MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. - Sudhir Kumar 001; Koichiro Tamura; Masatoshi Nei (Comput. Appl. Biosci., 1994)

Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. - Paul Walton Purdom Jr.; Phillip G. Bradford; Koichiro Tamura; Sudhir Kumar 001 (Bioinform., 2000)

MEGA2: molecular evolutionary genetics analysis software. - Sudhir Kumar 001; Koichiro Tamura; Ingrid B. Jakobsen; Masatoshi Nei (Bioinform., 2001)

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. - Sudhir Kumar 001; Koichiro Tamura; Masatoshi Nei (Briefings Bioinform., 2004)

Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. - Rajalakshmi Gurunathan; Bernard Van Emden; Sethuraman Panchanathan; Sudhir Kumar 001 (BMC Bioinform., 2004)

TimeTree: a public knowledge-base of divergence times among organisms. - S. Blair Hedges; Joel Dudley; Sudhir Kumar 001 (Bioinform., 2006)

Bioinformatics software for biologists in the genomics era. - Sudhir Kumar 001; Joel Dudley (Bioinform., 2007)

Lower bounds on multiple sequence alignment using exact 3-way alignment. - Charles J. Colbourn; Sudhir Kumar 001 (BMC Bioinform., 2007)

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. - Sudhir Kumar 001; Masatoshi Nei; Joel Dudley; Koichiro Tamura (Briefings Bioinform., 2008)

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. - Shuiwang Ji; Liang Sun 001; Rong Jin 001; Sudhir Kumar 001; Jieping Ye (Bioinform., 2008)

Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA. - Jieping Ye; Jianhui Chen; Ravi Janardan; Sudhir Kumar 001 (ACM Trans. Knowl. Discov. Data, 2008)

DrosophilaGene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. - Ying-Xin Li; Shuiwang Ji; Sudhir Kumar 001; Jieping Ye; Zhi-Hua Zhou (IJCAI, 2009)

Drosophila gene expression pattern annotation using sparse features and term-term interactions. - Shuiwang Ji; Lei Yuan 001; Ying-Xin Li; Zhi-Hua Zhou; Sudhir Kumar 001; Jieping Ye (KDD, 2009)

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. - Antonio Marco; Charlotte Konikoff; Timothy L. Karr; Sudhir Kumar 001 (Bioinform., 2009)

A bag-of-words approach for Drosophila gene expression pattern annotation. - Shuiwang Ji; Ying-Xin Li; Zhi-Hua Zhou; Sudhir Kumar 001; Jieping Ye (BMC Bioinform., 2009)

Biological Image Analysis via Matrix Approximation. - Jieping Ye; Ravi Janardan; Sudhir Kumar 001 (Encyclopedia of Data Warehousing and Mining, 2009)

TimeTree2: species divergence times on the iPhone. - Sudhir Kumar 001; S. Blair Hedges (Bioinform., 2011)

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. - Sudhir Kumar 001; Charlotte Konikoff; Bernard Van Emden; Christopher Busick; Kailah T. Davis; Shuiwang Ji; Lin-Wei Wu; Hector Ramos; Thomas Brody; Sethuraman Panchanathan; Jieping Ye; Timothy L. Karr; et al. (Bioinform., 2011)

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. - Vanessa E. Gray; Kimberly R. Kukurba; Sudhir Kumar 001 (Bioinform., 2012)

Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone. - Sudhir Kumar 001; Kelly Boccia; Michael McCutchan; Jieping Ye (Bioinform., 2012)

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. - Sudhir Kumar 001; Glen Stecher; Daniel Peterson; Koichiro Tamura (Bioinform., 2012)

Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval. - Lei Yuan 001; Alexander Woodard; Shuiwang Ji; Yuan Jiang 001; Zhi-Hua Zhou; Sudhir Kumar 001; Jieping Ye (BMC Bioinform., 2012)

Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. - Ying-Xin Li; Shuiwang Ji; Sudhir Kumar 001; Jieping Ye; Zhi-Hua Zhou (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Image-level and group-level models for Drosophila gene expression pattern annotation. - Qian Sun 002; Sherin Muckatira; Lei Yuan 001; Shuiwang Ji; Stuart J. Newfeld; Sudhir Kumar 001; Jieping Ye (BMC Bioinform., 2013)

A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. - Wenlu Zhang; Daming Feng; Rongjian Li; Andrey N. Chernikov; Nikos Chrisochoides; Christopher Osgood; Charlotte Konikoff; Stuart J. Newfeld; Sudhir Kumar 001; Shuiwang Ji (BMC Bioinform., 2013)

myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos. - Ivan Montiel; Charlotte Konikoff; Bremen L. Braun; Mary Packard; L. Sian Gramates; Qian Sun 002; Jieping Ye; Sudhir Kumar 001 (Bioinform., 2014)

MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. - Glen Stecher; Li Liu 035; Maxwell D. Sanderford; Daniel Peterson; Koichiro Tamura; Sudhir Kumar 001 (Bioinform., 2014)

Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. - Lei Yuan 001; Cheng Pan; Shuiwang Ji; Michael McCutchan; Zhi-Hua Zhou; Stuart J. Newfeld; Sudhir Kumar 001; Jieping Ye (Bioinform., 2014)

Predicting clone genotypes from tumor bulk sequencing of multiple samples. - Sayaka Miura; Karen Gomez; Oscar D. Murillo; Louise A. Huuki; Tracy Vu; Tiffany Buturla; Sudhir Kumar 001 (Bioinform., 2018)

Computational enhancement of single-cell sequences for inferring tumor evolution. - Sayaka Miura; Louise A. Huuki; Tiffany Buturla; Tracy Vu; Karen Gomez; Sudhir Kumar 001 (Bioinform., 2018)

PathFinder: Bayesian inference of clone migration histories in cancer. - Sudhir Kumar 001; Antonia Chroni; Koichiro Tamura; Maxwell D. Sanderford; Olumide Oladeinde; Vivian Aly; Tracy Vu; Sayaka Miura (Bioinform., 2020)

Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated. - Jose Barba-Montoya; Qiqing Tao; Sudhir Kumar 001 (Bioinform., 2020)

Somatic selection distinguishes oncogenes and tumor suppressor genes. - Pramod Chandrashekar; Navid Ahmadinejad; Junwen Wang; Aleksandar Sekulic; Jan B. Egan; Yan W. Asmann; Sudhir Kumar 001; Carlo Maley; Li Liu 035 (Bioinform., 2020)

A new method for inferring timetrees from temporally sampled molecular sequences. - Sayaka Miura; Koichiro Tamura; Qiqing Tao; Louise A. Huuki; Sergei L. Kosakovsky Pond; Jessica Priest; Jiamin Deng; Sudhir Kumar 001 (PLoS Comput. Biol., 2020)

Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis. - Wenlu Zhang; Rongjian Li; Tao Zeng; Qian Sun 002; Sudhir Kumar 001; Jieping Ye; Shuiwang Ji (IEEE Trans. Big Data, 2020)

TreeMap: a structured approach to fine mapping of eQTL variants. - Li Liu 035; Pramod Chandrashekar; Biao Zeng; Maxwell D. Sanderford; Sudhir Kumar 001; Greg Gibson (Bioinform., 2021)

Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies. - Qiqing Tao; Jose Barba-Montoya; Sudhir Kumar 001 (Bioinform., 2021)

Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. - Sudip Sharma; Sudhir Kumar 001 (Nat. Comput. Sci., 2021)

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. - Marcos A. Caraballo-Ortiz; Sayaka Miura; Maxwell D. Sanderford; Tenzin Dolker; Qiqing Tao; Steven Weaver; Sergei L. Kosakovsky Pond; Sudhir Kumar 001 (Bioinform., 2022)

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. - Nicholas J. Ose; Brandon M. Butler; Avishek Kumar; I. Can Kazan; Maxwell D. Sanderford; Sudhir Kumar 001; S. Banu Ozkan (PLoS Comput. Biol., 2022)

Discovering research articles containing evolutionary timetrees by machine learning. - Marija Stanojevic; Jovan Andjelkovic; Adrienne Kasprowicz; Louise A. Huuki; Jennifer Chao; S. Blair Hedges; Sudhir Kumar 001; Zoran Obradovic (Bioinform., 2023)

Molecular timetrees using relaxed clocks and uncertain phylogenies. - Jose Barba-Montoya; Sudip Sharma; Sudhir Kumar 001 (Frontiers Bioinform., 2023)

Completing a molecular timetree of apes and monkeys. - Jack M. Craig; Grace L. Bamba; Jose Barba-Montoya; S. Blair Hedges; Sudhir Kumar 001 (Frontiers Bioinform., 2023)

The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. - Jack M. Craig; Sudhir Kumar 001; S. Blair Hedges (Frontiers Bioinform., 2023)

Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. - Jared Huzar; Madelyn Shenoy; Maxwell D. Sanderford; Sudhir Kumar 001; Sayaka Miura (Frontiers Bioinform., 2023)

Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples. - Lei Cai; Zhengyang Wang; Rob Kulathinal; Sudhir Kumar 001; Shuiwang Ji (IEEE Trans. Neural Networks Learn. Syst., 2023)

Completing a molecular timetree of primates. - Jack M. Craig; S. Blair Hedges; Sudhir Kumar 001 (Frontiers Bioinform., 2024)