Moving towards genome-wide data integration for patient stratification with Integrate Any Omics.

Benjamin Haibe-Kains https://orcid.org/0000-0002-7684-0079 https://www.wikidata.org/entity/Q38639014 https://www.researcherid.com/rid/D-3702-2011 https://d-nb.info/gnd/1217869190

Shihao Ma Andy G. X. Zeng Benjamin Haibe-Kains Anna Goldenberg John E. Dick Bo Wang 0044 Moving towards genome-wide data integration for patient stratification with Integrate Any Omics. 29-42 2025 7 Nat. Mac. Intell. 1 https://doi.org/10.1038/s42256-024-00942-3 db/journals/natmi/natmi7.html#MaZHGDW25 streams/journals/natmi

Zeinab Navidi Jun Ma 0016 Esteban Miglietta Le Liu Anne E. Carpenter Beth A. Cimini Benjamin Haibe-Kains Bo Wang 0044 MorphoDiff: Cellular Morphology Painting with Diffusion Models. 2025 ICLR https://openreview.net/forum?id=PstM8YfhvI conf/iclr/2025 db/conf/iclr/iclr2025.html#NavidiMMLCCH025

Jing Shang James Bannon Benjamin Haibe-Kains Robert Tibshirani Lassoed Forests: Random Forests with Adaptive Lasso Post-selection. 2025 November abs/2511.06698 CoRR https://doi.org/10.48550/arXiv.2511.06698 db/journals/corr/corr2511.html#abs-2511-06698 streams/journals/corr

Caryn Geady Farnoosh Abbas Aghababazadeh Andres Kohan Scott Schuetze David Shultz Benjamin Haibe-Kains Radiomic-based prediction of lesion-specific systemic treatment response in metastatic disease. 102413 2024 116 Comput. Medical Imaging Graph. https://doi.org/10.1016/j.compmedimag.2024.102413 db/journals/cmig/cmig116.html#GeadyAKSSH24 streams/journals/cmig

Shihao Ma Andy G. X. Zeng Benjamin Haibe-Kains Anna Goldenberg John E. Dick Bo Wang 0044 Integrate Any Omics: Towards genome-wide data integration for patient stratification. 2024 abs/2401.07937 CoRR https://doi.org/10.48550/arXiv.2401.07937 db/journals/corr/corr2401.html#abs-2401-07937

Emily So Fengqing Yu Bo Wang 0044 Benjamin Haibe-Kains Reusability report: Evaluating reproducibility and reusability of a fine-tuned model to predict drug response in cancer patient samples. 792-798 2023 July 5 Nat. Mac. Intell. 7 https://doi.org/10.1038/s42256-023-00688-4 db/journals/natmi/natmi5.html#SoYWH23

Varsha Gouthamchand Ananya Choudhury Frank Hoebers Frederik Wesseling Mattea Welch Sejin Kim Benjamin Haibe-Kains Joanna Kazmierska Andre Dekker Johan van Soest Leonard Wee Privacy-Preserving Dashboard for F.A.I.R Head and Neck Cancer data supporting multi-centered collaborations. 11-21 2023 SWAT4HCLS https://ceur-ws.org/Vol-3415/paper-2.pdf conf/swat4ls/2023 db/conf/swat4ls/swat4hcls2023.html#GouthamchandCHW23

George Adam Benjamin Haibe-Kains Anna Goldenberg Maintaining Stability and Plasticity for Predictive Churn Reduction. 2023 abs/2305.04135 CoRR https://doi.org/10.48550/arXiv.2305.04135 db/journals/corr/corr2305.html#abs-2305-04135

Petr Smirnov Ian Smith Zhaleh Safikhani Wail Ba-alawi Farnoosh Khodakarami Eva Lin Yihong Yu Scott Martin Janosch Ortmann Tero Aittokallio Marc Hafner Benjamin Haibe-Kains Evaluation of statistical approaches for association testing in noisy drug screening data. 188 2022 23 BMC Bioinform. 1 https://doi.org/10.1186/s12859-022-04693-z https://www.wikidata.org/entity/Q112556783 db/journals/bmcbi/bmcbi23.html#SmirnovSSBKLYMO22

