3 May - 8 May 2026
Analysis and integration of transcriptome and proteome data
Vladimir Benes, Raffaele Calogero, Daria Fijalkowska, Jeroen Krijgsveld, Lennard Martens
Description OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells tissues and organisms operate in their biological context Among the key technologies driving this forward are next generation sequencing and proteomics as they provide powerful means to determine global expression levels of genes and proteins Both fields have matured to a degree that they have now become accessible to researchers in many areas of biology During this course participants will gain theoretical insight in the structure of sequencing and proteomic data and they will receive training in data analysis for the annotation quantification and statistical analysis of gene and protein expression using various computational tools In addition training will be provided in the use of Cytoscape to derive biological insights from the integration of both data types Audience This course is for biologists and biochemists who are starting to be involved in both next generation sequencing and mass spectrometry based proteomics but who are not experts in these fields Modules resources Principles of mRNA quantification Principles of protein identification and quantification Principles and application of bioinformatic tools for mining of transcriptome and proteome data Data integration by Cytoscape Learning outcomes The aim of this practical course is to provide insight in techniques that are frequently used for transcriptome and proteome analysis and to provide hands on experience turning primary data into information that can be used for further biological interpretation To achieve these goals participants will gain insight in the basic principles of gene expression analysis RNAseq data quantification and differential expression analysis protein identification and quantification and they will be trained in the use of software tools to analyse sequencing and proteomic data SearchGUI PeptideShaker MaxQuant In addition the course will provide insight in the complementarity of transcriptome and proteome data by their integrative analysis via Cytoscape What past participants say about the course An intensive and inspiring course with worldwide top researchers in bioinformatics Ideal for wet lab scientists who are now starting to work on RNA seq and proteomics analysis Marta Furtado Instituto de Medicina Molecular Portugal In this course I found lecturers and participants equally willing to share and learn This together with the high quality of each lecture and the care of the organisers contributed to make this week a life changing experience for me Maria Cristina Petrella Centre for Genomic Regulation CRG Spain Speakers Speakers trainers and staff Luca Alessandri University of Turin Italy Mathias Boulanger EMBL Heidelberg Germany Vladimir Benes EMBL Heidelberg Germany Raffaele Calogero University of Turin Italy Daria Fijalkowska University of Ghent Belgium Jeroen Krijgsveld German Cancer Research Centre DKFZ Germany Manjeet Kumar Florida Research Innovation Center USA Lennart Martens University of Ghent Belgium Gerben Menschaert University of Ghent Belgium Scooter Morris University of California San Francisco USA Santhust EMBL Heidelberg Germany Oliver Stegle EMBL Heidelberg DKFZ Germany Florin Walter EMBL Heidelberg Germany Scientific organisers Vladimir Benes EMBL Heidelberg Germany Raffaele Calogero University of Turin Italy Daria Fijalkowska University of Ghent Belgium Jeroen Krijgsveld German Cancer Research Centre DKFZ Germany Lennart Martens University of Ghent Belgium Course organisers Iva Gavran EMBL Heidelberg Germany Irena Provaznikova EMBL Heidelberg Germany Camilo Barbosa EMBL Heidelberg Germany Programme Are you on social media Post using EMBLDataIntegration and don t forget to tag EMBLEvents Day 1 Sunday 3 May 2026 Time Europe Berlin SessionLocation08 35 08 50Bus from hotel to EMBL bus stopPremier Inn Zentrum09 00 09 15Arrival welcome and safety introductionsCourtyard room09 15 11 00Lecture RNA seq cool but is it that simple Vladimir Benes EMBL Heidelberg GermanyCourtyard room11 00 11 30Coffee breakComputer Training Lab11 30 12 30Practical sessionRNAseq Reads to genesTrainers Raffaele Calogero University of Torino ItalyLuca Alessandri University of Torino ItalyMathias Boulanger EMBL Heidelberg GermanyComputer Training Lab12 30 13 30LunchEMBL Canteen13 30 16 00Practical sessionRNAseq Reads to genesTrainers Raffaele Calogero University of Torino ItalyLuca Alessandri University of Torino ItalyMathias Boulanger EMBL Heidelberg GermanyComputer Training Lab16 00 16 30Coffee breakComputer Training Lab16 30 18 30Q A on RNAseqRaffaele Calogero University of Torino ItalyLuca Alessandri University of Torino ItalyMathias Boulanger EMBL Heidelberg GermanyComputer Training Lab18 30 19 30Dinner in canteenEMBL Canteen19 30 Departure to hotelEMBL bus stop Day 2 Monday 4 May 2026 Time Europe Berlin SessionLocation08 35 08 50Bus from hotel to EMBL bus stopPremier Inn Zentrum09 00 10 30Practical theory Differential expression analysisRaffaele Calogero University of Torino ItalyComputer Training Lab10 30 11 00Coffee breakComputer Training Lab11 00 12 30Practical theory Batch correctionRaffaele Calogero University of Torino ItalyComputer Training Lab12 30 13 30LunchEMBL Canteen13 30 15 00Practical theory Batch correctionRaffaele Calogero University of Torino ItalyComputer Training Lab15 00 15 30Coffee breakComputer Training Lab15 30 17 30Lecture practical Ribosome profilingGerben Menschaert University of Ghent