METREE: a program package for inferring and testing minimum-evolution trees. - Andrey Rzhetsky; Masatoshi Nei (Comput. Appl. Biosci., 1994)

Fitting models of intron evolution to aldehyde dehydrogenase data. - Andrey Rzhetsky; Francisco José Ayala; Lily C. Hsu; Cheng Chang; Akira Yoshida (Mathematical Hierarchies and Biology, 1996)

A Knowledge Model for Analysis and Simulation of Regulatory Based on Information in Electronic Publications. - Andrey Rzhetsky; Tomohiro Koike; Sergey Kalachikov; Pauline Kra; Carol Friedman (AMIA, 1999)

Representing genomic knowledge in the UMLS semantic network. - Hong Yu 001; Carol Friedman; Andrey Rzhetsky; Pauline Kra (AMIA, 1999)

Using BLAST, A DNA and Protein Sequence Comparison Tool, for Finding Gene and Protein Names in Journal Articles. - Michael Krauthammer; Andrey Rzhetsky; Pavel Morozov; Carol Friedman (AMIA, 2000)

A knowledge model for analysis and simulation of regulatory networks. - Andrey Rzhetsky; Tomohiro Koike; Sergey Kalachikov; Shawn M. Gomez; Michael Krauthammer; Sabina H. Kaplan; Pauline Kra; James J. Russo; Carol Friedman (Bioinform., 2000)

GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways. - Andrey Rzhetsky; Michael Krauthammer; Tomohiro Koike; Pauline Kra; Shawn M. Gomez; Hong Yu 001; Pablo Ariel Duboué; Wubin Weng; Stephen B. Johnson; Vasileios Hatzivassiloglou; Carol Friedman (German Conference on Bioinformatics, 2001)

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. - Carol Friedman; Pauline Kra; Hong Yu 001; Michael Krauthammer; Andrey Rzhetsky (ISMB (Supplement of Bioinformatics), 2001)

Disambiguating proteins, genes, and RNA in text: a machine learning approach. - Vasileios Hatzivassiloglou; Pablo Ariel Duboué; Andrey Rzhetsky (ISMB (Supplement of Bioinformatics), 2001)

Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins. - Andrey Rzhetsky; Pavel Morozov (Pacific Symposium on Biocomputing, 2001)

Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. - Andrey Rzhetsky; Shawn M. Gomez (Bioinform., 2001)

Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. - Hong Yu 001; Vasileios Hatzivassiloglou; Carol Friedman; Andrey Rzhetsky; W. John Wilbur (AMIA, 2002)

Of truth and pathways: chasing bits of information through myriads of articles. - Michael Krauthammer; Pauline Kra; Ivan Iossifov; Shawn M. Gomez; George Hripcsak; Vasileios Hatzivassiloglou; Carol Friedman; Andrey Rzhetsky (ISMB, 2002)

Towards the Prediction of Complete Protein-Protein Interaction Networks. - Shawn M. Gomez; Andrey Rzhetsky (Pacific Symposium on Biocomputing, 2002)

Two biomedical sublanguages: a description based on the theories of Zellig Harris. - Carol Friedman; Pauline Kra; Andrey Rzhetsky (J. Biomed. Informatics, 2002)

Automatically identifying gene/protein terms in MEDLINE abstracts. - Hong Yu 001; Vasileios Hatzivassiloglou; Andrey Rzhetsky; W. John Wilbur (J. Biomed. Informatics, 2002)

Learning to predict protein-protein interactions from protein sequences. - Shawn M. Gomez; William Stafford Noble; Andrey Rzhetsky (Bioinform., 2003)

Probabilistic inference of molecular networks from noisy data sources. - Ivan Iossifov; Michael Krauthammer; Carol Friedman; Vasileios Hatzivassiloglou; Joel S. Bader; Kevin P. White; Andrey Rzhetsky (Bioinform., 2004)