Nikta Feizi Sisira Kadambat Nair Petr Smirnov Gangesh Beri Christopher Eeles Parinaz Nasr Esfahani Minoru Nakano Denis Tkachuk Anthony Mammoliti Evgeniya Gorobets Arvind Singh Mer Eva Lin Yihong Yu Scott Martin Marc Hafner Benjamin Haibe-Kains PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. 1348-1357 2022 50 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkab1084 https://www.wikidata.org/entity/Q112637653 db/journals/nar/nar50.html#FeiziNSBEENTMGM22

George-Alexandru Adam Chun-Hao Kingsley Chang Benjamin Haibe-Kains Anna Goldenberg Error Amplification When Updating Deployed Machine Learning Models. 715-740 2022 MLHC https://proceedings.mlr.press/v182/adam22a.html conf/mlhc/2022 db/conf/mlhc/mlhc2022.html#AdamCHG22

Xuelin Yang Louis Abraham Sejin Kim Petr Smirnov Feng Ruan Benjamin Haibe-Kains Robert Tibshirani FastCPH: Efficient Survival Analysis for Neural Networks. 2022 abs/2208.09793 CoRR https://doi.org/10.48550/arXiv.2208.09793 db/journals/corr/corr2208.html#abs-2208-09793

Hossein Sharifi-Noghabi Soheil Jahangiri-Tazehkand Petr Smirnov Casey Hon Anthony Mammoliti Sisira Kadambat Nair Arvind Singh Mer Martin Ester Benjamin Haibe-Kains Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models. 2021 22 Briefings Bioinform. 6 https://doi.org/10.1093/bib/bbab294 db/journals/bib/bib22.html#Sharifi-Noghabi21

Reza Reiazi Engy Abbas Petra Famiyeh Aria Rezaie Jennifer Y. Y. Kwan Tirth Patel Scott V. Bratman Tony Tadic Fei-Fei Liu Benjamin Haibe-Kains The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review. 104400 2021 133 Comput. Biol. Medicine https://doi.org/10.1016/j.compbiomed.2021.104400 db/journals/cbm/cbm133.html#ReiaziAFRKPBTLH21

Tahereh Javaheri Morteza Homayounfar Zohreh Amoozgar Reza Reiazi Fatemeh Homayounieh Engy Abbas Azadeh Laali Amir Reza Radmard Mohammad Hadi Gharib Seyed Ali Javad Mousavi Omid Ghaemi Rosa Babaei Hadi Karimi Mobin Mehdi Hosseinzadeh 0001 Rana Jahanban-Esfahlan Khaled Seidi Mannudeep K. Kalra Guanglan Zhang Lubomir T. Chitkushev Benjamin Haibe-Kains Reza Malekzadeh Reza Rawassizadeh CovidCTNet: an open-source deep learning approach to diagnose covid-19 using small cohort of CT images. 2021 4 npj Digit. Medicine https://doi.org/10.1038/s41746-021-00399-3 https://www.wikidata.org/entity/Q115009508 db/journals/npjdm/npjdm4.html#JavaheriHARHALR21

Sejin Kim Michal Kazmierski Benjamin Haibe-Kains Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. 223-231 2021 SPACA https://proceedings.mlr.press/v146/kim21a.html conf/spaca/2021 db/conf/spaca/spaca2021.html#KimKH21

Michal Kazmierski Mattea Welch Sejin Kim Chris McIntosh Katrina Rey-McIntyre Shao-Hui Huang Tirth Patel Tony Tadic Michael F. Milosevic Fei-Fei Liu Andrew Hope Scott V. Bratman Benjamin Haibe-Kains A Machine Learning Challenge for Prognostic Modelling in Head and Neck Cancer Using Multi-modal Data. 2021 abs/2101.11935 CoRR https://arxiv.org/abs/2101.11935 db/journals/corr/corr2101.html#abs-2101-11935

Michal Kazmierski Benjamin Haibe-Kains Lymph Node Graph Neural Networks for Cancer Metastasis Prediction. 2021 abs/2106.01711 CoRR https://arxiv.org/abs/2106.01711 db/journals/corr/corr2106.html#abs-2106-01711

Sisira Kadambat Nair Christopher Eeles Chantal Ho Gangesh Beri Esther Yoo Denis Tkachuk Amy Tang Parwaiz Nijrabi Petr Smirnov Heewon Seo Danyel Jennen Benjamin Haibe-Kains ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. W455-W462 2020 48 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkaa390 https://www.wikidata.org/entity/Q95287569 db/journals/nar/nar48.html#NairEHBYTTNSSJH20

Heewon Seo Denis Tkachuk Chantal Ho Anthony Mammoliti Aria Rezaie Seyed Ali Madani Tonekaboni Benjamin Haibe-Kains SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. W494-W501 2020 48 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkaa421 https://www.wikidata.org/entity/Q95650054 db/journals/nar/nar48.html#SeoTHMRTH20

Seyed Ali Madani Tonekaboni Andrew E. Brereton Zhaleh Safikhani Andreas Windemuth Benjamin Haibe-Kains Stephen MacKinnon Learning across label confidence distributions using Filtered Transfer Learning. 1117-1123 2020 ICMLA https://doi.org/10.1109/ICMLA51294.2020.00180 conf/icmla/2020 db/conf/icmla/icmla2020.html#TonekaboniBSWHM20 George-Alexandru Adam Chun-Hao Kingsley Chang Benjamin Haibe-Kains Anna Goldenberg Hidden Risks of Machine Learning Applied to Healthcare: Unintended Feedback Loops Between Models and Future Data Causing Model Degradation. 710-731 2020 MLHC http://proceedings.mlr.press/v126/adam20a.html conf/mlhc/2020 db/conf/mlhc/mlhc2020.html#AdamCHG20

Tahereh Javaheri Morteza Homayounfar Zohreh Amoozgar Reza Reiazi Fatemeh Homayounieh Engy Abbas Azadeh Laali Amir Reza Radmard Mohammad Hadi Gharib Seyed Ali Javad Mousavi Omid Ghaemi Rosa Babaei Hadi Karimi Mobin Mehdi Hosseinzadeh 0001 Rana Jahanban-Esfahlan Khaled Seidi Mannudeep K. Kalra Guanglan Zhang Lubomir T. Chitkushev Benjamin Haibe-Kains Reza Malekzadeh Reza Rawassizadeh CovidCTNet: An Open-Source Deep Learning Approach to Identify Covid-19 Using CT Image. 2020 abs/2005.03059 CoRR https://arxiv.org/abs/2005.03059 db/journals/corr/corr2005.html#abs-2005-03059

Seyed Ali Madani Tonekaboni Andrew E. Brereton Zhaleh Safikhani Andreas Windemuth Benjamin Haibe-Kains Stephen MacKinnon Learning across label confidence distributions using Filtered Transfer Learning. 2020 abs/2006.02528 CoRR https://arxiv.org/abs/2006.02528 db/journals/corr/corr2006.html#abs-2006-02528

Sejin Kim Michal Kazmierski Benjamin Haibe-Kains Deep-CR MTLR: a Multi-Modal Approach for Cancer Survival Prediction with Competing Risks. 2020 abs/2012.05765 CoRR https://arxiv.org/abs/2012.05765 db/journals/corr/corr2012.html#abs-2012-05765

Ladislav Rampásek Daniel Hidru Petr Smirnov Benjamin Haibe-Kains Anna Goldenberg Dr.VAE: improving drug response prediction via modeling of drug perturbation effects. 3743-3751 2019 35 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btz158 https://www.wikidata.org/entity/Q92237808 db/journals/bioinformatics/bioinformatics35.html#RampasekHSHG19

Seyed Ali Madani Tonekaboni Venkata Satya Kumar Manem Nehme El-Hachem Benjamin Haibe-Kains SIGN: similarity identification in gene expression. 4830-4833 2019 35 Bioinform. 22 https://doi.org/10.1093/bioinformatics/btz485 https://www.wikidata.org/entity/Q92744012 db/journals/bioinformatics/bioinformatics35.html#TonekaboniMEH19

Deena M. A. Gendoo Robert E. Denroche Amy Zhang Nikolina Radulovich Gun Ho Jang Mathieu Lemire Sandra Fischer Dianne Chadwick Ilinca M. Lungu Emin Ibrahimov Ping-Jiang Cao Lincoln D. Stein Julie M. Wilson John M. S. Bartlett Ming-Sound Tsao Neesha Dhani David Hedley Steven Gallinger Benjamin Haibe-Kains Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. 2019 15 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1006596 https://www.wikidata.org/entity/Q61798360 db/journals/ploscb/ploscb15.html#GendooDZRJLFCLI19

Arvind Singh Mer Petr Smirnov Benjamin Haibe-Kains Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data. 557 2019 BCB https://doi.org/10.1145/3307339.3343176 conf/bcb/2019 db/conf/bcb/bcb2019.html#MerSH19

George Adam Petr Smirnov Benjamin Haibe-Kains Anna Goldenberg Reducing Adversarial Example Transferability Using Gradient Regularization. 2019 abs/1904.07980 CoRR http://arxiv.org/abs/1904.07980 db/journals/corr/corr1904.html#abs-1904-07980

Seyed Ali Madani Tonekaboni Laleh Soltan Ghoraie Venkata Satya Kumar Manem Benjamin Haibe-Kains Predictive approaches for drug combination discovery in cancer. 263-276 2018 19 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbw104 https://www.wikidata.org/entity/Q39018410 db/journals/bib/bib19.html#TonekaboniGMH18

Aliyu Musa Laleh Soltan Ghoraie Shu-Dong Zhang Galina V. Glazko Olli Yli-Harja Matthias Dehmer Benjamin Haibe-Kains Frank Emmert-Streib A review of connectivity map and computational approaches in pharmacogenomics. 506-523 2018 19 Briefings Bioinform. 3 https://doi.org/10.1093/bib/bbw112 https://www.wikidata.org/entity/Q36244997 db/journals/bib/bib19.html#MusaGZGYDHE18

Fupan Yao Seyed Ali Madani Tonekaboni Zhaleh Safikhani Petr Smirnov Nehme El-Hachem Mark Freeman 0002 Venkata Satya Kumar Manem Benjamin Haibe-Kains Tissue specificity of in vitro drug sensitivity. 158-166 2018 25 J. Am. Medical Informatics Assoc. 2 https://doi.org/10.1093/jamia/ocx062 https://www.wikidata.org/entity/Q47655442 db/journals/jamia/jamia25.html#YaoTSSEFMH18

Petr Smirnov Victor Kofia Alexander Maru Mark Freeman 0002 Chantal Ho Nehme El-Hachem George-Alexandru Adam Wail Ba-alawi Zhaleh Safikhani Benjamin Haibe-Kains PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. D994-D1002 2018 46 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkx911 https://www.wikidata.org/entity/Q47134581 db/journals/nar/nar46.html#SmirnovKMFHEABS18

George-Alexandru Adam Petr Smirnov Anna Goldenberg David Duvenaud Benjamin Haibe-Kains Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples. 2018 abs/1808.06645 CoRR http://arxiv.org/abs/1808.06645 db/journals/corr/corr1808.html#abs-1808-06645

Sean Davis 0001 Marcel Ramos Lori A. Shepherd Nitesh Turaga Ludwig Geistlinger Martin T. Morgan Benjamin Haibe-Kains Levi Waldron Orchestrating a community-developed computational workshop and accompanying training materials. 1656 2018 7 F1000Research https://doi.org/10.12688/f1000research.16516.1 https://www.wikidata.org/entity/Q58001642 db/journals/f1000research/f1000research7.html#DavisRSTGMHW18

Aliyu Musa Laleh Soltan Ghoraie Shu-Dong Zhang Galina V. Glazko Olli Yli-Harja Matthias Dehmer Benjamin Haibe-Kains Frank Emmert-Streib A review of connectivity map and computational approaches in pharmacogenomics. 903 2017 18 Briefings Bioinform. 5 https://doi.org/10.1093/bib/bbx023 https://www.wikidata.org/entity/Q87648094 db/journals/bib/bib18.html#MusaGZGYDHE17