BelgiumCourtyard room17 30 18 30Flash talk presentationsCourtyard room18 30 20 00BBQ dinnerBBQ platz20 15Departure to hotelATC entrance Day 3 Tuesday 5 May 2026 Time Europe Berlin SessionLocation08 35 08 50Bus from hotel to EMBL bus stopPremier Inn Zentrum09 00 10 00Introduction to ProteomicsJeroen Krijgsveld German Cancer Research Centre DKFZ GermanyCourtyard room10 00 11 00Practical session peptide and protein identificationJeroen Krijgsveld German Cancer Research Centre DKFZ GermanyComputer Training Lab11 00 11 30Coffee breakComputer Training Lab11 30 12 00Practical session peptide and protein identificationJeroen Krijgsveld German Cancer Research Centre DKFZ GermanyComputer Training Lab12 00 13 00LunchEMBL Canteen13 00 13 30Lecture Bioinformatics for proteomicsLennart Martens University of Ghent BelgiumCourtyard room13 30 14 30Q A to Bioinformatics for proteomicsLennart Martens University of Ghent BelgiumComputer Training Lab14 30 15 00Coffee BreakComputer Training Lab15 00 18 30Practical session Turning data into information peptide and protein identification database searchingLennart Martens University of Ghent BelgiumComputer Training Lab18 30 19 00Pizza dinnerRooftop Lounge19 00 20 00Pub quiz and drinksRooftop Lounge20 15Departure to hotelATC entrance Day 4 Wednesday 6 May 2026 Time Europe Berlin SessionLocation08 35 08 50Bus from hotel to EMBL bus stopPremier Inn Zentrum09 00 10 00Lecture Introduction to DIA proteomics data analysisDaria Fijalkowska University of Ghent BelgiumCourtyard room10 00 10 30Coffee breakComputer Training Lab10 30 12 00Practical Session DIA proteomics data analysisDaria Fijalkowska University of Ghent BelgiumComputer Training Lab12 00 13 00LunchEMBL Canteen13 00 14 30Practical Session DIA proteomics data analysisDaria Fijalkowska University of Ghent BelgiumComputer Training Lab14 30 15 00Coffee breakComputer Training Lab15 00 16 00Q A to Bioinformatic tools for data comparison and integrationScooter Morris University of California San Francisco USACourtyard room16 00 17 00Practical session Introduction to CytoscapeManjeet Kumar Florida Research and Innovation Center Cleveland Clinic Florida USAJohn Scooter Morris University of California San Francisco USASanthust EMBL Heidelberg GermanyComputer Training Lab17 15Departure to hotelFree eveningEMBL bus stop Day 5 Thursday 7 May 2026 Time Europe Berlin SessionLocation08 35 08 50Bus from hotel to EMBL bus stopPremier Inn Zentrum09 00 10 00Lecture MOFA data integration talkOliver Stegle EMBL Heidelberg GermanyCourtyard room10 00 10 30Coffee breakCourtyard room10 30 12 00Practical session MOFA data integrationFlorin Walter EMBL Heidelberg GermanyComputer Training Lab12 00 13 00LunchEMBL Canteen13 00 14 30Practical session Introduction to CytoscapeManjeet Kumar Florida Research and Innovation Center Cleveland Clinic Florida USAJohn Scooter Morris University of California San Francisco USASanthust EMBL Heidelberg GermanyComputer Training Lab and Courtyard room14 30 15 00Coffee breakCourtyard room15 00 16 15Practical session Introduction to CytoscapeManjeet Kumar Florida Research and Innovation Center Cleveland Clinic Florida USAJohn Scooter Morris University of California San Francisco USASanthust EMBL Heidelberg GermanyComputer Training Lab and Courtyard room16 15 17 45GeneCore and Proteomics Core facilities toursCourtyard room17 50 18 15Departure to downtownEMBL bus stop19 00 22 00Downtown dinner Day 6 Friday 8 May 2026 Time Europe Berlin SessionLocation08 35 08 50Bus from hotel to EMBL bus stopPremier Inn Zentrum09 00 12 00Practical session Data integrationwith flexible coffee breakManjeet Kumar Florida Research and Innovation Center Cleveland Clinic Florida USAJohn Scooter Morris University of California San Francisco USAComputer Training Lab and Courtyard room12 00 13 00LunchEMBL Canteen13 00 15 00Practical session Data integrationManjeet Kumar Florida Research and Innovation Center Cleveland Clinic Florida USAJohn Scooter Morris University of California San Francisco USAComputer Training Lab and Courtyard room15 00 15 30Course wrap up and farewellCourtyard room15 40Departure to train stationEMBL bus stop Practical information Registration fees The course is limited to 24 participants For selection purposes please note that your application will not be considered without a letter of motivation Registration fees Your registration for this course includes Admission to the event Meals and coffee breaks Course materials Access to the e learning platform A letter to support your visa application for more information check the Travel and accommodation tab Accommodation and travel are not included in the fees participants are expected to book and pay their own expenses Academia 740PhD Student 740Industry 1250 Confirmation and payment The registration fee should be paid only after acceptance to the course The results will be announced approximately 2 3 weeks after the application deadline Cancellation policy If you are no longer able to take part in the course please inform your course contact responsible for this event Your registration and the submitted motivation letter will be deleted Please also check our Terms and Conditions for the cancellation policy Further details For further information about registration please refer to the FAQ page Submitting a motivation letter After you have logged in and successfully registered you will receive an email asking you to submit your motivation letter Click on the link provided and enter your motivation letter in the text box provided Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering Instructions