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Zaugg Group

Systems (epi)genetics to study the basis of complex traits and diseases

Publications

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Publication year

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis.

Lim B, Kamal A, Gomez Ramos B, Adrian Segarra JM, Ibarra IL, Dignas L, Kindinger T, Volz K, Rahbari M, Rahbari N, Poisel E, Kafetzopoulou K, Böse L, Breinig M, Heide D, Gallage S, Barragan Avila JE, Wiethoff H, Berest I, Schnabellehner S, Schneider M, Becker J, Helm D, Grimm D, Mäkinen T, Tschaharganeh DF, Heikenwalder M, Zaugg JB, Mall M

Nature genetics, 2025

doi:10.1038/s41588-025-02081-w.

Transcriptional profiling unveils molecular subgroups of adaptive and maladaptive right ventricular remodeling in pulmonary hypertension.

Khassafi F, Chelladurai P, Valasarajan C, Nayakanti SR, Martineau S, Sommer N, Yokokawa T, Boucherat O, Kamal A, Kiely DG, Swift AJ, Alabed S, Omura J, Breuils-Bonnet S, Kuenne C, Potus F, Günther S, Savai R, Seeger W, Looso L, Lawrie A, Zaugg JB, Tello K, Provencher S, Bonnet S, Pullamsetti SS

Nature cardiovascular research, 2023

doi:10.1038/s44161-023-00338-3.

Operation of a TCA cycle subnetwork in the mammalian nucleus.

Kafkia E, Andres-Pons A, Ganter K, Seiler M, Smith TS, Andrejeva A, Jouhten P, Pereira F, Franco C, Kuroshchenkova A, Leone S, Sawarkar R, Boston R, Thaventhiran J, Zaugg JB, Lilley KS, Lancrin C, Beck M, Patil KR

Science advances, 2022

doi:10.1126/sciadv.abq5206.

Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response.

Scheller M, Ludwig AK, Göllner S, Rohde C, Krämer S, Stäble S, Janssen M, Müller JA, He L, Bäumer N, Arnold C, Gerß J, Schönung M, Thiede C, Niederwieser C, Niederwieser D, Serve H, Berdel WE, Thiem U, Hemmerling I, Leuschner F, Plass C, Schlesner M, Zaugg J, Milsom MD, Trumpp A, Pabst C, Lipka DB, Müller-Tidow C

Nature cancer, 2021

doi:10.1038/s43018-021-00213-9.

