Sudhir Kumar

53 papers A* 3Journal 49
YearRankTypeTitle / Venue / Authors
2026 J jnl
Evolutionary dynamics of early and late mutational signatures in metastatic cancer.
Frontiers Bioinform.
Anastasia Yankovskiy, Sudhir Kumar, Sayaka Miura
2025 J jnl
Completing a molecular timetree of Afrotheria.
Frontiers Bioinform.
Jack M. Craig, Whitney L. Fisher, Allan S. Thomas, S. Blair Hedges, Sudhir Kumar
2025 J jnl
GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data.
Frontiers Bioinform.
Ryan M. Tobin, Shikha Singh, Sudhir Kumar, Sayaka Miura
2025 J jnl
Integrating phylogenies with chronology to assemble the tree of life.
Frontiers Bioinform.
Jose Barba-Montoya, Jack M. Craig, Sudhir Kumar
2024 J jnl
Completing a molecular timetree of primates.
Frontiers Bioinform.
Jack M. Craig, S. Blair Hedges, Sudhir Kumar
2023 J jnl
Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data.
Frontiers Bioinform.
Jared Huzar, Madelyn Shenoy, Maxwell D. Sanderford, Sudhir Kumar, Sayaka Miura
2023 J jnl
Completing a molecular timetree of apes and monkeys.
Frontiers Bioinform.
Jack M. Craig, Grace L. Bamba, Jose Barba-Montoya, S. Blair Hedges, Sudhir Kumar
2023 J jnl
Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples.
IEEE Trans. Neural Networks Learn. Syst.
Lei Cai, Zhengyang Wang, Rob Kulathinal, Sudhir Kumar, Shuiwang Ji
2023 J jnl
Discovering research articles containing evolutionary timetrees by machine learning.
Bioinform.
Marija Stanojevic, Jovan Andjelkovic, Adrienne Kasprowicz, Louise A. Huuki, Jennifer Chao, S. Blair Hedges, Sudhir Kumar, Zoran Obradovic
2023 J jnl
Molecular timetrees using relaxed clocks and uncertain phylogenies.
Frontiers Bioinform.
Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar
2023 J jnl
The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen.
Frontiers Bioinform.
Jack M. Craig, Sudhir Kumar, S. Blair Hedges
2022 J jnl
Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants.
PLoS Comput. Biol.
Nicholas J. Ose, Brandon M. Butler, Avishek Kumar, I. Can Kazan, Maxwell D. Sanderford, Sudhir Kumar, S. Banu Ozkan
2022 J jnl
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.
Bioinform.
Marcos A. Caraballo-Ortiz, Sayaka Miura, Maxwell D. Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L. Kosakovsky Pond, Sudhir Kumar
2021 J jnl
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies.
Bioinform.
Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar
2021 J jnl
Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps.
Nat. Comput. Sci.
Sudip Sharma, Sudhir Kumar
2021 J jnl
TreeMap: a structured approach to fine mapping of eQTL variants.
Bioinform.
Li Liu, Pramod Chandrashekar, Biao Zeng, Maxwell D. Sanderford, Sudhir Kumar, Greg Gibson
2020 J jnl
A new method for inferring timetrees from temporally sampled molecular sequences.
PLoS Comput. Biol.
Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar
2020 J jnl
Deep Low-Shot Learning for Biological Image Classification and Visualization from Limited Training Samples.
CoRR
Lei Cai, Zhengyang Wang, Rob Kulathinal, Sudhir Kumar, Shuiwang Ji
2020 J jnl
Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis.
IEEE Trans. Big Data
Wenlu Zhang, Rongjian Li, Tao Zeng, Qian Sun, Sudhir Kumar, Jieping Ye, Shuiwang Ji
2020 J jnl
PathFinder: Bayesian inference of clone migration histories in cancer.
Bioinform.
Sudhir Kumar, Antonia Chroni, Koichiro Tamura, Maxwell D. Sanderford, Olumide Oladeinde, Vivian Aly, Tracy Vu, Sayaka Miura
2020 J jnl
Somatic selection distinguishes oncogenes and tumor suppressor genes.
Bioinform.
Pramod Chandrashekar, Navid Ahmadinejad, Junwen Wang, Aleksandar Sekulic, Jan B. Egan, Yan W. Asmann, Sudhir Kumar, Carlo Maley, Li Liu
2020 J jnl
Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated.
Bioinform.
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
2018 J jnl
Computational enhancement of single-cell sequences for inferring tumor evolution.
Bioinform.
Sayaka Miura, Louise A. Huuki, Tiffany Buturla, Tracy Vu, Karen Gomez, Sudhir Kumar
2018 J jnl
Predicting clone genotypes from tumor bulk sequencing of multiple samples.
Bioinform.
Sayaka Miura, Karen Gomez, Oscar D. Murillo, Louise A. Huuki, Tracy Vu, Tiffany Buturla, Sudhir Kumar
2015 A* conf
Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis.
KDD
Wenlu Zhang, Rongjian Li, Tao Zeng, Qian Sun, Sudhir Kumar, Jieping Ye, Shuiwang Ji
2014 J jnl
Automated annotation of developmental stages of
Bioinform.
Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye
2014 J jnl
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation.
Bioinform.
Glen Stecher, