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Guojing Cong, Frank Chao, Daniel L. Svoboda, Jeremy N. Erickson, Michele R. Balik-Meisner, Deepak Mav, Dhiral P. Phadke, Elizabeth H. Scholl, Ruchir R. Shah, Scott S. Auerbach

Nicolas Borisov, Maksim Sorokin, Anton Buzdin

Zeynep Kucukakcali, Sami Akbulut, Cemil Colak

Ding-Fan Guo, Lin-Wei Fan, Qi Wen, Jin-Ke Wang, Yun-Hui Liang, Qi Feng, Ting Wang, Kun-He Zhang

Fei Deng, Yongfeng Zhang, Lanjing Zhang

Wenbo Chen, Bingjun Yan, Aidong Xu, Xin Mu, Xiufang Zhou, Maowei Jiang, Changgang Wang, Rui Li, Jie Huang, Junhua Dong

A S Escobedo-Muñoz, Diego Carmona-Campos, Armando G G Trapaga, Julio A Freyre-González

Shuai Li, Yaqiang Guo, Chenxi Huo, Lin Zhu, Caixia Shi, Risu Na, Mingjuan Gu, Wenguang Zhang

Saud Alqahtani, Taha Alqahtani, Krishnaraju Venkatesan, Durgaramani Sivadasan, Rehab Ahmed, Hassabelrasoul Elfadil, Premalatha Paulsamy, Kalaiselvi Periannan

Li Wang, Jinjin Wang, Yutong Wang, Ting Niu, Ailin Zhao

Elio Nushi, François P Douillard, Katja Selby, Benjamin A Blount, Oliver J Pennington, Nigel P Minton, Miia Lindström, Antti Honkela

Fei Deng, Catherine H. Feng, Nan Gao, Lanjing Zhang

Yuning Cheng, Si-Mei Xu, Kristina Santucci, Grace Lindner, Michael Janitz

Beibei Wang, Yihui Luan

Beibei Wang, Fengzhu Sun, Yihui Luan

Shuqiong Zheng, Weixiong Zeng, Qianyun Wu, Weimin Li, Zilong He, Enze Li, Chong Tang, Xiang Xue, Genggeng Qin, Bin Zhang, Honglei Yin

Daniel Skubleny, Sunita Ghosh, Jennifer Spratlin, Daniel E. Schiller, Gina R. Rayat

Mathias N. Stokholm, Maria B. Rabaglino, Haja N. Kadarmideen

Katelyn A. McKenzie, Jonathan D. Mahnken

Meng Zhou, Siqi Bao, Tongyang Gong, Qiang Wang, Jie Sun, Jiaqi Li, Minyi Lu, Wanyuan Sun, Jianzhong Su, Hongyan Chen, Zhihua Liu

Zhang Chen, Liqun Chen, Zhengwei Ma, Kangkang Xu, Yu Zhou, Wenjing Shen

Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi, Nafiseh Ghorbanpour Farshbaf, Abolfazl Barzegar, Ulf Schmitz

Nicolas Borisov, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Ella Kim, Denis Kuzmin, Betul Karademir-Yilmaz, Anton Buzdin

Ruxu Sun, Hongjing Zhu, Ying Wang, Jianan Wang, Chao Jiang, Qiuchen Cao, Yeran Zhang, Yichen Zhang, Songtao Yuan, Qinghuai Liu

Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni

Zi-Xin Qin, Guo-Zhong Chen, Qian-Qian Yang, Ying-Jian Wu, Chu-Qing Sun, Xiao-Man Yang, Mei Luo, Chun-Rong Yi, Jun Zhu, Wei-Hua Chen, Zhi Liu

Supawan Jamnongsong, Patipark Kueanjinda, Pongsakorn Buraphat, Phuwanat Sakornsakolpat, Kulthida Vaeteewoottacharn, Seiji Okada, Siwanon Jirawatnotai, Somponnat Sampattavanich

Nicolas Borisov, Anton Buzdin

Weixiong Zeng, Wei Li, Kaibin Huang, Zhenzhou Lin, Hui Dai, Zilong He, Renyi Liu, Zhaodong Zeng, Genggeng Qin, Weiguo Chen, Yongming Wu

Ilaha Isali, Phillip McClellan, Adam Calaway, Megan Prunty, Phillip Abbosh, Kirtishri Mishra, Lee Ponsky, Sarah Markt, Sarah P Psutka, Laura Bukavina