Ngoc Cam Pham Benjamin Haibe-Kains Pau Bellot Gianluca Bontempi Patrick E. Meyer 0001 Study of Meta-analysis strategies for network inference using information-theoretic approaches. 15:1-15:14 2017 10 BioData Min. 1 https://doi.org/10.1186/s13040-017-0136-6 https://www.wikidata.org/entity/Q38796769 db/journals/biodatamining/biodatamining10.html#PhamHBBM17

Lavanya Kannan Marcel Ramos Angela Re Nehme Hachem Zhaleh Safikhani Deena M. A. Gendoo Sean Davis 0001 David Gomez-Cabrero Robert Castelo Kasper D. Hansen Vincent J. Carey Martin Morgan Aedín C. Culhane Benjamin Haibe-Kains Levi Waldron Public data and open source tools for multi-assay genomic investigation of disease. 603-615 2016 17 Briefings Bioinform. 4 https://doi.org/10.1093/bib/bbv080 https://www.wikidata.org/entity/Q28596241 db/journals/bib/bib17.html#KannanRRHSGDGCH16

Deena M. A. Gendoo Natchar Ratanasirigulchai Markus S. Schröder Laia Paré Joel S. Parker Aleix Prat Benjamin Haibe-Kains Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. 1097-1099 2016 32 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btv693 https://www.wikidata.org/entity/Q40274876 db/journals/bioinformatics/bioinformatics32.html#GendooRSPPPH16

Petr Smirnov Zhaleh Safikhani Nehme Hachem Dong Wang Adrian She Catharina Olsen Mark Freeman 0002 Heather Marie Selby Deena M. A. Gendoo Patrick Grossmann Andrew H. Beck Hugo J. W. L. Aerts Mathieu Lupien Anna Goldenberg Benjamin Haibe-Kains PharmacoGx: an R package for analysis of large pharmacogenomic datasets. 1244-1246 2016 32 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btv723 https://www.wikidata.org/entity/Q38812641 db/journals/bioinformatics/bioinformatics32.html#SmirnovSHWSOFSG16

Solaiappan Manimaran Heather Marie Selby Kwame Okrah Claire Ruberman Jeffrey T. Leek John Quackenbush Benjamin Haibe-Kains Héctor Corrada Bravo W. Evan Johnson BatchQC: interactive software for evaluating sample and batch effects in genomic data. 3836-3838 2016 32 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btw538 https://www.wikidata.org/entity/Q31122464 db/journals/bioinformatics/bioinformatics32.html#ManimaranSORLQH16

Zhaleh Safikhani Nehme Hachem Petr Smirnov Mark Freeman 0002 Anna Goldenberg Nicolai J. Birkbak Andrew H. Beck Hugo J. W. L. Aerts John Quackenbush Benjamin Haibe-Kains Safikhani et al. reply. E2-E4 2016 540 Nat. 7631 https://doi.org/10.1038/nature19839 https://www.wikidata.org/entity/Q53840848 db/journals/nature/nature540.html#SafikhaniHSFGBB16

Deena M. A. Gendoo Benjamin Haibe-Kains MM2S: personalized diagnosis of medulloblastoma patients and model systems. 6 2016 11 Source Code Biol. Medicine 1 https://doi.org/10.1186/s13029-016-0053-y https://www.wikidata.org/entity/Q39858199 db/journals/scfbm/scfbm11.html#GendooH16

Ngoc Cam Pham Benjamin Haibe-Kains Pau Bellot Gianluca Bontempi Patrick E. Meyer 0001 Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches. 76-83 2016 DEXA Workshops https://doi.org/10.1109/DEXA.2016.030 https://doi.ieeecomputersociety.org/10.1109/DEXA.2016.030 conf/dexaw/2016 db/conf/dexaw/dexaw2016.html#PhamHBB016

Prasad Patil Pierre-Olivier Bachant-Winner Benjamin Haibe-Kains Jeffrey T. Leek Test set bias affects reproducibility of gene signatures. 2318-2323 2015 31 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btv157 https://www.wikidata.org/entity/Q35829697 db/journals/bioinformatics/bioinformatics31.html#PatilBHL15

