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Harvard Wai Hann Hui, Weijia Kong, Wilson Wen Bin Goh

Barbora Orlikova-Boyer, Anne Lorant, Sruthi Reddy Gajulapalli, Claudia Cerella, Michael Schnekenburger, Jin-Young Lee, Ji Yeon Paik, Yejin Lee, David Siegel, David Ross, Byung Woo Han, Thi Kim Yen Nguyen, Christo Christov, Hyoung Jin Kang, Mario Dicato, Marc Diederich

Auob Rustamzadeh, Abbas Tafakhori, Armin Ariaei, Mahdi Heydari, Mehran Ebrahimi Shah-abadi, Farhad Seif

Douglas V. N. P. Oliveira, Edyta Biskup, Colm J. O’Rourke, Julie L. Hentze, Jesper B. Andersen, Claus Høgdall, Estrid V. Høgdall

Nikita A Verheyden, Melina Klostermann, Mirko Brüggemann, Hanna M Steede, Anica Scholz, Shady Amr, Chiara Lichtenthaeler, Christian Münch, Tobias Schmid, Kathi Zarnack, Andreas Krueger

Mohammad Elahimanesh, Nafiseh Shokri, Elmira Mahdinia, Payam Mohammadi, Najmeh Parvaz, Mohammad Najafi

Yuan Liu, Jinzhu Lin, Menglong Li, Zhining Wen

Jacopo Vegni, Ying Sun, Stefan E. Seemann, Martina Zappaterra, Roberta Davoli, Stefania Dall’Olio, Jan Gorodkin, Paolo Zambonelli

Christopher M. Dunn, Cassandra Sturdy, Cassandra Velasco, Leoni Schlupp, Emmaline Prinz, Vladislav Izda, Liubov Arbeeva, Yvonne M. Golightly, Amanda E. Nelson, Matlock A. Jeffries

Youngsic Jeon, Tae Kyeom Kang, Wook-Bin Lee, Sang Hoon Jung, Young-Joo Kim

Aggeliki K. Meligova, Dimitra Siakouli, Sotiria Stasinopoulou, Despoina S. Xenopoulou, Maria Zoumpouli, Vassiliki Ganou, Eleni-Fani Gkotsi, Aristotelis Chatziioannou, Olga Papadodima, Eleftherios Pilalis, Michael N. Alexis, Dimitra J. Mitsiou

Antonella L. Bastone, Violetta Dziadek, Philipp John-Neek, Friederike Mansel, Jenni Fleischauer, Eric Agyeman-Duah, Dirk Schaudien, Oliver Dittrich-Breiholz, Adrian Schwarzer, Axel Schambach, Michael Rothe

Nora Yujia Payne, Johann A Gagnon-Bartsch

Ryszard Kubinski, Jean-Yves Djamen-Kepaou, Timur Zhanabaev, Alex Hernandez-Garcia, Stefan Bauer, Falk Hildebrand, Tamas Korcsmaros, Sani Karam, Prévost Jantchou, Kamran Kafi, Ryan D. Martin

JingYang Niu, Wei Xu, DongMing Wei, Kun Qian, Qian Wang

Jingyang Niu, Jing Yang, Yuyu Guo, Kun Qian, Qian Wang

Alejandra Avalos-Pacheco, David Rossell, Richard S. Savage

Gustavo Bravo Ruiz, Michele Tinti, Melanie Ridgway, David Horn

Michael Kenn, Rudolf Karch, Dan Cacsire Castillo-Tong, Christian F. Singer, Heinz Koelbl, Wolfgang Schreiner

Qingqin S. Li, Diana Cai

Akram Ghantous, Alexei Novoloaca, Liacine Bouaoun, Cyrille Cuenin, Marie-Pierre Cros, Ya Xu, Hector Hernandez-Vargas, Momodou K. Darboe, Andrew M. Prentice, Sophie E. Moore, Yun Yun Gong, Zdenko Herceg, Michael N. Routledge

Michael Kenn, Dan Cacsire Castillo-Tong, Christian F. Singer, Michael Cibena, Heinz Kölbl, Wolfgang Schreiner

Elisa Ferrari, Alessandra Retico, Davide Bacciu

Michael Schubert, Maria Colomé-Tatché, Floris Foijer

Albert Eric Schultze, Bindu Bennet, Jessica Caverly Rae, Alan Y. Chiang, Kendall Frazier, Paula Katavolos, LuAnn McKinney, Daniel J. Patrick, Niraj Tripathi