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. - Andrey Rzhetsky; Ivan Iossifov; Tomohiro Koike; Michael Krauthammer; Pauline Kra; Mitzi Morris; Hong Yu 001; Pablo Ariel Duboué; Wubin Weng; W. John Wilbur (J. Biomed. Informatics, 2004)

The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology. - Mark Borodovsky; Andrey Rzhetsky; Dmitrij Frishman (Bioinform., 2005)

Mining biomedical texts for disease-related pathways. - Andrey Rzhetsky (BioNLP@NAACL-HLT, 2006)

New directions in biomedical text annotation: definitions, guidelines and corpus construction. - W. John Wilbur; Andrey Rzhetsky; Hagit Shatkay (BMC Bioinform., 2006)

Imitating Manual Curation of Text-Mined Facts in Biomedicine. - Raul Rodriguez-Esteban; Ivan Iossifov; Andrey Rzhetsky (PLoS Comput. Biol., 2006)

Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. - Hagit Shatkay; Fengxia Pan; Andrey Rzhetsky; W. John Wilbur (Bioinform., 2008)

Quantitative systems-level determinants of drug targets. - Lixia Yao; Andrey Rzhetsky (BMC Bioinform., 2008)

Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans. - Ivan Iossifov; Raul Rodriguez-Esteban; Ilya Mayzus; Kathleen J. Millen; Andrey Rzhetsky (PLoS Comput. Biol., 2009)

Getting Started in Text Mining: Part Two. - Andrey Rzhetsky; Michael R. Seringhaus; Mark B. Gerstein (PLoS Comput. Biol., 2009)

How to Get the Most out of Your Curation Effort. - Andrey Rzhetsky; Hagit Shatkay; W. John Wilbur (PLoS Comput. Biol., 2009)

Discovering and Counting Biomedical Verbs. - Sonjia Waxmonsky; John Goldsmith; Andrey Rzhetsky (ICMLA, 2010)

Understanding Etiology of Complex Neurodevelopmental Disorders: Two Approaches. - Andrey Rzhetsky (AIME, 2011)

A distributed look-up architecture for text mining applications using MapReduce. - Atilla Soner Balkir; Ian T. Foster; Andrey Rzhetsky (SC, 2011)

Representation of research hypotheses. - Larisa N. Soldatova; Andrey Rzhetsky (J. Biomed. Semant., 2011)

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis. - Anna Divoli; Eneida A. Mendonça; James A. Evans; Andrey Rzhetsky (PLoS Comput. Biol., 2011)

War of Ontology Worlds: Mathematics, Computer Code, or Esperanto? - Andrey Rzhetsky; James A. Evans (PLoS Comput. Biol., 2011)

Benchmarking Ontologies: Bigger or Better? - Lixia Yao; Anna Divoli; Ilya Mayzus; James A. Evans; Andrey Rzhetsky (PLoS Comput. Biol., 2011)

Global and Local Approach of Part-of-Speech Tagging for Large Corpora. - Shi Yu; Robert Grossman; Andrey Rzhetsky (AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text, 2012)

Representation of probabilistic scientific knowledge. - Larisa N. Soldatova; Andrey Rzhetsky; Kurt De Grave; Ross D. King (J. Biomed. Semant., 2013)

Tradition and Innovation in Scientists' Research Strategies - Jacob G. Foster; Andrey Rzhetsky; James A. Evans (CoRR, 2013)

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. - Chun-Chi Liu; Yu-Ting Tseng; Wenyuan Li 006; Chia-Yu Wu; Ilya Mayzus; Andrey Rzhetsky; Fengzhu Sun; Michael S. Waterman; Jeremy J. W. Chen; Preet M. Chaudhary; Joseph Loscalzo; Edward Crandall; et al. (Nucleic Acids Res., 2014)

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy. - David R. Blair; Kanix Wang; Svetlozar Nestorov; James A. Evans; Andrey Rzhetsky (PLoS Comput. Biol., 2014)

Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability. - Andrey Rzhetsky; Steven C. Bagley; Kanix Wang; Christopher S. Lyttle; Edwin H. Cook Jr.; Russ B. Altman; Robert D. Gibbons (PLoS Comput. Biol., 2014)

The Big Mechanism Program: Changing How Science Is Done. - Andrey Rzhetsky (DAMDID/RCDL, 2016)

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning. - Ji-Sung Kim; Andrey Rzhetsky (CoRR, 2017)

Centralized "big science" communities more likely generate non-replicable results. - Valentin Danchev; Andrey Rzhetsky; James A. Evans (CoRR, 2018)

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning. - Ji-Sung Kim; Xin Gao 001; Andrey Rzhetsky (PLoS Comput. Biol., 2018)

BioRelEx 1.0: Biological Relation Extraction Benchmark. - Hrant Khachatrian; Lilit Nersisyan; Karen Hambardzumyan; Tigran Galstyan; Anna Hakobyan; Arsen Arakelyan; Andrey Rzhetsky; Aram Galstyan (BioNLP@ACL, 2019)

Detecting signal from science: The structure of research communities and prior knowledge improves prediction of genetic regulatory experiments. - Alexander V. Belikov; Andrey Rzhetsky; James A. Evans (CoRR, 2020)

Measurable health effects associated with the daylight saving time shift. - Hanxin Zhang; Torsten Dahlén; Atif Ali Khan; Gustaf Edgren; Andrey Rzhetsky (PLoS Comput. Biol., 2020)

Soft Sensing Transformer: Hundreds of Sensors are Worth a Single Word. - Chao Zhang 050; Jaswanth K. Yella; Yu Huang 017; Xiaoye Qian; Sergei Petrov; Andrey Rzhetsky; Sthitie Bom (IEEE BigData, 2021)

Lightweight Mobile Automated Assistant-to-physician for Global Lower-resource Areas. - Chao Zhang; Hanxin Zhang; Atif Ali Khan; Ted Kim; Olasubomi Omoleye; Oluwamayomikun Abiona; Amy Lehman; Christopher O. Olopade; Olufunmilayo I. Olopade; Pedro Lopes; Andrey Rzhetsky (CoRR, 2021)

Observable variations in human sex ratio at birth. - Yanan Long; Qi Chen; Henrik Larsson; Andrey Rzhetsky (PLoS Comput. Biol., 2021)

Prediction of robust scientific facts from literature. - Alexander V. Belikov; Andrey Rzhetsky; James A. Evans (Nat. Mach. Intell., 2022)

OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics. - Jonathan M. Matthews; Brooke Schuster; Sara Saheb Kashaf; Ping Liu 002; Rakefet Ben-Yishay; Dana Ishay-Ronen; Evgeny Izumchenko; Le Shen; Christopher R. Weber; Margaret Bielski; Sonia S. Kupfer; Mustafa Bilgic 001; et al. (PLoS Comput. Biol., 2022)

The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. - Gengjie Jia; Yu Li 006; Xue Zhong; Kanix Wang; Milton Pividori; Rabab Alomairy; Aniello Esposito; Hatem Ltaief; Chikashi Terao; Masato Akiyama; Koichi Matsuda; David E. Keyes; et al. (Nat. Comput. Sci., 2023)

Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. - Gengjie Jia; Yu Li 006; Xue Zhong; Kanix Wang; Milton Pividori; Rabab Alomairy; Aniello Esposito; Hatem Ltaief; Chikashi Terao; Masato Akiyama; Koichi Matsuda; David E. Keyes; et al. (Nat. Comput. Sci., 2023)

An effective encoding of human medical conditions in disease space provides a versatile framework for deciphering disease associations. - Tianxin Xu; Yu Li 006; Xin Gao 001; Andrey Rzhetsky; Gengjie Jia (Quant. Biol., 2025)