Swneke D. Bailey Carl Virtanen Benjamin Haibe-Kains Mathieu Lupien ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. 3057-3059 2015 31 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btv321 https://www.wikidata.org/entity/Q36344543 db/journals/bioinformatics/bioinformatics31.html#BaileyVHL15

Kimberly Glass John Quackenbush Dimitrios Spentzos Benjamin Haibe-Kains Guo-Cheng Yuan A network model for angiogenesis in ovarian cancer. 115:1-115:17 2015 16 BMC Bioinform. https://doi.org/10.1186/s12859-015-0551-y https://www.wikidata.org/entity/Q35534413 db/journals/bmcbi/bmcbi16.html#GlassQSHY15

Frank Emmert-Streib Ricardo de Matos Simoes Galina V. Glazko Simon S. McDade Benjamin Haibe-Kains Andreas Holzinger Matthias Dehmer Frederick Campbell Functional and genetic analysis of the colon cancer network. S6 2014 15 BMC Bioinform. S-6 https://doi.org/10.1186/1471-2105-15-S6-S6 https://www.wikidata.org/entity/Q34153290 db/journals/bmcbi/bmcbi15S.html#Emmert-StreibSGMHHDC14

Benjamin Frederick Ganzfried Markus Riester Benjamin Haibe-Kains Thomas Risch Svitlana Tyekucheva Ina Jazic Xin Victoria Wang Mahnaz Ahmadifar Michael J. Birrer Giovanni Parmigiani Curtis Huttenhower Levi Waldron curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. 2013 2013 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bat013 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625954/ https://www.wikidata.org/entity/Q30611147 db/journals/biodb/biodb2013.html#GanzfriedRHRTJWABPHW13

Markus S. Schröder Daniel Gusenleitner John Quackenbush Aedín C. Culhane Benjamin Haibe-Kains RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. 666-668 2013 29 Bioinform. 5 https://doi.org/10.1093/bioinformatics/bts708 https://www.wikidata.org/entity/Q36638518 db/journals/bioinformatics/bioinformatics29.html#SchroderGQCH13

Nicolas De Jay Simon Papillon-Cavanagh Catharina Olsen Nehme Hachem Gianluca Bontempi Benjamin Haibe-Kains mRMRe: an R package for parallelized mRMR ensemble feature selection. 2365-2368 2013 29 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btt383 https://www.wikidata.org/entity/Q34793900 db/journals/bioinformatics/bioinformatics29.html#JayPOHBH13

Simon Papillon-Cavanagh Nicolas De Jay Nehme Hachem Catharina Olsen Gianluca Bontempi Hugo J. W. L. Aerts John Quackenbush Benjamin Haibe-Kains Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity. 597-602 2013 20 J. Am. Medical Informatics Assoc. 4 https://doi.org/10.1136/amiajnl-2012-001442 https://www.wikidata.org/entity/Q37039879 db/journals/jamia/jamia20.html#Papillon-CavanaghJHOBAQH13

Benjamin Haibe-Kains Nehme El-Hachem Nicolai J. Birkbak Andrew C. Jin Andrew H. Beck Hugo J. W. L. Aerts John Quackenbush Inconsistency in large pharmacogenomic studies. 389-393 2013 504 Nat. 7480 https://doi.org/10.1038/nature12831 https://www.wikidata.org/entity/Q34541198 db/journals/nature/nature504.html#Haibe-KainsEBJB13

Andrew H. Beck Nicholas W. Knoblauch Marco M. Hefti Jennifer Kaplan Stuart J. Schnitt Aedín C. Culhane Markus S. Schröder Thomas Risch John Quackenbush Benjamin Haibe-Kains Significance Analysis of Prognostic Signatures. 2013 9 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1002875 https://www.wikidata.org/entity/Q34568149 db/journals/ploscb/ploscb9.html#BeckKHKSCSRQH13

Benjamin Haibe-Kains Catharina Olsen Amira Djebbari Gianluca Bontempi Mick Correll Christopher Bouton John Quackenbush Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. 866-875 2012 40 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkr1050 https://www.wikidata.org/entity/Q35631178 db/journals/nar/nar40.html#Haibe-KainsODBCBQ12

Aedín C. Culhane Markus S. Schröder Razvan Sultana Shaita C. Picard Enzo N. Martinelli Caroline Kelly Benjamin Haibe-Kains Misha Kapushesky Anne-Alyssa St Pierre William Flahive Kermshlise C. Picard Daniel Gusenleitner Gerald Papenhausen Niall O'Connor Mick Correll John Quackenbush GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. 1060-1066 2012 40 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkr901 https://www.wikidata.org/entity/Q35630836 db/journals/nar/nar40.html#CulhaneSSPMKHKPFPGPOCQ12

Markus S. Schröder Aedín C. Culhane John Quackenbush Benjamin Haibe-Kains survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. 3206-3208 2011 27 Bioinform. 22 https://doi.org/10.1093/bioinformatics/btr511 https://www.wikidata.org/entity/Q35526651 db/journals/bioinformatics/bioinformatics27.html#SchroderCQH11

Qiyuan Li Aron C. Eklund Nicolai J. Birkbak Christine Desmedt Benjamin Haibe-Kains Christos P. Sotiriou W. Fraser Symmans Lajos Pusztai Søren Brunak Andrea L. Richardson Zoltan Szallasi Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. 310 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-310 https://www.wikidata.org/entity/Q33974305 db/journals/bmcbi/bmcbi12.html#LiEBDHSSPBRS11

Gianluca Bontempi Benjamin Haibe-Kains Christine Desmedt Christos P. Sotiriou John Quackenbush Multiple-input multiple-output causal strategies for gene selection. 458 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-458 https://www.wikidata.org/entity/Q34083912 db/journals/bmcbi/bmcbi12.html#BontempiHDSQ11

Benjamin Haibe-Kains Christine Desmedt Christos P. Sotiriou Gianluca Bontempi A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? 2200-2208 2008 24 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btn374 https://www.wikidata.org/entity/Q33352632 db/journals/bioinformatics/bioinformatics24.html#Haibe-KainsDSB08

Benjamin Haibe-Kains Christine Desmedt Sherene Loi Mauro Delorenzi Christos P. Sotiriou Gianluca Bontempi Computational Intelligence in Clinical Oncology: Lessons Learned from an Analysis of a Clinical Study. 237-268 2008 Computational Intelligence in Biomedicine and Bioinformatics https://doi.org/10.1007/978-3-540-70778-3_10 https://www.wikidata.org/entity/Q57660188 series/sci/2008-151 db/series/sci/sci151.html#Haibe-KainsDLDSB08 Engy Abbas Louis Abraham George Adam George-Alexandru Adam Hugo J. W. L. Aerts Farnoosh Abbas Aghababazadeh Mahnaz Ahmadifar Tero Aittokallio Zohreh Amoozgar Wail Ba-alawi Rosa Babaei Pierre-Olivier Bachant-Winner Swneke D. Bailey James Bannon John M. S. Bartlett Andrew H. Beck Pau Bellot Gangesh Beri Nicolai J. Birkbak Michael J. Birrer Gianluca Bontempi Christopher Bouton Scott V. Bratman Héctor Corrada Bravo Andrew E. Brereton Søren Brunak Frederick Campbell Ping-Jiang Cao Vincent CareyVincent J. Carey Anne E. Carpenter Robert Castelo Dianne Chadwick Chun-Hao ChangChun-Hao Kingsley Chang Lubomir T. Chitkushev Ananya Choudhury Beth A. Cimini Mick Correll Aedín C. Culhane Sean R. DavisSean Davis 0001 Matthias Dehmer Andre Dekker Mauro Delorenzi Robert E. Denroche Christine Desmedt Neesha Dhani John E. Dick Amira Djebbari David Duvenaud Christopher Eeles Aron C. Eklund Frank Emmert-Streib Parinaz Nasr Esfahani Martin Ester Petra Famiyeh Nikta Feizi Sandra Fischer William Flahive Mark Freeman 0002 Steven Gallinger Benjamin Frederick Ganzfried Caryn Geady Ludwig Geistlinger Deena M. A. Gendoo Omid Ghaemi Mohammad Hadi Gharib Laleh Soltan Ghoraie Kimberly Glass Galina V. Glazko Anna Goldenberg David Gomez-Cabrero Evgeniya Gorobets Varsha Gouthamchand Patrick Grossmann Daniel Gusenleitner Nehme HachemNehme El-Hachem Marc Hafner Kasper D. Hansen David Hedley Marco M. Hefti Daniel Hidru Chantal Ho Frank Hoebers Andreas Holzinger Morteza Homayounfar Fatemeh Homayounieh Casey Hon Andrew Hope Mehdi Hosseinzadeh 0001 Shao-Hui Huang Curtis Huttenhower Emin Ibrahimov Rana Jahanban-Esfahlan Soheil Jahangiri-Tazehkand Gun Ho Jang Tahereh Javaheri Nicolas De Jay Ina Jazic Danyel Jennen Andrew C. Jin W. Evan Johnson Mannudeep K. Kalra Lavanya Kannan Jennifer Kaplan Misha Kapushesky Joanna Kazmierska Michal Kazmierski Caroline Kelly Farnoosh Khodakarami Sejin Kim Nicholas W. Knoblauch Victor Kofia Andres Kohan Jennifer Y. Y. Kwan Azadeh Laali Jeffrey T. Leek Mathieu Lemire Qiyuan Li Eva Lin Fei-Fei Liu Le Liu Sherene Loi Ilinca M. Lungu Mathieu Lupien Jun Ma 0016 Shihao Ma Stephen MacKinnon Reza Malekzadeh Anthony Mammoliti Venkata Satya Kumar Manem Solaiappan Manimaran Scott Martin Enzo N. Martinelli Alexander Maru Simon S. McDade Chris McIntosh Arvind Singh Mer Patrick E. Meyer 0001 Esteban Miglietta Michael F. Milosevic Hadi Karimi Mobin Martin MorganMartin T. Morgan Seyed Ali Javad Mousavi Aliyu Musa Sisira Kadambat Nair Minoru Nakano Zeinab Navidi Parwaiz Nijrabi Niall O'Connor Kwame Okrah Catharina Olsen Janosch Ortmann Gerald Papenhausen Simon Papillon-Cavanagh Laia Paré Joel S. Parker Giovanni Parmigiani Tirth Patel Prasad Patil Ngoc Cam Pham Kermshlise C. Picard Shaita C. Picard Anne-Alyssa St Pierre Aleix Prat Lajos Pusztai John Quackenbush Amir Reza Radmard Nikolina Radulovich Marcel Ramos Ladislav Rampásek Natchar Ratanasirigulchai Reza Rawassizadeh Angela Re Reza Reiazi Katrina Rey-McIntyre Aria Rezaie Andrea L. Richardson Markus Riester Thomas Risch Feng Ruan Claire Ruberman Zhaleh Safikhani Stuart J. Schnitt Markus S. Schröder Scott Schuetze Khaled Seidi Heather Marie Selby Heewon Seo Jing Shang Hossein Sharifi-Noghabi Adrian She Lori A. Shepherd David Shultz Ricardo de Matos Simoes Petr Smirnov Ian Smith Emily So Johan van Soest Christos P. Sotiriou Dimitrios Spentzos Lincoln SteinLincoln D. Stein Razvan Sultana W. Fraser Symmans Zoltan Szallasi Tony Tadic Amy Tang Robert Tibshirani Denis Tkachuk Seyed Ali Madani Tonekaboni Ming-Sound Tsao Nitesh Turaga Svitlana Tyekucheva Carl Virtanen Levi Waldron Bo Wang 0044 Dong Wang Xin Victoria Wang Leonard Wee Mattea Welch Frederik Wesseling Julie M. Wilson Andreas Windemuth Xuelin Yang Fupan Yao Olli Yli-Harja Esther Yoo Fengqing Yu Yihong Yu Guo-Cheng Yuan Andy G. X. Zeng Amy Zhang Guanglan Zhang Shu-Dong Zhang