Qingqin S. Li, Yu Sun, Tania Wang

Christopher M. Dunn, Michael C. Nevitt, John A. Lynch, Matlock A. Jeffries

Sebastian Ohse, Melanie Boerries, Hauke Busch

Jiajianghui Li, Zining Wu, Deqiang Zheng, Yue Sun, Sisi Wang, Yuxiang Yan

Anna Papiez, Michal Marczyk, Joanna Polanska, Andrzej Polanski

Igor H. Wierzbicki, Anaamika Campeau, Diana Dehaini, Maya Holay, Xiaoli Wei, Trever Greene, Man Ying, Jenna S. Sands, Anne Lamsa, Elina Zuniga, Kit Pogliano, Ronnie H. Fang, Christopher N. LaRock, Liangfang Zhang, David J. Gonzalez

Robin Gradin, Malin Lindstedt, Henrik Johansson

Jeffrey W. Tyner, Cristina E. Tognon, Daniel Bottomly, Beth Wilmot, Stephen E. Kurtz, Samantha L. Savage, Nicola Long, Anna Reister Schultz, Elie Traer, Melissa Abel, Anupriya Agarwal, Aurora Blucher, Uma Borate, Jade Bryant, Russell Burke, Amy Carlos, Richie Carpenter, Joseph Carroll, Bill H. Chang, Cody Coblentz, Amanda d’Almeida, Rachel Cook, Alexey Danilov, Kim-Hien T. Dao, Michie Degnin, Deirdre Devine, James Dibb, David K. Edwards, Christopher A. Eide, Isabel English, Jason Glover, Rachel Henson, Hibery Ho, Abdusebur Jemal, Kara Johnson, Ryan Johnson, Brian Junio, Andy Kaempf, Jessica Leonard, Chenwei Lin, Selina Qiuying Liu, Pierrette Lo, Marc M. Loriaux, Samuel Luty, Tara Macey, Jason MacManiman, Jacqueline Martinez, Motomi Mori, Dylan Nelson, Ceilidh Nichols, Jill Peters, Justin Ramsdill, Angela Rofelty, Robert Schuff, Robert Searles, Erik Segerdell, Rebecca L. Smith, Stephen E. Spurgeon, Tyler Sweeney, Aashis Thapa, Corinne Visser, Jake Wagner, Kevin Watanabe-Smith, Kristen Werth, Joelle Wolf, Libbey White, Amy Yates, Haijiao Zhang, Christopher R. Cogle, Robert H. Collins, Denise C. Connolly, Michael W. Deininger, Leylah Drusbosky, Christopher S. Hourigan, Craig T. Jordan, Patricia Kropf, Tara L. Lin, Micaela E. Martinez, Bruno C. Medeiros, Rachel R. Pallapati, Daniel A. Pollyea, Ronan T. Swords, Justin M. Watts, Scott J. Weir, David L. Wiest, Ryan M. Winters, Shannon K. McWeeney, Brian J. Druker

M. Umut Caglar, Adam J. Hockenberry, Claus O. Wilke

Junfang Chen, Emanuel Schwarz

Seunggeun Lee, Wei Sun, Fred A. Wright, Fei Zou

Samanwoy Mukhopadhyay, Pravat K. Thatoi, Abhay D. Pandey, Bidyut K. Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj K. Mohapatra

Roman Hornung, David Causeur, Christoph Bernau, Anne-Laure Boulesteix

Junghyun Jung, Kyoungyoung Hah, Woosuk Lee, Wonhee Jang

Roman Hornung, Anne-Laure Boulesteix, David Causeur

Zhixiang Lin, Can Yang, Ying Zhu, John Duchi, Yao Fu, Yong Wang, Bai Jiang, Mahdi Zamanighomi, Xuming Xu, Mingfeng Li, Nenad Sestan, Hongyu Zhao, Wing Hung Wong

Elisa M Noll, Christian Eisen, Albrecht Stenzinger, Elisa Espinet, Alexander Muckenhuber, Corinna Klein, Vanessa Vogel, Bernd Klaus, Wiebke Nadler, Christoph Rösli, Christian Lutz, Michael Kulke, Jan Engelhardt, Franziska M Zickgraf, Octavio Espinosa, Matthias Schlesner, Xiaoqi Jiang, Annette Kopp-Schneider, Peter Neuhaus, Marcus Bahra, Bruno V Sinn, Roland Eils, Nathalia A Giese, Thilo Hackert, Oliver Strobel, Jens Werner, Markus W Büchler, Wilko Weichert, Andreas Trumpp, Martin R Sprick

