R, Schmidt S, Hennig M, Kirschner K, Sterner R

Biochemistry, 2002

doi:10.1021/bi026092h.

The genome sequence of the malaria mosquito Anopheles gambiae

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL

Science (New York, N.Y.), 2002

doi:10.1126/science.1076181.

A genomic switch at the transition from cell proliferation to terminal differentiation in the Drosophila eye.

Jasper H, Benes V, Atzberger A, Sauer S, Ansorge W, Bohmann D

Developmental cell, 2002

doi:10.1016/s1534-5807(02)00297-6.

A common evolutionary origin of two elementary enzyme folds

Höcker B, Schmidt S, Sterner R

FEBS letters, 2002

doi:10.1016/s0014-5793(01)03232-x.

Functional equivalency of amphioxus and vertebrate Pax258 transcription factors suggests that the activation of mid-hindbrain specific genes in vertebrates occurs via the recruitment of Pax regulatory elements

Krelová J, Holland LZ, Schubert M, Burgtorf C, Benes V, Kozmik Z

Gene, 2002

doi:10.1016/s0378-1119(01)00840-x.

A versatile structural domain analysis server using profile weight matrices

Schmidt S, Bork P, Dandekar T

Journal of chemical information and computer sciences, 2002

doi:10.1021/ci010374r.

The genomic response of the Drosophila embryo to JNK signaling.

Jasper H, Benes V, Schwager C, Sauer S, Clauder-Münster S, Ansorge W, Bohmann D

Developmental cell, 2001

doi:10.1016/s1534-5807(01)00045-4.

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert TH, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S, European Union Chromosome 3 Arabidopsis Sequencing Consortium, Institute for Genomic Research, Kazusa DNA Research Institute

Nature, 2000

doi:10.1038/35048706.

A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation

Fukami M, Kirsch S, Schiller S, Richter A, Benes V, Franco B, Muroya K, Rao E, Merker S, Niesler B, Ballabio A, Ansorge W, Ogata T, Rappold GA

American journal of human genetics, 2000

doi:10.1086/303047.

Point mutation of bacterial artificial chromosomes by ET recombination

Muyrers JP, Zhang Y, Benes V, Testa G, Ansorge W, Stewart AF

EMBO reports, 2000

doi:10.1093/embo-reports/kvd049.

An estimate of large-scale sequencing accuracy

Hill F, Gemünd C, Benes V, Ansorge W, Gibson TJ

EMBO reports, 2000

doi:10.1093/embo-reports/kvd015.

Genetic diversity of Borrelia burgdorferi sensu lato in ticks from mainland Portugal

De Michelis S, Sewell HS, Collares-Pereira M, Santos-Reis M, Schouls LM, Benes V, Holmes EC, Kurtenbach K

Journal of clinical microbiology, 2000

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Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines

Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC

Proceedings of the National Academy of Sciences of the United States of America, 2000

doi:10.1073/pnas.97.12.6619.

Progress in Arabidopsis genome sequencing and functional genomics

Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansroge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Bountry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Rose M

Journal of biotechnology, 2000

doi:10.1016/s0168-1656(00)00195-4.

BAC trimming: minimizing clone overlaps

Hill F, Benes V, Thomasova D, Stewart AF, Kafatos FC, Ansorge W

Genomics, 2000

doi:10.1006/geno.1999.6106.

Sequence and expression of the kettin gene in Drosophila melanogaster and Caenorhabditis elegans

Kolmerer B, Clayton J, Benes V, Allen T, Ferguson C, Leonard K, Weber U, Knekt M, Ansorge W, Labeit S, Bullard B

Journal of molecular biology, 2000

doi:10.1006/jmbi.1999.3461.

Genomic locus and promoter region of rat Smad7, an important antagonist of TGFbeta signaling

Stopa M, Benes V, Ansorge W, Gressner AM, Dooley S

Mammalian genome : official journal of the International Mammalian Genome Society, 2000

doi:10.1007/s003350010032.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert TH, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR

Nature, 1999

doi:10.1038/47134.