Nicolas Borisov, Maksim Sorokin, Marianna Zolotovskaya, Constantin Borisov, Anton Buzdin

Yuri Belotti, Elaine Lim, Chwee Lim

Malik Qasaimeh, Rand Abu Hammour, Muneer Bani Yassein, Raad S. Al‐Qassas, Juan Alfonso Lara Torralbo, David Lizcano

Geoffroy Andrieux, Sajib Chakraborty

Weihao Chen, Pâmela A. Alexandre, Gabriela Ribeiro, Heidge Fukumasu, Wei Sun, Antonio Reverter, Yutao Li

Yazeed Zoabi, Noam Shomron

François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jennifer J. Hill

Kailin Tang, Xuejie Ji, Mengdi Zhou, Zeliang Deng, Yuwei Huang, Genhui Zheng, Zhiwei Cao

Yuri Belotti, Su Bin Lim, Narayanan Gopalakrishna Iyer, Wan-Teck Lim, Chwee Teck Lim

Zhixian Liu, Zehang Jiang, Nan Wu, Guoren Zhou, Xiaosheng Wang

Franziska Linke, Macha Aldighieri, Anbarasu Lourdusamy, Anna M Grabowska, Snow Stolnik, Ian D Kerr, Catherine LR Merry, Beth Coyle

Müge Yalçin, Rukeia El-Athman, Koliane Ouk, Josef Priller, Angela Relógio

Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira

Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, Christine A. Wells

Frans M. van der Kloet, Jeroen Buurmans, Martijs J. Jonker, Age K. Smilde, Johan A. Westerhuis

Mohamed Alloghani, Dhiya Al-Jumeily, Jamila Mustafina, Abir Hussain, Ahmed J. Aljaaf

Xiaomei Li, Lin Liu, Gregory J. Goodall, Andreas Schreiber, Taosheng Xu, Jiuyong Li, Thuc D. Le

Sadia Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine Pelch, Gilbert B. Wilshire, Trupti Joshi

Timothy J Peters, Hugh J French, Stephen T Bradford, Ruth Pidsley, Clare Stirzaker, Hilal Varinli, Shalima Nair, Wenjia Qu, Jenny Song, Katherine A Giles, Aaron L Statham, Helen Speirs, Terence P Speed, Susan J Clark

Fernando M. Delgado, Francisco Gómez-Vela

Shuai Jiang, Si-Jin Cheng, Li-Chen Ren, Qian Wang, Yu-Jian Kang, Yang Ding, Mei Hou, Xiao-Xu Yang, Yuan Lin, Nan Liang, Ge Gao

Jaclyn N. Taroni, Peter C. Grayson, Qiwen Hu, Sean Eddy, Matthias Kretzler, Peter A. Merkel, Casey S. Greene

Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola

Ian Duran, Roberto Leandro, Jose Guevara-Coto

Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim

Carly A. Bobak, Alexander J. Titus, Jane E. Hill

L. D. Mora, O. Azofeifa, D. Diaz, J. A. Guevara-Coto

Matthew J. Emmett, Mitchell A. Lazar

Chao Chen, Qingtuan Meng, Yan Xia, Chaodong Ding, Le Wang, Rujia Dai, Lijun Cheng, Preethi Gunaratne, Richard A. Gibbs, Shishi Min, Cristian Coarfa, Jeffrey G. Reid, Chunling Zhang, Chuan Jiao, Yi Jiang, Gina Giase, Amber Thomas, Dominic Fitzgerald, Tonya Brunetti, Annie Shieh, Cuihua Xia, Yongjun Wang, Yunpeng Wang, Judith A. Badner, Elliot S. Gershon, Kevin P. White, Chunyu Liu

Weidong Zhang, Jing Wang, Sandeep Menon

Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, Phil J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett A. Mason, Josie B. Garner, Leah C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain, Michael E. Goddard