Jacob J. Hughey, Atul J. Butte

2024	Thinking points for effective batch correction on biomedical data Briefings in Bioinformatics Harvard Wai Hann Hui, Weijia Kong, Wilson Wen Bin Goh
2024	Antileukemic potential of methylated indolequinone MAC681 through immunogenic necroptosis and PARP1 degradation Biomarker Research Barbora Orlikova-Boyer, Anne Lorant, Sruthi Reddy Gajulapalli, Claudia Cerella, Michael Schnekenburger, Jin-Young Lee, Ji Yeon Paik, Yejin Lee, David Siegel, David Ross, Byung Woo Han, Thi Kim Yen Nguyen, Christo Christov, Hyoung Jin Kang, Mario Dicato, Marc Diederich
2024	Targeting Caspases 3/6 and Cathepsins L/B May Decrease Laminopathy-Induced Apoptosis in Alzheimer’s Disease Journal of Alzheimer's Disease Auob Rustamzadeh, Abbas Tafakhori, Armin Ariaei, Mahdi Heydari, Mehran Ebrahimi Shah-abadi, Farhad Seif
2024	Developing a DNA Methylation Signature to Differentiate High-Grade Serous Ovarian Carcinomas from Benign Ovarian Tumors Molecular Diagnosis & Therapy Douglas V. N. P. Oliveira, Edyta Biskup, Colm J. O’Rourke, Julie L. Hentze, Jesper B. Andersen, Claus Høgdall, Estrid V. Høgdall
2024	A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match Nucleic Acids Research Nikita A Verheyden, Melina Klostermann, Mirko Brüggemann, Hanna M Steede, Anica Scholz, Shady Amr, Chiara Lichtenthaeler, Christian Münch, Tobias Schmid, Kathi Zarnack, Andreas Krueger
2024	Differential gene expression patterns in ST-elevation Myocardial Infarction and Non-ST-elevation Myocardial Infarction Scientific Reports Mohammad Elahimanesh, Nafiseh Shokri, Elmira Mahdinia, Payam Mohammadi, Najmeh Parvaz, Mohammad Najafi
2023	Computational Methods in Engineering & the Sciences Yuan Liu, Jinzhu Lin, Menglong Li, Zhining Wen
2023	RNA-Seq Study on the Longissimus thoracis Muscle of Italian Large White Pigs Fed Extruded Linseed with or without Antioxidants and Polyphenols Animals Jacopo Vegni, Ying Sun, Stefan E. Seemann, Martina Zappaterra, Roberta Davoli, Stefania Dall’Olio, Jan Gorodkin, Paolo Zambonelli
2023	Peripheral Blood DNA Methylation–Based Machine Learning Models for Prediction of Knee Osteoarthritis Progression: Biologic Specimens and Data From the Osteoarthritis Initiative and Johnston County Osteoarthritis Project Arthritis & Rheumatology Christopher M. Dunn, Cassandra Sturdy, Cassandra Velasco, Leoni Schlupp, Emmaline Prinz, Vladislav Izda, Liubov Arbeeva, Yvonne M. Golightly, Amanda E. Nelson, Matlock A. Jeffries
2023	Gene Signatures and Associated Transcription Factors of Allergic Rhinitis: KLF4 Expression Is Associated with Immune Response BioMed Research International Youngsic Jeon, Tae Kyeom Kang, Wook-Bin Lee, Sang Hoon Jung, Young-Joo Kim
2023	ERβ1 Sensitizes and ERβ2 Desensitizes ERα-Positive Breast Cancer Cells to the Inhibitory Effects of Tamoxifen, Fulvestrant and Their Combination with All-Trans Retinoic Acid International Journal of Molecular Sciences Aggeliki K. Meligova, Dimitra Siakouli, Sotiria Stasinopoulou, Despoina S. Xenopoulou, Maria Zoumpouli, Vassiliki Ganou, Eleni-Fani Gkotsi, Aristotelis Chatziioannou, Olga Papadodima, Eleftherios Pilalis, Michael N. Alexis, Dimitra J. Mitsiou
2023	Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants Molecular Therapy - Methods & Clinical Development Antonella L. Bastone, Violetta Dziadek, Philipp John-Neek, Friederike Mansel, Jenni Fleischauer, Eric Agyeman-Duah, Dirk Schaudien, Oliver Dittrich-Breiholz, Adrian Schwarzer, Axel Schambach, Michael Rothe
2022	Separating and reintegrating latent variables to improve classification of genomic data Biostatistics Nora Yujia Payne, Johann A Gagnon-Bartsch
2022	Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease Frontiers in Genetics Ryszard Kubinski, Jean-Yves Djamen-Kepaou, Timur Zhanabaev, Alex Hernandez-Garcia, Stefan Bauer, Falk Hildebrand, Tamas Korcsmaros, Sani Karam, Prévost Jantchou, Kamran Kafi, Ryan D. Martin
2022	Deep Learning Framework for Integrating Multibatch Calibration, Classification, and Pathway Activities Analytical Chemistry JingYang Niu, Wei Xu, DongMing Wei, Kun Qian, Qian Wang
2022	Joint deep learning for batch effect removal and classification toward MALDI MS based metabolomics BMC Bioinformatics Jingyang Niu, Jing Yang, Yuyu Guo, Kun Qian, Qian Wang
2022	Heterogeneous Large Datasets Integration Using Bayesian Factor Regression Bayesian Analysis Alejandra Avalos-Pacheco, David Rossell, Richard S. Savage
2022	Control of Variant Surface Glycoprotein Expression by CFB2 in Trypanosoma brucei and Quantitative Proteomic Connections to Translation and Cytokinesis mSphere Gustavo Bravo Ruiz, Michele Tinti, Melanie Ridgway, David Horn
2022	Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer Journal of Personalized Medicine Michael Kenn, Rudolf Karch, Dan Cacsire Castillo-Tong, Christian F. Singer, Heinz Koelbl, Wolfgang Schreiner
2021	Integrated miRNA-Seq and mRNA-Seq Study to Identify miRNAs Associated With Alzheimer’s Disease Using Post-mortem Brain Tissue Samples Frontiers in Neuroscience Qingqin S. Li, Diana Cai
2021	Aflatoxin Exposure during Early Life Is Associated with Differential DNA Methylation in Two-Year-Old Gambian Children International Journal of Molecular Sciences Akram Ghantous, Alexei Novoloaca, Liacine Bouaoun, Cyrille Cuenin, Marie-Pierre Cros, Ya Xu, Hector Hernandez-Vargas, Momodou K. Darboe, Andrew M. Prentice, Sophie E. Moore, Yun Yun Gong, Zdenko Herceg, Michael N. Routledge
2020	The nucleosome remodeling and deacetylase complex has prognostic significance and associates with immune microenvironment in skin cutaneous melanoma International Immunopharmacology Xinhua Liu, Ju Wang
2020	Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers BioMed Research International Michael Kenn, Dan Cacsire Castillo-Tong, Christian F. Singer, Michael Cibena, Heinz Kölbl, Wolfgang Schreiner
2020	Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI) Artificial Intelligence in Medicine Elisa Ferrari, Alessandra Retico, Davide Bacciu
2020	Gene networks in cancer are biased by aneuploidies and sample impurities Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms Michael Schubert, Maria Colomé-Tatché, Floris Foijer
2020	Scientific Regulatory Policy Committee Points to Consider*: Nuisance Factors, Block Effects, and Batch Effects in Nonclinical Safety Assessment Studies Toxicologic Pathology Albert Eric Schultze, Bindu Bennet, Jessica Caverly Rae, Alan Y. Chiang, Kendall Frazier, Paula Katavolos, LuAnn McKinney, Daniel J. Patrick, Niraj Tripathi
2020	Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions Clinical Epigenetics Qingqin S. Li, Yu Sun, Tania Wang
2019	A pilot study of peripheral blood DNA methylation models as predictors of knee osteoarthritis radiographic progression: data from the Osteoarthritis Initiative (OAI) Scientific Reports Christopher M. Dunn, Michael C. Nevitt, John A. Lynch, Matlock A. Jeffries
2019	Blind normalization of public high-throughput databases PeerJ Computer Science Sebastian Ohse, Melanie Boerries, Hauke Busch
2019	Bioinformatics analysis of the regulatory lncRNA‑miRNA‑mRNA network and drug prediction in patients with hypertrophic cardiomyopathy Molecular Medicine Reports Jiajianghui Li, Zining Wu, Deqiang Zheng, Yue Sun, Sisi Wang, Yuxiang Yan
2019	BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm Bioinformatics Anna Papiez, Michal Marczyk, Joanna Polanska, Andrzej Polanski
2019	Group A Streptococcal S Protein Utilizes Red Blood Cells as Immune Camouflage and Is a Critical Determinant for Immune Evasion Cell Reports Igor H. Wierzbicki, Anaamika Campeau, Diana Dehaini, Maya Holay, Xiaoli Wei, Trever Greene, Man Ying, Jenna S. Sands, Anne Lamsa, Elina Zuniga, Kit Pogliano, Ronnie H. Fang, Christopher N. LaRock, Liangfang Zhang, David J. Gonzalez