Sec61beta, a subunit of the protein translocation channel, is required during Drosophila development

Valcárcel R, Weber U, Jackson DB, Benes V, Ansorge W, Bohmann D, Mlodzik M

Journal of cell science, 1999

doi:.

Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources

Kal AJ, van Zonneveld AJ, Benes V, van den Berg M, Koerkamp MG, Albermann K, Strack N, Ruijter JM, Richter A, Dujon B, Ansorge W, Tabak HF

Molecular biology of the cell, 1999

doi:10.1091/mbc.10.6.1859.

Bacteriophage phi29 early protein p17 is conditionally required for the first rounds of viral DNA replication

Crucitti P, Lázaro JM, Benes V, Salas M

Gene, 1998

doi:10.1016/s0378-1119(98)00167-x.

Systematic gain-of-function genetics in Drosophila

Rørth P, Szabo K, Bailey A, Laverty T, Rehm J, Rubin GM, Weigmann K, Milán M, Benes V, Ansorge W, Cohen SM

Development (Cambridge, England), 1998

doi:.

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana

Bevan M, Bancroft I, Bent E, Love K, Goodman H, Dean C, Bergkamp R, Dirkse W, Van Staveren M, Stiekema W, Drost L, Ridley P, Hudson SA, Patel K, Murphy G, Piffanelli P, Wedler H, Wedler E, Wambutt R, Weitzenegger T, Pohl TM, Terryn N, Gielen J, Villarroel R, De Clerck R, Van Montagu M, Lecharny A, Auborg S, Gy I, Kreis M, Lao N, Kavanagh T, Hempel S, Kotter P, Entian KD, Rieger M, Schaeffer M, Funk B, Mueller-Auer S, Silvey M, James R, Montfort A, Pons A, Puigdomenech P, Douka A, Voukelatou E, Milioni D, Hatzopoulos P, Piravandi E, Obermaier B, Hilbert H, Düsterhöft A, Moores T, Jones JD, Eneva T, Palme K, Benes V, Rechman S, Ansorge W, Cooke R, Berger C, Delseny M, Voet M, Volckaert G, Mewes HW, Klosterman S, Schueller C, Chalwatzis N

Nature, 1998

doi:10.1038/35140.

Strawberry vein banding virus--definitive member of the genus Caulimovirus

Petrzik K, Benes V, Mráz I, Honetslegrová-Fránová J, Ansorge W, Spak J

Virus genes, 1998

doi:10.1023/a:1008039024963.

Bacteriophage B103: complete DNA sequence of its genome and relationship to other Bacillus phages

Pecenková T, Benes V, Paces J, Vlcek C, Paces V

Gene, 1997

doi:10.1016/s0378-1119(97)00363-6.

Automated cycle sequencing with Taquenase: protocols for internal labeling, dye primer and "doublex" simultaneous sequencing

Voss H, Nentwich U, Duthie S, Wiemann S, Benes V, Zimmermann J, Ansorge W

BioTechniques, 1997

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Direct primer walking on P1 plasmid DNA

Benes V, Kilger C, Voss H, Pääbo S, Ansorge W

BioTechniques, 1997

doi:10.2144/97231bm21.

Simultaneous loading of 200 sample lanes for DNA sequencing on vertical and horizontal, standard and ultrathin gels

Erfle H, Ventzki R, Voss H, Rechmann S, Benes V, Stegemann J, Ansorge W

Nucleic acids research, 1997

doi:10.1093/nar/25.11.2229.

DNA sequencing and analysis of 130 kb from yeast chromosome XV

Voss H, Benes V, Andrade MA, Valencia A, Rechmann S, Teodoru C, Schwager C, Paces V, Sander C, Ansorge W

Yeast (Chichester, England), 1997

doi:10.1002/(sici)1097-0061(19970615)13:7<655::aid-yea120>3.0.co;2-i.

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI

Bussey H, Storms RK, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell B, Badcock K, Benes V, Botstein D, Bowman S, Brückner M, Carpenter J, Cherry JM, Chung E, Churcher C, Coster F, Davis K, Davis RW, Dietrich FS, Delius H, DiPaolo T, Hani J

Nature, 1997

doi:10.1038/387s103.