Include your relevant skills experience and qualifications showing why you would be suitable for the course Explain why you would like to attend including what you can contribute and how you think you will benefit from the course Please note The limit of 2 000 characters refers to manually typed text and excludes spaces If an error occurs try using a different web browser preferably Google Chrome or Mozilla Firefox If you copy paste the text into the form hidden formatting might still be included which may cause the text to exceed the 2 000 character limit resulting in an error message We recommend you clear all formatting before pasting in the text If you have special symbols in your text make sure you are using Unicode characters otherwise these will not be recognised For detailed instructions please watch our video on how to submit a course motivation letter Further details For further information about registration and motivation letter submission please refer to the FAQ page Financial assistance Financial assistance Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waivers travel grants and childcare grants Your place in the meeting is only confirmed by paying the registration fee which is mandatory even when receiving a fee waiver Registration fee waiver The fee waiver will cover the registration sum that you have paid to attend the course Travel grant The travel grant will cover the cost of travel airfare train bus taxi accommodation visa and is provided up to specified caps which are normally as follows up to 400 for participants travelling to an EMBL Course within Europe up to 1000 for participants travelling to an EMBL Course from outside Europe The organisers may reduce the grant cap to accommodate more participants Recipients will be notified of their travel cap amount when they are informed of the outcome of their application Original receipts must be provided with your signature for all costs incurred within two months of completion of travel Scanned copies cannot be accepted Childcare grants There is the possibility to apply for a childcare grant to offset child care costs incurred by participants speakers trainers and organisers when attending a course Eligible costs include but are not limited to fees for a babysitter or child care facility and travel costs for a caregiver Please note that priority will be given to early stage researchers There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants EMBO accessibility grant For EMBO Practical Course participants with accessibility needs there is the possibility to apply for an accessibility grant to offset costs incurred by participants or speakers when participating at a course Eligible costs include costs incurred for equipment or adaptations to the course environment or travel costs for an event companion to assist the participant or speaker during the course where necessary While we do our best to accommodate needs please note that extensive changes to the course environment might not be possible Priority will be given to early stage researchers A maximum amount of 500 can be awarded per participant applying for an EMBO accessibility grant In order to apply for this grant for EMBO Practical Courses you must be registered by the application deadline Application Whether you are attending onsite or virtually to apply for financial assistance please follow the steps in the application system During the process of submitting your motivation letter to the system you will be asked which type of grant you want to apply for Applications for financial support will not affect the outcome of your selection results Information about the grant will be sent out shortly after the motivation letter deadline Results Grant allocations are announced by email to all applicants after the selection results Allocation results do not impact your selection to the course Selection for financial assistance is based on scientific merit your current work or study location the reasons for needing financial support and the impact this event will have on your career Please note that for childcare grants priority will be given to early stage researchers Further details Check out this list of external funding opportunities For further information about financial assistance please refer to the FAQ page Travel and accommodation Visa We can send you a registration confirmation to support your visa procedure not an official invitation letter Please contact the Conference Officer responsible for your event For more information please see here Travel If you are travelling to Heidelberg via aeroplane train car or long distance bus you can find useful information here Accommodation Accommodation is not included in the registration fee 24 single rooms have been reserved for 6 nights from Saturday 2 May to Friday 8 May 2026 at a downtown Heidelberg hotel Premier Inn Heidelberg City Centre After the selection process selected participants should contact the hotel directly to make a booking with a booking code PRO26 01 by the deadline of Friday 3 April 2026 We recommend that all course participants stay at the dedicated hotel for the course Local transportation Course shuttle buses Shuttle buses will go from the dedicated hotel to EMBL and back mornings and evenings A bus schedule and location of the bus stops will be made available prior to the meeting Other local transportation In addition to the shuttle busses there is also the public bus 28 that serves the EMBL campus and taxis can be easily booked at any time For more information see here Further details Address EMBL Heidelberg Meyerhofstra e 