Nathan T. Johnson, Andi Dhroso, Katelyn J. Hughes, Dmitry Korkin

Weidong Zhang, Bo Huang, Jing Wang, Sandeep Menon

Jennifer M Franks, Guoshuai Cai, Michael L Whitfield

Christina Bligaard Pedersen, Finn Cilius Nielsen, Maria Rossing, Lars Rønn Olsen

Jeffrey A. Thompson, Brock C. Christensen, Carmen J. Marsit

Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene

Yufen Song, Zhaohui Yan

Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene

Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene

Minseung Kim, Navneet Rai, Violeta Zorraquino, Ilias Tagkopoulos

Jing Qin, Bin Yan, Yaohua Hu, Panwen Wang, Junwen Wang

2026	Transplatformer: translating toxicogenomic profiles between generations of platforms BMC Bioinformatics Guojing Cong, Frank Chao, Daniel L. Svoboda, Jeremy N. Erickson, Michele R. Balik-Meisner, Deepak Mav, Dhiral P. Phadke, Elizabeth H. Scholl, Ruchir R. Shah, Scott S. Auerbach
2025	Handbook of Translational Transcriptomics Nicolas Borisov, Maksim Sorokin, Anton Buzdin
2025	Prediction of genomic biomarkers for endometriosis using the transcriptomic dataset World Journal of Clinical Cases Zeynep Kucukakcali, Sami Akbulut, Cemil Colak
2025	Dual tissue mRNA and serum protein signatures improve risk stratification in hepatocellular carcinoma npj Precision Oncology Ding-Fan Guo, Lin-Wei Fan, Qi Wen, Jin-Ke Wang, Yun-Hui Liang, Qi Feng, Ting Wang, Kun-He Zhang
2025	Toward the Best Generalizable Performance of Machine Learning in Modeling Omic and Clinical Data Laboratory Investigation Fei Deng, Yongfeng Zhang, Lanjing Zhang
2025	An intelligent matching method for the equivalent circuit of electrochemical impedance spectroscopy based on Random Forest Journal of Materials Science & Technology Wenbo Chen, Bingjun Yan, Aidong Xu, Xin Mu, Xiufang Zhou, Maowei Jiang, Changgang Wang, Rui Li, Jie Huang, Junhua Dong
2025	How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO Briefings in Bioinformatics A S Escobedo-Muñoz, Diego Carmona-Campos, Armando G G Trapaga, Julio A Freyre-González
2025	Machine Learning-Based Analysis of Differentially Expressed Genes in the Muscle Transcriptome Between Beef Cattle and Dairy Cattle International Journal of Molecular Sciences Shuai Li, Yaqiang Guo, Chenxi Huo, Lin Zhu, Caixia Shi, Risu Na, Mingjuan Gu, Wenguang Zhang
2025	Unveiling Pharmacogenomics Insights into Circular RNAs: Toward Precision Medicine in Cancer Therapy Biomolecules Saud Alqahtani, Taha Alqahtani, Krishnaraju Venkatesan, Durgaramani Sivadasan, Rehab Ahmed, Hassabelrasoul Elfadil, Premalatha Paulsamy, Kalaiselvi Periannan
2025	A disulfidptosis‐related gene signature predicts prognosis and immune‐metabolic landscape in multiple myeloma British Journal of Haematology Li Wang, Jinjin Wang, Yutong Wang, Ting Niu, Ailin Zhao
2025	A supervised Bayesian method for time (re)annotation of transcriptomics data NAR Genomics and Bioinformatics Elio Nushi, François P Douillard, Katja Selby, Benjamin A Blount, Oliver J Pennington, Nigel P Minton, Miia Lindström, Antti Honkela
2025	Normalization and Selecting Non-Differentially Expressed Genes Improve Machine Learning Modelling of Cross-Platform Transcriptomic Data Transactions on Artificial Intelligence Fei Deng, Catherine H. Feng, Nan Gao, Lanjing Zhang
2024	Machine learning and related approaches in transcriptomics Biochemical and Biophysical Research Communications Yuning Cheng, Si-Mei Xu, Kristina Santucci, Grace Lindner, Michael Janitz
2024	Evaluation of normalization methods for predicting quantitative phenotypes in metagenomic data analysis Frontiers in Genetics Beibei Wang, Yihui Luan
2024	Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity Scientific Reports Beibei Wang, Fengzhu Sun, Yihui Luan
2024	Predictive Models for Suicide Attempts in Major Depressive Disorder and the Contribution of EPHX2: A Pilot Integrative Machine Learning Study Depression and Anxiety Shuqiong Zheng, Weixiong Zeng, Qianyun Wu, Weimin Li, Zilong He, Enze Li, Chong Tang, Xiang Xue, Genggeng Qin, Bin Zhang, Honglei Yin
2024	Feature-specific quantile normalization and feature-specific mean–variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data BMC Bioinformatics Daniel Skubleny, Sunita Ghosh, Jennifer Spratlin, Daniel E. Schiller, Gina R. Rayat
2024	GEDI: An R Package for Integration of Transcriptomic Data from Multiple Platforms for Bioinformatics Applications Current Protocols Mathias N. Stokholm, Maria B. Rabaglino, Haja N. Kadarmideen
2024	Estimator of Agreement with Covariate Adjustment Journal of Agricultural, Biological and Environmental Statistics Katelyn A. McKenzie, Jonathan D. Mahnken
2023	The transcriptional landscape and diagnostic potential of long non-coding RNAs in esophageal squamous cell carcinoma Nature Communications Meng Zhou, Siqi Bao, Tongyang Gong, Qiang Wang, Jie Sun, Jiaqi Li, Minyi Lu, Wanyuan Sun, Jianzhong Su, Hongyan Chen, Zhihua Liu
2023	Joint modeling for early predictions of Li-ion battery cycle life and degradation trajectory Energy Zhang Chen, Liqun Chen, Zhengwei Ma, Kangkang Xu, Yu Zhou, Wenjing Shen
2023	Network-Based and Machine-Learning Approaches Identify Diagnostic and Prognostic Models for EMT-Type Gastric Tumors Genes Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi, Nafiseh Ghorbanpour Farshbaf, Abolfazl Barzegar, Ulf Schmitz
2023	Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns Frontiers in Molecular Biosciences Nicolas Borisov, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Ella Kim, Denis Kuzmin, Betul Karademir-Yilmaz, Anton Buzdin
2023	Circular RNA expression and the competitive endogenous RNA network in pathological, age-related macular degeneration events: A cross-platform normalization study The Journal of Biomedical Research Ruxu Sun, Hongjing Zhu, Ying Wang, Jianan Wang, Chao Jiang, Qiuchen Cao, Yeran Zhang, Yichen Zhang, Songtao Yuan, Qinghuai Liu
2023	Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously Communications Biology Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni
2023	Cross-Platform Transcriptomic Data Integration, Profiling, and Mining in Vibrio cholerae Microbiology Spectrum Zi-Xin Qin, Guo-Zhong Chen, Qian-Qian Yang, Ying-Jian Wu, Chu-Qing Sun, Xiao-Man Yang, Mei Luo, Chun-Rong Yi, Jun Zhu, Wei-Hua Chen, Zhi Liu
2022	Comprehensive drug response profiling and pan-omic analysis identified therapeutic candidates and prognostic biomarkers for Asian cholangiocarcinoma iScience Supawan Jamnongsong, Patipark Kueanjinda, Pongsakorn Buraphat, Phuwanat Sakornsakolpat, Kulthida Vaeteewoottacharn, Seiji Okada, Siwanon Jirawatnotai, Somponnat Sampattavanich
2022	Comprehensive Library of Drug Response and Pan-Omic Analysis Identified Therapeutic Candidates and Accompanying Prognostic Biomarkers for Asian Cholangiocarcinoma SSRN Electronic Journal Supawan Jamnongsong, Patipark Kueanjinda, Pongsakorn Buraphat, Phuwanat Sakornsakolpat, Kulthida Vaeteewoottacharn, Seiji Okada, Siwanon Jirawatnotai, Somponnat Sampattavanich
2022	Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect Biomedicines Nicolas Borisov, Anton Buzdin
2022	Big data and computational advancements for next generation of Microbial Biotechnology Microbial Biotechnology Zulema Udaondo
2022	Predicting futile recanalization, malignant cerebral edema, and cerebral herniation using intelligible ensemble machine learning following mechanical thrombectomy for acute ischemic stroke Frontiers in Neurology Weixiong Zeng, Wei Li, Kaibin Huang, Zhenzhou Lin, Hui Dai, Zilong He, Renyi Liu, Zhaodong Zeng, Genggeng Qin, Weiguo Chen, Yongming Wu
2022	Gene network profiling in muscle-invasive bladder cancer: A systematic review and meta-analysis Urologic Oncology: Seminars and Original Investigations Ilaha Isali, Phillip McClellan, Adam Calaway, Megan Prunty, Phillip Abbosh, Kirtishri Mishra, Lee Ponsky, Sarah Markt, Sarah P Psutka, Laura Bukavina
