On this page
- What motivates us
- Our approach
- Outputs (recent highlights)
- Current and future work
- Work with us
- Important publications
- Group members
- Former members
Group leaders: Wolfgang Huber, Sascha Dietrich and Junyan Lu
What motivates us
Why do some cancer treatments elicit response in some patients but not others? How do cancers become resistant to treatment? These are major clinical and scientific challenges. We aim to understand the molecular biological mechanisms that underlie them. We hope to contribute to new treatment strategies, improvements to existing therapies with adjuvants or combinatorics, and better patient stratifications.
Our approach
We use a systems medicine approach that combines ex-vivo drug perturbation profiling on primary cells from lymphoma and leukaemia patients, single-cell multi-omics, and spatial omics. By machine learning / AI based-multi-modal integration and careful computational biology, we aim to dissect the interaction between tumour cells, the tumour microenvironment and the immune system, and modern cancer treatments such as targeted compounds and immunotherapies.
Our joint expertise brings together:
- Applied bioinformatics and biomedical data science
- Access to samples from large, systematic clinical studies and biobanks
- Direct clinical experience with the cancer entities we study
- Cutting-edge single cell and spatial omics instrumentation
- Statistical method development
Outputs (recent highlights)
We demonstrated feasibility in a routine clinical setting of an assay for newly diagnosed blood cancers to record ex-vivo their response to a panel of drugs and return the results to the treating physician with 7-day turnaround [Liebers, Bruch et al., Nature Cancer 2023]. We showed the utility of multi-omics factor analysis (MOFA) to discover an important new type of biological heterogeneity in CLL [Lu, Cannizzaro et al, Nature Cancer 2021]. We studied the impact of the tumour microenvironment on treatment response and disease outcomes via cytokines [Bruch, Giles et al., Molecular Systems Biology 2022] and and via T cells [Roider et al., Nature Cell Biology 2024]. We contributed to safety improvements of CAR T cell therapies [Kobbe et al., NEJM 2024].
Current and future work
Our current and future work is organized along three lines:
- Enhance data-driven statistical analysis with machine deep learning / AI models that represent prior knowledge of molecular biological networks and of cell-, tissue- and organ-scale spatial organisation
- Identify proteomic and metabolic biomarkers for predicting treatment response, by combining mass-spectrometry with multi-omics
- Push the boundaries of spatial omics for predictive and biology-based understanding of the response to immunotherapies (immune checkpoint inhibitors, bispecific antibodies, CAR T cells)
Work with us
We are continually looking for energetic and ambitious researchers at different levels (master thesis, doctoral research, postdoc, research software engineer etc.) to join our team — get in touch!
We particularly welcome candidates who will be able to contribute to technology development and scaling in spatial omics of cancer tissues and models, in statistical bioinformatics and data science, and/or the use of deep learning tools for bioimage analysis and for biological knowledge representation.
Important publications
Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.
Lindenhofer D, Bauman JR, Hawkins JA, Fitzgerald D, Yildiz U, Jung H, Korosteleva A, Marttinen M, Kueblbeck M, Zaugg JB, Noh KM, Dietrich S, Huber W, Stegle O, Steinmetz LM.
Nat Methods. 2025 Oct;22(10):2032-2041. doi: 10.1038/s41592-025-02805-0. Epub 2025 Sep 1. PMID: 40890552
Disease-specific U1 spliceosomal RNA mutations in mature B-cell neoplasms.
Nadeu F, Shuai S, Clot G, Hilton LK, Diaz-Navarro A, Martín S, Royo R, Baumann T, Kulis M, López-Oreja I, Cossio M, Lu J, Ljungström V, Young E, Plevova K, Knisbacher BA, Lin Z, Hahn CK, Bousquets P, Alcoceba M, González M, Colado E, Payer ÁR, Aymerich M, Terol MJ, Rivas-Delgado A, Enjuanes A, Ruiz-Gaspà S, Chatzikonstantinou T, Hägerstrand D, Jylhä C, Skaftason A, Mansouri L, Stranska K, Doubek M, van Gastel-Mol EJ, Davis Z, Walewska R, Scarfò L, Trentin L, Visentin A, Parikh SA, Rabe KG, Moia R, Armand M, Rossi D, Davi F, Gaidano G, Kay NE, Shanafelt TD, Ghia P, Oscier D, Langerak AW, Beà S, López-Guillermo A, Neuberg D, Wu CJ, Getz G, Pospisilova S, Stamatopoulos K, Rosenquist R, Huber W, Zenz T, Colomer D, Martín-Subero JI, Delgado J, Morin RD, Stein LD, Puente XS, Campo E.