1 69117 Heidelberg Germany For more information about travel and accommodation please refer to the FAQ page On site information Here you will find useful information for when you are onsite at the event Catering All meals and coffee breaks are included in the registration fee Our catering staff will prepare a variety of vegetarian meals meat and fish dishes soups pasta fresh fruit and vegetables as well as a variety of desserts Please wear your badge at all times when serving yourself No food or drinks are allowed in the auditorium Internet Wi Fi is available on campus using the EMBL Events network and the event specific password which will be provided on site The eduroam network secure worldwide roaming access service developed for the international research and education community is also available Photography During the conference an EMBL Photographer may be taking photos If you would not like to appear in these please inform the photographer or a member of the Course and Conference Office Charging stations There are lockers available next to the stairs leading down into the Auditorium You will find some of those equipped with sockets to charge your smartphone tablet etc In most places the electricity is 220 volts AC 50 cycles An adaptor and a plug that fits the German socket may be needed for your appliances laptop i e American Japanese etc A USB charging station for electronic devices is available at the registration desk Printing We can help to print your boarding pass train ticket Please send it to events embl de and collect your print outs at the registration desk Luggage There are lockers available on site to store your luggage which require a 2 EURO coin to operate There is another luggage room on level E0 which is free to use but remains unlocked during the conference Lost and found Lost and Found items are kept at the registration desk until the end of the conference Nursing room There is a nursing room available in the ATC Rooftop Lounge on level A29 Room for prayers meditation and yoga There is a room for prayer yoga and meditation located on level E0 behind the Auditorium Please be respectful of others using the room EMBL campus map Health and safety notes Please take a moment to read our health and safety policy Do not smoke in any EMBL building Eating and drinking is prohibited in the Auditorium and all laboratories Do not enter any restricted areas or the laboratories unless instructed to do so If first aid is required The first aid room is located next to the ATC Registration Desk room 10 205 Dial the Emergency number 222 from any EMBL internal phone only Be prepared to answer the following questions Where is the accident What happened How many injured Emergency number 06221 387 7821 from mobile phones Please report all accidents to the conference officer at the registration desk In case of fire Press the nearest fire alarm button or the Emergency number 222 from any internal phone A loud fire alarm will go off if an evacuation is required On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points Do not use the lifts Beyond first aid The Heidelberg University Hospital or Universit tsklinikum has a 24 hour accident and emergency facility and is at Im Neuenheimer Feld 672 It is a 8km or a 20 minute taxi ride away from EMBL In a medical emergency the ambulance service generally transports patients to this hospital Please remember to bring your own medication if needed to the conference Note that the next pharmacy is a 4 minute drive from the EMBL but for many medications you will be required to see a doctor to get a prescription Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg The EMBL course and conference office team are able to advise you on where to turn for emergency or non emergency medical treatment in Heidelberg and can assist you in making appointments and or arranging transport to get to the pharmacy or a doctor of your choice if necessary Please note we are not however permitted to personally accompany you off campus Sightseeing A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing Technical requirements and event software Additional software The EMBL eCampus learning platform will be used to collaborate communicate and network with all of the course participants All participants will receive information on how to join shortly before the course We recommend using Chrome Safari or Mozilla Firefox browsers for eCampus Zoom will be used for the live talks and Q A sessions More information will be provided closer to the start of the course Other information While using the software during the course please make sure you have nothing 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OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Systems biology is a still expanding field of research aiming to understand at the molecular level how cells, tissues, and organisms operate in their biological context. Among the key technologies driving this forward, are next-generation sequencing and proteomics as they provide powerful means to determine global expression levels of genes and proteins. Both fields have matured to a degree that they have now become accessible to researchers in many areas of biology. During this course, participants will gain theoretical insight in the structure of sequencing and proteomic data, and they will receive training in data analysis for the annotation, quantification, and statistical analysis of gene and protein expression using various computational tools. In addition, training will be provided in the use...
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