Genetic effects on gene expression across human tissues

Aguet F, Brown AA, Castel SE, Davis JR, He Y, Jo B, Mohammadi P, Park Y, Parsana P, Segre AV, Strober BJ, Zappala Z, Cummings BB, Gelfand ET, Hadley K, Huang KH, Lek M, Li X, Nedzel JL, Nguyen DY, Noble MS, Sullivan TJ, Tukiainen T, MacArthur DG, Getz G, Management NP, Addington A, Guan P, Koester S, Little AR, Lockhart NC, Moore HM, Rao A, Struewing JP, Volpi S, Collection B, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley D, Mash DC, Davis DA, Sobin L, Barcus ME, Branton PA, Grp EMW, Abell NS, Balliu B, Delaneau O, Fresard L, Gamazon ER, Garrido-Martin D, Gewirtz ADH, Gliner G, Gloudemans MJ, Han B, He AZ, Hormozdiari F, Li X, Liu B, Kang EY, McDowell IC, Ongen H, Palowitch JJ, Peterson CB, Quon G, Ripke S, Saha A, Shabalin AA, Shimko TC, Sul JH, Teran NA, Tsang EK, Zhang H, Zhou YH, Bustamante CD, Cox NJ, Guigo R, Kellis M, McCarthy MI, Conrad DF, Eskin E, Li G, Nobel AB, Sabatti C, Stranger BE, Wen X, Wright FA, Ardlie KG, Dermitzakis ET, Lappalainen T, Battle A, Brown CD, Engelhardt BE, Montgomery SB, Aguet F, Ardlie KG, Cummings BB, Gelfand ET, Getz G, Hadley K, Handsaker RE, Huang KH, Kashin S, Karczewski KJ, Lek M, Li X, MacArthur DG, Nedzel JL, Nguyen DT, Noble MS, Segre AV, Trowbridge CA, Tukiainen T, Abell NS, Balliu B, Barshir R, Basha O, Battle A, Bogu GK, Brown A, Brown CD, Castel SE, Chen LS, Chiang C, Conrad DF, Cox NJ, Damani FN, Davis JR, Delaneau O, Dermitzakis ET, Engelhardt BE, Eskin E, Ferreira PG, Fresard L, Gamazon ER, Garrido-Martin D, Gewirtz ADH, Gliner G, Gloudemans MJ, Guigo R, Hall IM, Han B, He Y, Hormozdiari F, Howald C, Im HK, Jo B, Kang EY, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy MI, McDowell IC, Mohammadi P, Monlong J, Montgomery SB, Munoz-Aguirre M, Ndungu AW, Nicolae DL, Nobel AB, Oliva M, Ongen H, Palowitch JJ, Panousis N, Papasaikas P, Park Y, Parsana P, Payne AJ, Peterson CB, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Scott AJ, Shabalin AA, Sodaei R, Stephens M, Stranger BE, Strober BJ, Sul JH, Tsang EK, Urbut S, De Bunt MV, Wang G, Wen X, Wright FA, Xi HS, Yeger-Lotem E, Zappala Z, Zaugg JB, Zhou YH, Akey JM, Bates D, Chan J, Chen LS, Claussnitzer M, Demanelis K, Diegel M, Doherty JA, Feinberg AP, Fernando MS, Halow J, Hansen KD, Haugen E, Hickey PF, Hou L, Jasmine F, Jian R, Jiang L, Johnson A, Kaul R, Kellis M, Kibriya MG, Lee K, Li JB, Li Q, Li X, Lin J, Lin S, Linder S, Linke C, Liu Y, Maurano MT, Molinie B, Montgomery SB, Nelson J, Neri FJ, Oliva M, Park Y, Pierce BL, Rinaldi NJ, Rizzardi LF, Sandstrom R, Skol A, Smith KS, Snyder MP, Stamatoyannopoulos J, Stranger BE, Tang H, Tsang EK, Wang L, Wang M, Van Wittenberghe N, Wu F, Zhang R, Fund NC, Nierras CR, Nci N, Branton PA, Carithers LJ, Guan P, Moore HM, Rao A, Vaught JB, Nhgri N, Gould SE, Lockart NC, Martin C, Struewing JP, Volpi S, Nimh N, Addington AM, Koester SE, Nida N, Little AR, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley DR, Davis DA, Mash DC, Undale AH, Smith AM, Tabor DE, Roche NV, McLean JA, Vatanian N, Robinson KL, Sobin L, Barcus ME, Valentino KM, Qi L, Hunter S, Hariharan P, Singh S, Um KS, Matose T, Tomaszewski MM, Study E, Barker LK, Mosavel M, Siminoff LA, Traino HM, Flicek P, Juettemann T, Ruffier M, Sheppard D, Taylor K, Trevanion SJ, Zerbino DR, Craft B, Goldman M, Haeussler M, Kent WJ, Lee CM, Paten B, Rosenbloom KR, Vivian J, Zhu J

NATURE, 2017

doi:10.1038/nature24277.

Dynamic landscape and regulation of RNA editing in mammals

Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Amaswami GR, Ariyoshi K, Gupte A, Keegan LP, George CX, Amu AR, Huang N, Pollina EA, Leeman DS, Ustighi AR, Goh YPS, Hawla AC, Del Sal G, Peltz G, Runet AB, Onrad DFC, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB

NATURE, 2017

doi:10.1038/nature24041.

Landscape of X chromosome inactivation across human tissues.

Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Ummings BBC, Astel SEC, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG

Nature, 2017

doi:10.1038/nature24265.

Extensive variation in chromatin states across humans

Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M

Science (New York, N.Y.), 2013

doi:10.1126/science.1242510.

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