Leukemia. 2025 Sep;39(9):2076-2086. doi: 10.1038/s41375-025-02667-7. Epub 2025 Jun 30. PMID: 40588565
Spatialproteomics – an interoperable toolbox for analyzing highly multiplexed fluorescence image data.
Matthias Meyer-Bender, Harald Vöhringer, Christina Schniederjohann, Sarah Koziel, Erin Chung, Ekaterina Popova, Alexander Brobeil, Lisa-Maria Held, Aamir Munir, Scverse Community, Sascha Dietrich, Peter-Martin Bruch, and Wolfgang Huber.
bioRχiv, May 2025.
DOI:10.1101/2025.04.29.651202 – Preprint – EuropePMC.
IAP dependency of T-cell prolymphocytic leukemia identified by high-throughput drug screening.
Pohly MF, Putzker K, Scheinost S, Ben Taarit L, Walther T, Kummer S, Wertheimer T, Lin M, Do THL, Handler K, Michler J, Kivioja J, Bach K, Kisele S, Kim J, Dietrich S, Bornhauser B, Wong WW, Becher B, Moor A, Lewis J, Ficht X, Lu J, Huber W, Zenz T.
Blood. 2025 May 15;145(20):2336-2352. doi: 10.1182/blood.2024027171. PMID: 39869826
BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia.
Chong SJF, Lu J, Valentin R, Lehmberg TZ, Eu JQ, Wang J, Zhu F, Kong LR, Fernandes SM, Zhang J, Herbaux C, Goh BC, Brown JR, Niemann CU, Huber W, Zenz T, Davids MS.
Mol Cancer. 2025 Mar 3;24(1):62. doi: 10.1186/s12943-025-02260-7. PMID: 40025512
Blocking the CD39/CD73 pathway synergizes with anti-CD20 bispecific antibody in nodal B-cell lymphoma.
Kolbe C, Kauer J, Brinkmann B, Dreger P, Huber W, Müller-Tidow C, Dietrich S, Roider T. J
Immunother Cancer. 2025 Jan 30;13(1):e009245. doi: 10.1136/jitc-2024-009245. PMID: 39884778
SpatialData: an open and universal data framework for spatial omics.
Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O.
Nat Methods. 2025 Jan;22(1):58-62. doi: 10.1038/s41592-024-02212-x. Epub 2024 Mar 20. PMID: 38509327
Multiplexed Immunophenotyping of Lymphoma Tissue Samples.
Schniederjohann C, Bruch PM, Dietrich S, Neumann F.
Methods Mol Biol. 2025;2865:375-393. doi: 10.1007/978-1-0716-4188-0_16.PMID: 39424733
Aggressive Lymphoma after CD19 CAR T-Cell Therapy.
Kobbe G, Brüggemann M, Baermann BN, Wiegand L, Trautmann H, Yousefian S, Libertini S, Menssen HD, Maier HJ, Ulrich P, Gao J, Bruch PM, Liebers N, Radujkovic A, Seifert M, Schniederjohann C, Paramasivam N, Fitzgerald D, Seidel M, Esposito I, Germing U, Cadeddu RP, Nachtkamp K, Jäger P, Ulrych T, Fischer JC, Rox JM, Giesel F, Koch R, Antoch G, Distler JHW, Meuth SG, Jacobsen M, Hübschmann D, Lu J, Iaccarino I, Haas S, Damm F, Dietrich S.
N Engl J Med. 2024 Oct 3;391(13):1217-1226. doi: 10.1056/NEJMoa2402730.PMID: 39589371
Multimodal and spatially resolved profiling identifies distinct patterns of T-cell infiltration in nodal B-cell lymphoma entities.
Tobias Roider, Marc A. Baertsch, Donnacha Fitzgerald, Harald Vöhringer, Berit J. Brinkmann, Felix Czernilofsky, Mareike Knoll, Laura Llaó-Cid, Peter-Martin Bruch, Nora Liebers, Christian M. Schürch, Verena Passerini, Alexander Brobeil, Gunhild Mechtersheimer, Carsten Müller-Tidow, Oliver Weigert, Martina Seiffert, Garry P. Nolan, Wolfgang Huber, and Sascha Dietrich
Nature Cell Biology 2024, Feb 20 volume 26, pages 478–489, DOI:10.1038/s41556-024-01358-2
A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity.
Donnacha Fitzgerald, Tobias Roider, Marc-Andrea Baertsch, Artur Kibler, Anastasiia Horlova, Erin Chung, Harald Vöhringer, Anna Mathioudaki, Bettina Budeus, Verena Passerini, Mareike Knoll, Johannes Mammen, Linsha Li, Léandra Caillé, Felix Czernilofsky, Peter-Martin Bruch, Nora Liebers, Matthias Meyer-Bender, Oliver Weigert, Judith Zaugg, Garry Nolan, Marc Seifert, Sascha Dietrich, and Wolfgang Huber.
bioRχiv, 2023. DOI:10.1101/2023.11.06.565756 – Preprint – EuropePMC.
Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial.
Liebers N, Bruch PM, Terzer T, Hernandez-Hernandez M, Paramasivam N, Fitzgerald D, Altmann H, Roider T, Kolb C, Knoll M, Lenze A, Platzbecker U, Röllig C, Baldus C, Serve H, Bornhäuser M, Hübschmann D, Müller-Tidow C, Stölzel F, Huber W, Benner A, Zenz T, Lu J, Dietrich S.
Nat Cancer. 2023 Oct 2. doi: 10.1038/s43018-023-00645-5. Online ahead of print.PMID: 37783805
Comparing the value of mono- versus coculture for high-throughput compound screening in hematological malignancies
Sophie A. Herbst, Vladislav Kim, Tobias Roider, Eva C. Schitter, Peter-Martin Bruch, Nora Liebers, Carolin Kolb, Mareike Knoll, Junyan Lu, Peter Dreger, Carsten Müller-Tidow, Thorsten Zenz, Wolfgang Huber, Sascha Dietrich
Blood advances June 23, 2023 https://doi.org/10.1182/bloodadvances.2022009652.
Retrospective analysis of hematopoietic cell transplantation for blastic plasmacytoid dendritic cell neoplasm: conditioning intensity matters.
Bruch PM, Dietrich S, Finel H, Boumendil A, Greinix H, Heinicke T, Bethge W, Beelen D, Schmid C, Martin H, Castagna L, Scheid C, Schäfer-Eckart K, Bittenbring J, Finke J, Sengeloev H, Heiblig M, Cornelissen J, Chevallier P, Mohty M, Robinson S, Montoto S, Dreger P.
Leukemia. 2023 Feb;37(2):465-472. doi: 10.1038/s41375-022-01782-z. Epub 2022 Dec 22.PMID: 36550212
Venetoclax synergizes with gilteritinib in FLT3 wild-type high-risk acute myeloid leukemia by suppressing MCL-1.
Janssen M, Schmidt C, Bruch PM, Blank MF, Rohde C, Waclawiczek A, Heid D, Renders S, Göllner S, Vierbaum L, Besenbeck B, Herbst SA, Knoll M, Kolb C, Przybylla A, Weidenauer K, Ludwig AK, Fabre M, Gu M, Schlenk RF, Stölzel F, Bornhäuser M, Röllig C, Platzbecker U, Baldus C, Serve H, Sauer T, Raffel S, Pabst C, Vassiliou G, Vick B, Jeremias I, Trumpp A, Krijgsveld J, Müller-Tidow C, Dietrich S.
Blood. 2022 Dec 15;140(24):2594-2610. doi: 10.1182/blood.2021014241.PMID: 35857899
Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis.
Gegner HM, Naake T, Dugourd A, Müller T, Czernilofsky F, Kliewer G, Jäger E, Helm B, Kunze-Rohrbach N, Klingmüller U, Hopf C, Müller-Tidow C, Dietrich S, Saez-Rodriguez J, Huber W, Hell R, Poschet G, Krijgsveld J.
Front Mol Biosci. 2022 Dec 20;9:961448. doi: 10.3389/fmolb.2022.961448. eCollection 2022.PMID: 36605986
Single-cell multi-omic and spatial analysis of nodal B cell non-Hodgkin lymphomas reveals plasticity in B cell maturation as a driver of intratumor heterogeneity.
Donnacha Fitzgerald, Tobias Roider, Marc-A. Baertsch, Harald Vöhringer, Mareike Knoll, Bettina Budeus, Artur Kibler, Anna Mathioudaki, Léandra Caillé, Linsha Li, Johannes Mammen, Marc Seifert, Wolfgang Huber, and Sascha Dietrich.
Blood, 140:742, November 2022. DOI:10.1182/blood-2022-156210
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.
Nat Biotechnol. 2022 Nov 24. doi: 10.1038/s41587-022-01551-4. Online ahead of print.PMID: 36424487
Multimodal and spatially resolved profiling identifies distinct patterns of T-cell infiltration in nodal B-cell lymphoma entities
Roider T, Marc A. Baertsch et al
bioRxiv Nov 8, 2022
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia.
Herbst SA, Vesterlund M, Helmboldt AJ, Jafari R, Siavelis I, Stahl M, Schitter EC, Liebers N, Brinkmann BJ, Czernilofsky F, Roider T, Bruch PM, Iskar M, Kittai A, Huang Y, Lu J, Richter S, Mermelekas G, Umer HM, Knoll M, Kolb C, Lenze A, Cao X, Österholm C, Wahnschaffe L, Herling C, Scheinost S, Ganzinger M, Mansouri L, Kriegsmann K, Kriegsmann M, Anders S, Zapatka M, Del Poeta G, Zucchetto A, Bomben R, Gattei V, Dreger P, Woyach J, Herling M, Müller-Tidow C, Rosenquist R, Stilgenbauer S, Zenz T, Huber W, Tausch E, Lehtiö J, Dietrich S.
Nat Commun. 2022 Oct 20;13(1):6226. doi: 10.1038/s41467-022-33385-8.PMID: 36266272
Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling.
Batzilla A, Lu J, Kivioja J, Putzker K, Lewis J, Zenz T, Huber W.
PLoS Comput Biol. 2022 Aug 22;18(8):e1010438. doi: 10.1371/journal.pcbi.1010438. eCollection 2022 Aug.PMID: 35994503
Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL.
Bruch PM, Giles HA, Kolb C, Herbst SA, Becirovic T, Roider T, Lu J, Scheinost S, Wagner L, Huellein J, Berest I, Kriegsmann M, Kriegsmann K, Zgorzelski C, Dreger P, Zaugg JB, Müller-Tidow C, Zenz T, Huber W, Dietrich S.
Mol Syst Biol. 2022 Aug;18(8):e10855. doi: 10.15252/msb.202110855. PMID: 35959629
Networks and graphs discovery in metabolomics data analysis and interpretation
A Amara, C Frainay, F Jourdan, T Naake, S Neumann et al
Frontiers in Molecular Biosciences, 08. March 2022, 223
Humoral and cellular responses after COVID-19 vaccination in anti-CD20-treated lymphoma patients.
Liebers N, Speer C, Benning L, Bruch PM, Kraemer I, Meissner J, Schnitzler P, Kräusslich HG, Dreger P, Mueller-Tidow C, Poschke I, Dietrich S.
Blood. 2022 Jan 6;139(1):142-147. doi: 10.1182/blood.2021013445.PMID: 34669919
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
Alina Batzilla, Junyan Lu, Jarno Kivioja, Kerstin Putzker, Joe Lewis, Thorsten Zenz, Wolfgang Huber
bioRxiv 2022.01.11.475864; doi: https://doi.org/10.1101/2022.01.11.475864
MatrixQCvis: shiny-based interactive data quality exploration for omics data.
Naake T, Huber W.
Bioinformatics. 2021 Nov 12;38(4):1181-2. doi: 10.1093/bioinformatics/btab748. Online ahead of print. PMID: 34788796
Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake.
Zimoń M, Huang Y, Trasta A, Halavatyi A, Liu JZ, Chen CY, Blattmann P, Klaus B, Whelan CD, Sexton D, John S, Huber W, Tsai EA, Pepperkok R, Runz H.
Nat Commun. 2021 Nov 5;12(1):6411. doi: 10.1038/s41467-021-26761-3. PMID: 34741066
Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia.
Lu J, Cannizzaro E, Meier-Abt F, Scheinost S, Bruch PM, Giles HA, Lütge A, Hüllein J, Wagner L, Giacopelli B, Nadeu F, Delgado J, Campo E, Mangolini M, Ringshausen I, Böttcher M, Mougiakakos D, Jacobs A, Bodenmiller B, Dietrich S, Oakes CC, Zenz T, Huber W.
Nat Cancer. 2021 Aug;2(8):853-864. doi: 10.1038/s43018-021-00216-6. Epub 2021 Jul 1. PMID: 34423310
Mapping drug-microenvironment-genetic interplay in CLL reveals trisomy 12 as a modulator of microenvironmental signals
Peter-Martin Bruch, Holly A. R. Giles, Carolin Kolb, Sophie A. Herbst, Tina Becirovic, Tobias Roider, Junyan Lu, Sebastian Scheinost, Lena Wagner, Jennifer Huellein, Ivan Berest, Mark Kriegsmann, Katharina Kriegsmann, Christiane Zgorzelski, Peter Dreger, Judith B. Zaugg, Carsten Müller-Tidow, Thorsten Zenz, Wolfgang Huber, Sascha Dietrich
biorxiv https://doi.org/10.1101/2021.07.23.453514
Polatuzumab vedotin as a salvage and bridging treatment in relapsed or refractory large B-cell lymphomas.
Liebers N, Duell J, Fitzgerald D, Kerkhoff A, Noerenberg D, Kaebisch E, Acker F, Fuhrmann S, Leng C, Welslau M, Chemnitz J, Middeke JM, Weber T, Holtick U, Trappe R, Pfannes R, Liersch R, Spoer C, Fuxius S, Gebauer N, Caillé L, Geer T, Koenecke C, Keller U, Claus R, Mougiakakos D, Mayer S, Huettmann A, Pott C, Trummer A, Wulf G, Brunnberg U, Bullinger L, Hess G, Mueller-Tidow C, Glass B, Lenz G, Dreger P, Dietrich S.
Blood Adv. 2021 Jul 13;5(13):2707-2716. doi: 10.1182/bloodadvances.2020004155. PMID: 34196677
The Protein Landscape of Chronic Lymphocytic Leukemia (CLL).
Meier-Abt F, Lu J, Cannizzaro E, Pohly MF, Kummer S, Pfammatter S, Kunz L, Collins BC, Nadeu F, Lee KS, Xue P, Gwerder M, Roiss M, Hüllein J, Scheinost S, Dietrich S, Campo E, Huber W, Aebersold R, Zenz T.
Blood. 2021 Jun 29:blood.2020009741. doi: 10.1182/blood.2020009741. Online ahead of print. PMID: 34189564
Transformation and Preprocessing of Single-Cell RNA-Seq Data
Constantin Ahlmann-Eltze, Wolfgang Huber
Biorxiv June 25, 2021 https://doi.org/10.1101/2021.06.24.449781
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data.
Ahlmann-Eltze C, Huber W.
Bioinformatics. 2021 Apr 5;36(24):5701-5702. doi: 10.1093/bioinformatics/btaa1009. PMID: 33295604
The impact of SAMHD1 expression and mutation status in mantle cell lymphoma: An analysis of the MCL Younger and Elderly trial.
Roider T, Wang X, Hüttl K, Müller-Tidow C, Klapper W, Rosenwald A, Stewart JP, de Castro DG, Dreger P, Hermine O, Kluin-Nelemans HC, Grabe N, Dreyling M, Pott C, Ott G, Hoster E, Dietrich S.