2019	Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects PLOS ONE Robin Gradin, Malin Lindstedt, Henrik Johansson
2018	Functional genomic landscape of acute myeloid leukaemia Nature Jeffrey W. Tyner, Cristina E. Tognon, Daniel Bottomly, Beth Wilmot, Stephen E. Kurtz, Samantha L. Savage, Nicola Long, Anna Reister Schultz, Elie Traer, Melissa Abel, Anupriya Agarwal, Aurora Blucher, Uma Borate, Jade Bryant, Russell Burke, Amy Carlos, Richie Carpenter, Joseph Carroll, Bill H. Chang, Cody Coblentz, Amanda d’Almeida, Rachel Cook, Alexey Danilov, Kim-Hien T. Dao, Michie Degnin, Deirdre Devine, James Dibb, David K. Edwards, Christopher A. Eide, Isabel English, Jason Glover, Rachel Henson, Hibery Ho, Abdusebur Jemal, Kara Johnson, Ryan Johnson, Brian Junio, Andy Kaempf, Jessica Leonard, Chenwei Lin, Selina Qiuying Liu, Pierrette Lo, Marc M. Loriaux, Samuel Luty, Tara Macey, Jason MacManiman, Jacqueline Martinez, Motomi Mori, Dylan Nelson, Ceilidh Nichols, Jill Peters, Justin Ramsdill, Angela Rofelty, Robert Schuff, Robert Searles, Erik Segerdell, Rebecca L. Smith, Stephen E. Spurgeon, Tyler Sweeney, Aashis Thapa, Corinne Visser, Jake Wagner, Kevin Watanabe-Smith, Kristen Werth, Joelle Wolf, Libbey White, Amy Yates, Haijiao Zhang, Christopher R. Cogle, Robert H. Collins, Denise C. Connolly, Michael W. Deininger, Leylah Drusbosky, Christopher S. Hourigan, Craig T. Jordan, Patricia Kropf, Tara L. Lin, Micaela E. Martinez, Bruno C. Medeiros, Rachel R. Pallapati, Daniel A. Pollyea, Ronan T. Swords, Justin M. Watts, Scott J. Weir, David L. Wiest, Ryan M. Winters, Shannon K. McWeeney, Brian J. Druker
2018	Predicting bacterial growth conditions from mRNA and protein abundances PLOS ONE M. Umut Caglar, Adam J. Hockenberry, Claus O. Wilke
2017	Methods in Molecular Biology Junfang Chen, Emanuel Schwarz
2017	An improved and explicit surrogate variable analysis procedure by coefficient adjustment Biometrika Seunggeun Lee, Wei Sun, Fred A. Wright, Fei Zou
2017	Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock PLOS ONE Samanwoy Mukhopadhyay, Pravat K. Thatoi, Abhay D. Pandey, Bidyut K. Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj K. Mohapatra
2017	Improving cross-study prediction through addon batch effect adjustment or addon normalization Bioinformatics Roman Hornung, David Causeur, Christoph Bernau, Anne-Laure Boulesteix
2017	Meta-analysis of microarray datasets for the risk assessment of coplanar polychlorinated biphenyl 77 (PCB77) on human health Toxicology and Environmental Health Sciences Junghyun Jung, Kyoungyoung Hah, Woosuk Lee, Wonhee Jang
2016	Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment BMC Bioinformatics Roman Hornung, Anne-Laure Boulesteix, David Causeur
2016	Simultaneous dimension reduction and adjustment for confounding variation Proceedings of the National Academy of Sciences Zhixiang Lin, Can Yang, Ying Zhu, John Duchi, Yao Fu, Yong Wang, Bai Jiang, Mahdi Zamanighomi, Xuming Xu, Mingfeng Li, Nenad Sestan, Hongyu Zhao, Wing Hung Wong
2016	CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma Nature Medicine Elisa M Noll, Christian Eisen, Albrecht Stenzinger, Elisa Espinet, Alexander Muckenhuber, Corinna Klein, Vanessa Vogel, Bernd Klaus, Wiebke Nadler, Christoph Rösli, Christian Lutz, Michael Kulke, Jan Engelhardt, Franziska M Zickgraf, Octavio Espinosa, Matthias Schlesner, Xiaoqi Jiang, Annette Kopp-Schneider, Peter Neuhaus, Marcus Bahra, Bruno V Sinn, Roland Eils, Nathalia A Giese, Thilo Hackert, Oliver Strobel, Jens Werner, Markus W Büchler, Wilko Weichert, Andreas Trumpp, Martin R Sprick
2015	Robust meta-analysis of gene expression using the elastic net Nucleic Acids Research Jacob J. Hughey, Atul J. Butte
2015
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