2022	Shambhala‐2: A Protocol for Uniformly Shaped Harmonization of Gene Expression Profiles of Various Formats Current Protocols Nicolas Borisov, Maksim Sorokin, Marianna Zolotovskaya, Constantin Borisov, Anton Buzdin
2022	The Role of the Extracellular Matrix and Tumor-Infiltrating Immune Cells in the Prognostication of High-Grade Serous Ovarian Cancer Cancers Yuri Belotti, Elaine Lim, Chwee Lim
2022	Advanced security testing using a cyber‐attack forecasting model: A case study of financial institutions Journal of Software: Evolution and Process Malik Qasaimeh, Rand Abu Hammour, Muneer Bani Yassein, Raad S. Al‐Qassas, Juan Alfonso Lara Torralbo, David Lizcano
2021	Editorial: Integration of Multi-Omics Techniques in Cancer Frontiers in Genetics Geoffroy Andrieux, Sajib Chakraborty
2021	Identification of Predictor Genes for Feed Efficiency in Beef Cattle by Applying Machine Learning Methods to Multi-Tissue Transcriptome Data Frontiers in Genetics Weihao Chen, Pâmela A. Alexandre, Gabriela Ribeiro, Heidge Fukumasu, Wei Sun, Antonio Reverter, Yutao Li
2021	Methods in Molecular Biology Yazeed Zoabi, Noam Shomron
2021	Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data Scientific Reports François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jennifer J. Hill
2021	Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer Nucleic Acids Research Kailin Tang, Xuejie Ji, Mengdi Zhou, Zeliang Deng, Yuwei Huang, Genhui Zheng, Zhiwei Cao
2021	Prognostic Matrisomal Gene Panel and Its Association with Immune Cell Infiltration in Head and Neck Carcinomas Cancers Yuri Belotti, Su Bin Lim, Narayanan Gopalakrishna Iyer, Wan-Teck Lim, Chwee Teck Lim
2021	Classification of gastric cancers based on immunogenomic profiling Translational Oncology Zhixian Liu, Zehang Jiang, Nan Wu, Guoren Zhou, Xiaosheng Wang
2021	3D hydrogels reveal medulloblastoma subgroup differences and identify extracellular matrix subtypes that predict patient outcome The Journal of Pathology Franziska Linke, Macha Aldighieri, Anbarasu Lourdusamy, Anna M Grabowska, Snow Stolnik, Ian D Kerr, Catherine LR Merry, Beth Coyle
2020	Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington’s Disease Cancers Müge Yalçin, Rukeia El-Athman, Koliane Ouk, Josef Priller, Angela Relógio
2020	Merging microarray studies to identify a common gene expression signature to several structural heart diseases BioData Mining Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira
2020	A simple, scalable approach to building a cross-platform transcriptome atlas PLOS Computational Biology Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, Christine A. Wells
2020	Increased comparability between RNA-Seq and microarray data by utilization of gene sets PLOS Computational Biology Frans M. van der Kloet, Jeroen Buurmans, Martijs J. Jonker, Age K. Smilde, Johan A. Westerhuis
2020	Unsupervised and Semi-Supervised Learning Mohamed Alloghani, Dhiya Al-Jumeily, Jamila Mustafina, Abir Hussain, Ahmed J. Aljaaf
2020	A novel single-cell based method for breast cancer prognosis PLOS Computational Biology Xiaomei Li, Lin Liu, Gregory J. Goodall, Andreas Schreiber, Taosheng Xu, Jiuyong Li, Thuc D. Le
2019	Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data Frontiers in Genetics Sadia Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine Pelch, Gilbert B. Wilshire, Trupti Joshi
2019	Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements Bioinformatics Timothy J Peters, Hugh J French, Stephen T Bradford, Ruth Pidsley, Clare Stirzaker, Hilal Varinli, Shalima Nair, Wenjia Qu, Jenny Song, Katherine A Giles, Aaron L Statham, Helen Speirs, Terence P Speed, Susan J Clark
2019	Computational methods for Gene Regulatory Networks reconstruction and analysis: A review Artificial Intelligence in Medicine Fernando M. Delgado, Francisco Gómez-Vela
2019	An expanded landscape of human long noncoding RNA Nucleic Acids Research Shuai Jiang, Si-Jin Cheng, Li-Chen Ren, Qian Wang, Yu-Jian Kang, Yang Ding, Mei Hou, Xiao-Xu Yang, Yuan Lin, Nan Liang, Ge Gao