Int J Cancer. 2021 Jan 1;148(1):150-160. doi: 10.1002/ijc.33202. Epub 2020 Aug 15. PMID: 32638373
Miniaturized Drug Sensitivity and Resistance Test on Patient-Derived Cells Using Droplet-Microarray.
Popova AA, Dietrich S, Huber W, Reischl M, Peravali R, Levkin PA.
SLAS Technol. 2020 Aug 13:2472630320934432. doi: 10.1177/2472630320934432. Online ahead of print. PMID: 32791934
The impact of SAMHD1 expression and mutation status in mantle cell lymphoma: An analysis of the MCL Younger and Elderly trial.
Roider T, Wang X, Hüttl K, Müller-Tidow C, Klapper W, Rosenwald A, Stewart JP, Gonzalez de Castro D, Dreger P, Hermine O, Kluin-Nelemans HC, Grabe N, Dreyling M, Pott C, Ott G, Hoster E, Dietrich S.
Int J Cancer. 2020 Jul 7. doi: 10.1002/ijc.33202. Online ahead of print. PMID: 32638373
Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels.
Roider T, Seufert J, Uvarovskii A, Frauhammer F, Bordas M, Abedpour N, Stolarczyk M, Mallm JP, Herbst SA, Bruch PM, Balke-Want H, Hundemer M, Rippe K, Goeppert B, Seiffert M, Brors B, Mechtersheimer G, Zenz T, Peifer M, Chapuy B, Schlesner M, Müller-Tidow C, Fröhling S, Huber W, Anders S, Dietrich S.
Nat Cell Biol. 2020 Jul;22(7):896-906. doi: 10.1038/s41556-020-0532-x. Epub 2020 Jun 15. PMID: 32541878
Survey of ex vivo drug combination effects in chronic lymphocytic leukemia reveals synergistic drug effects and genetic dependencies.
Lukas M, Velten B, Sellner L, Tomska K, Hüellein J, Walther T, Wagner L, Muley C, Wu B, Oleś M, Dietrich S, Jethwa A, Bohnenberger H, Lu J, Huber W, Zenz T.
Leukemia. 2020 May 13. doi: 10.1038/s41375-020-0846-5. Online ahead of print. PMID: 32404973
BRAF inhibitor treatment in classic hairy cell leukemia: a long-term follow-up study of patients treated outside clinical trials.
Liebers N, Roider T, Bohn JP, Haberbosch I, Pircher A, Ferstl B, Ebnöther M, Wendtner CM, Dearden C, Follows GA, Ho AD, Müller-Tidow C, Dreger P, Troussard X, Zenz T, Dietrich S.
Leukemia 2020 May;34(5):1454-1457. doi: 10.1038/s41375-019-0646-y. Epub 2019 Nov 18. PMID: 31740808
Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB.
Cell Rep. 2019 Dec 3;29(10):3147-3159.e12. doi: 10.1016/j.celrep.2019.10.106. PMID: 31801079
Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O.
Mol Syst Biol. 2018 Jun 20;14(6):e8124. doi: 10.15252/msb.20178124. PMID:29925568
Drug-perturbation-based stratification of blood cancer.
Dietrich S, Oleś M, Lu J, Sellner L, Anders S, Velten B, Wu B, Hüllein J, da Silva Liberio M, Walther T, Wagner L, Rabe S, Ghidelli-Disse S, Bantscheff M, Oleś AK, Słabicki M, Mock A, Oakes CC, Wang S, Oppermann S, Lukas M, Kim V, Sill M, Benner A, Jauch A, Sutton LA, Young E, Rosenquist R, Liu X, Jethwa A, Lee KS, Lewis J, Putzker K, Lutz C, Rossi D, Mokhir A, Oellerich T, Zirlik K, Herling M, Nguyen-Khac F, Plass C, Andersson E, Mustjoki S, von Kalle C, Ho AD, Hensel M, Dürig J, Ringshausen I, Zapatka M, Huber W, Zenz T.