The nucleotide sequence of Saccharomyces cerevisiae chromosome XV

Dujon B, Albermann K, Aldea M, Alexandraki D, Ansorge W, Arino J, Benes V, Bohn C, Bolotin-Fukuhara M, Bordonné R, Boyer J, Camasses A, Casamayor A, Casas C, Chéret G, Cziepluch C, Daignan-Fornier B, Dang DV, de Haan M, Delius H, Durand P, Fairhead C, Feldmann H, Gaillon L, Kleine K

Nature, 1997

doi:10.1038/387s098.

The nucleotide sequence of Saccharomyces cerevisiae chromosome XII

Johnston M, Hillier L, Riles L, Albermann K, André B, Ansorge W, Benes V, Brückner M, Delius H, Dubois E, Düsterhöft A, Entian KD, Floeth M, Goffeau A, Hebling U, Heumann K, Heuss-Neitzel D, Hilbert H, Hilger F, Kleine K, Kötter P, Louis EJ, Messenguy F, Mewes HW, Hoheisel JD

Nature, 1997

doi:10.1038/387s087.

Molecular characterization of two high affinity sulfate transporters in Saccharomyces cerevisiae

Cherest H, Davidian JC, Thomas D, Benes V, Ansorge W, Surdin-Kerjan Y

Genetics, 1997

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Reducing "double sequences" in automated DNA sequencing with T7 DNA polymerase and internal labeling

Wiemann S, Schilke A, Rechmann S, Zimmermann J, Voss H, Ansorge W

BioTechniques, 1996

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"Doublex" fluorescent DNA sequencing: two independent sequences obtained simultaneously in one reaction with internal labeling and unlabeled primers

Wiemann S, Stegemann J, Zimmermann J, Voss H, Benes V, Ansorge W

Analytical biochemistry, 1996

doi:10.1006/abio.1996.0068.

Sequencing 39,350 bp of Saccharomyces cerevisiae chromosome XII utilizing ordered shotgun libraries

Scholler P, Benes V, Voss H, Ansorge W, Hoheisel JD

DNA sequence : the journal of DNA sequencing and mapping, 1996

doi:10.3109/10425179609020872.

Nucleotide sequence and analysis of the centromeric region of yeast chromosome IX

Voss H, Tamames J, Teodoru C, Valencia A, Sensen C, Wiemann S, Schwager C, Zimmermann J, Sander C, Ansorge W

Yeast (Chichester, England), 1995

doi:10.1002/yea.320110109.

Simultaneous on-line DNA sequencing on both strands with two fluorescent dyes

Wiemann S, Stegemann J, Grothues D, Bosch A, Estivill X, Schwager C, Zimmermann J, Voss H, Ansorge W

Analytical biochemistry, 1995

doi:10.1006/abio.1995.1015.

High speed on-line DNA sequencing on ultrathin slab gels

Stegemann J, Schwager C, Erfle H, Hewitt N, Voss H, Zimmermann J, Ansorge W

Nucleic acids research, 1991

doi:10.1093/nar/19.3.675.

Automated fluorescent sequencing of lambda DNA

Voss H, Zimmermann J, Schwager C, Erfle H, Stegemann J, Stucky K, Ansorge W

Nucleic acids research, 1990

doi:10.1093/nar/18.17.5314.

Automated fluorescent sequencing of cosmid DNA

Voss H, Zimmermann J, Schwager C, Erfle H, Stegemann J, Stucky K, Ansorge W

Nucleic acids research, 1990

doi:10.1093/nar/18.4.1066.

A simplified protocol for fast plasmid DNA sequencing

Zimmermann J, Voss H, Schwager C, Stegemann J, Erfle H, Stucky K, Kristensen T, Ansorge W

Nucleic acids research, 1990

doi:10.1093/nar/18.4.1067.

Direct genomic fluorescent on-line sequencing and analysis using in vitro amplification of DNA

Voss H, Schwager C, Wirkner U, Sproat B, Zimmermann J, Rosenthal A, Erfle H, Stegemann J, Ansorge W

Nucleic acids research, 1989

doi:10.1093/nar/17.7.2517.