2019	MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease Cell Systems Jaclyn N. Taroni, Peter C. Grayson, Qiwen Hu, Sean Eddy, Matthias Kretzler, Peter A. Merkel, Casey S. Greene
2019	Multiplatform biomarker identification using a data-driven approach enables single-sample classification BMC Bioinformatics Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola
2019	2019 IV Jornadas Costarricenses de Investigación en Computación e Informática (JoCICI) Ian Duran, Roberto Leandro, Jose Guevara-Coto
2019	Compendiums of cancer transcriptomes for machine learning applications Scientific Data Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
2019	Comparison of common machine learning models for classification of tuberculosis using transcriptional biomarkers from integrated datasets Applied Soft Computing Carly A. Bobak, Alexander J. Titus, Jane E. Hill
2019	2019 IV Jornadas Costarricenses de Investigación en Computación e Informática (JoCICI) L. D. Mora, O. Azofeifa, D. Diaz, J. A. Guevara-Coto
2019	Integrative regulation of physiology by histone deacetylase 3 Nature Reviews Molecular Cell Biology Matthew J. Emmett, Mitchell A. Lazar
2018	The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders Science Translational Medicine Chao Chen, Qingtuan Meng, Yan Xia, Chaodong Ding, Le Wang, Rujia Dai, Lijun Cheng, Preethi Gunaratne, Richard A. Gibbs, Shishi Min, Cristian Coarfa, Jeffrey G. Reid, Chunling Zhang, Chuan Jiao, Yi Jiang, Gina Giase, Amber Thomas, Dominic Fitzgerald, Tonya Brunetti, Annie Shieh, Cuihua Xia, Yongjun Wang, Yunpeng Wang, Judith A. Badner, Elliot S. Gershon, Kevin P. White, Chunyu Liu
2018	Advancing cancer drug development through precision medicine and innovative designs Journal of Biopharmaceutical Statistics Weidong Zhang, Jing Wang, Sandeep Menon
2018	Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues BMC Genomics Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, Phil J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett A. Mason, Josie B. Garner, Leah C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain, Michael E. Goddard
2018	Biological classification with RNA-seq data: Can alternatively spliced transcript expression enhance machine learning classifiers? RNA Nathan T. Johnson, Andi Dhroso, Katelyn J. Hughes, Dmitry Korkin
2018	ICSA Book Series in Statistics Weidong Zhang, Bo Huang, Jing Wang, Sandeep Menon
2018	Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data Bioinformatics Jennifer M Franks, Guoshuai Cai, Michael L Whitfield
2018	Using microarray‐based subtyping methods for breast cancer in the era of high‐throughput RNA sequencing Molecular Oncology Christina Bligaard Pedersen, Finn Cilius Nielsen, Maria Rossing, Lars Rønn Olsen
2018	Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts Scientific Reports Jeffrey A. Thompson, Brock C. Christensen, Carmen J. Marsit
2017	ADAGE signature analysis: differential expression analysis with data-defined gene sets BMC Bioinformatics Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
2017	Exploring of the molecular mechanism of rhinitis via bioinformatics methods Molecular Medicine Reports Yufen Song, Zhaohui Yan
2017	Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks Cell Systems Jie Tan, Georgia Doing, Kimberley A. Lewis, Courtney E. Price, Kathleen M. Chen, Kyle C. Cady, Barret Perchuk, Michael T. Laub, Deborah A. Hogan, Casey S. Greene
2017	A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma BMC Genomics Gregory P. Way, Robert J. Allaway, Stephanie J. Bouley, Camilo E. Fadul, Yolanda Sanchez, Casey S. Greene
2016	Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli Nature Communications Minseung Kim, Navneet Rai, Violeta Zorraquino, Ilias Tagkopoulos
2016	Applications of integrative OMICs approaches to gene regulation studies Quantitative Biology Jing Qin, Bin Yan, Yaohua Hu, Panwen Wang, Junwen Wang
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