J Clin Invest. 2018 Jan 2;128(1):427-445. doi: 10.1172/JCI93801. Epub 2017 Dec 11.PMID:29227286
Data-driven hypothesis weighting increases detection power in genome-scale multiple testing.
Ignatiadis N, Klaus B, Zaugg JB, Huber W.
Nat Methods. 2016 Jul;13(7):577-80. doi: 10.1038/nmeth.3885.
PMID:27240256
BRAF inhibition in hairy cell leukemia with low-dose vemurafenib.
Dietrich S, Pircher A, Endris V, Peyrade F, Wendtner CM, Follows GA, Hüllein J, Jethwa A, Ellert E, Walther T, Liu X, Dyer MJ, Elter T, Brummer T, Zeiser R, Hermann M, Herold M, Weichert W, Dearden C, Haferlach T, Seiffert M, Hallek M, von Kalle C, Ho AD, Gaehler A, Andrulis M, Steurer M, Zenz T.
Blood. 2016 Jun 9;127(23):2847-55. doi: 10.1182/blood-2015-11-680074.
PMID: 26941398
A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells.
Breinig M, Klein FA, Huber W, Boutros M.
Mol Syst Biol. 2015 Dec 23;11(12):846. doi: 10.15252/msb.20156400.
PMID: 26700849
Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells.
Brennecke P, Reyes A, Pinto S, Rattay K, Nguyen M, Küchler R, Huber W, Kyewski B, Steinmetz LM. Nat Immunol. 2015 Sep;16(9):933-41. doi: 10.1038/ni.3246.
PMID: 26237553
Recurrent CDKN1B (p27) mutations in hairy cell leukemia.
Dietrich S, Hüllein J, Lee SC, Hutter B, Gonzalez D, Jayne S, Dyer MJ, Oleś M, Else M, Liu X, Słabicki M, Wu B, Troussard X, Dürig J, Andrulis M, Dearden C, von Kalle C, Granzow M, Jauch A, Fröhling S, Huber W, Meggendorfer M, Haferlach T, Ho AD, Richter D, Brors B, Glimm H, Matutes E, Abdel Wahab O, Zenz T.
Blood. 2015 Aug 20;126(8):1005-8. doi: 10.1182/blood-2015-04-643361.
PMID: 26065650
Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP.
Hauer C, Curk T, Anders S, Schwarzl T, Alleaume AM, Sieber J, Hollerer I, Bhuvanagiri M, Huber W, Hentze MW, Kulozik AE.
Nat Commun. 2015 Aug 11;6:7921. doi: 10.1038/ncomms8921.
PMID: 26260686
A map of directional genetic interactions in a metazoan cell.
Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M.
Elife. 2015 Mar 6;4. doi: 10.7554/eLife.05464.
PMID:25748138
Orchestrating high-throughput genomic analysis with Bioconductor.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.
Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.
PMID: 25633503
Continued response off treatment after BRAF inhibition in refractory hairy cell leukemia.
Dietrich S, Hüllein J, Hundemer M, Lehners N, Jethwa A, Capper D, Acker T, Garvalov BK, Andrulis M, Blume C, Schulte C, Mandel T, Meissner J, Fröhling S, von Kalle C, Glimm H, Ho AD, Zenz T.
J Clin Oncol. 2013 Jul 1;31(19):e300-3. doi: 10.1200/JCO.2012.45.9495. No abstract available.
PMID:23690412
Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping.
Laufer C, Fischer B, Billmann M, Huber W, Boutros M.
Nat Methods. 2013 May;10(5):427-31. doi: 10.1038/nmeth.2436.
PMID:23563794
BRAF inhibition in refractory hairy-cell leukemia.
Dietrich S, Glimm H, Andrulis M, von Kalle C, Ho AD, Zenz T.
N Engl J Med. 2012 May 24;366(21):2038-40. doi: 10.1056/NEJMc1202124.
PMID:22621641
Group members
Shubham Agrawal
Data Engineer/Technical Assistant
Lu Group, Institute for Computational Biomedicine, Medical Faculty Heidelberg, Heidelberg University
shubham.agrawal@uni-heidelberg.de
Antonia-Eugenia Angeli-Terzidou
PhD Student
Dietrich Group, Department of Internal Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Medical Center
Phone: + 49 6221 56-1949
Antonia.Angeli-Terzidou@med.uni-heidelberg.de
Peter-Martin Bruch, MD
Physician Scientist
Dietrich Group, Department of Internal Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Medical Center
Phone: + 49 6221 56-39066
Peter-Martin.Bruch@med.uni-heidelberg.de
Erin Kim Chung
PhD student (EMBL International PhD Programme – EIPP)
Huber Group, EMBL
Phone: +49 6221 387-8131
erin.chung@embl.de
Felix Czernilofsky, MD
Physician Scientist
Dietrich Group, Department of Internal Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Medical Center
Phone: + 49 6221 56-1949
Felix.Czernilofsky@med.uni-heidelberg.de
Jiaojiao He
PhD Student
Lu Group, Institute for Computational Biomedicine, Medical Faculty Heidelberg, Heidelberg University
jiaojiao.he@stud.uni-heidelberg.de
Anastasiia Horlova
PhD student (EMBL International PhD Programme – EIPP)
Huber Group, EMBL
Phone: +49 6221 387 8151
anastasiia.horlova@embl.de
Sviatoslav Kharuk
PhD student (EMBL International PhD Programme – EIPP)
Huber Group, EMBL
Phone: +49 6221 387-8131
sviatoslav.kharuk@embl.de
Sarah Patricia Koziel
PhD Student
Dietrich Group
Qian-Wu Liao
PhD Student
Lu Group, Institute for Computational Biomedicine, Medical Faculty Heidelberg, Heidelberg University
QianWu.Liao@stud.uni-heidelberg.de
Nora Liebers, MD
Physician Scientist
Dietrich Group, Department of Internal Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Medical Center
Phone: + 49 6221 56-39066
Nora.Liebers@med.uni-heidelberg.de
Caroline Lohoff
PhD student
Lu Group, Institute for Computational Biomedicine, Medical Faculty Heidelberg, Heidelberg University
caroline.lohoff@uni-heidelberg.de
Matthias Meyer-Bender
PhD student (EMBL International PhD Programme – EIPP)
Huber Group, EMBL
Phone: +49 6221 387-8151
matthias.meyerbender@embl.de
Stefan Peidli, PhD
Postdoc
Huber Group, EMBL
Phone: +49 6221 387-8151
stefan.peidli@embl.de
Giada Sandrini, PhD
Postdoc
Lu Group, Institute for Computational Biomedicine, Medical Faculty Heidelberg, Heidelberg University
Christina Schniederjohann
PhD Student
Dietrich Group, Department of Internal Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Medical Center
Phone: + 49 6221 56-6539
Christina.Schniederjohann@med.uni-heidelberg.de
Marc Seifert, PhD
Staff Scientist
Dietrich Group, Department of Internal Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Medical Center
Vladimir Vutov, PhD
Postdoc
Lu Group, Institute for Computational Biomedicine, Medical Faculty Heidelberg, Heidelberg University
vladimir.vutov@uni-heidelberg.de
Former members
Constantin Ahlmann-Eltze
PhD student (EMBL International PhD Programme – EIPP)
Hosna Baniadam, PhD student (EMBL International PhD Programme – EIPP)
Berit Brinkmann, PhD Postdoc
Klemens Tümay Capraz, PhD student (EMBL International PhD Programme – EIPP)
Holly Giles, PhD
Postdoc
Donnacha Fitzgerald, PhD student (EMBL International PhD Programme – EIPP)
Laleh Haghverdi, PhD
Postdoc
Alexander Helmboldt, PhD
Postdoc
Sophie Herbst, PhD
Postdoc
Jennifer Hüllein
Data Manager
Vladislav Kim
PhD student (EMBL International PhD Programme – EIPP)
Carolin Kolb
Technician
Junyan Lu, PhD
Expert in Machine Learning
Thomas Naake, PhD, Postdoc
Tobias Roider, MD
Petr Smirnov, PhD, Postdoc
Marta Stolarczyk, PhD
Postdoc
Britta Velten
PhD student (EMBL International PhD Programme – EIPP)
Harald Vöhringer, PhD Postdoc
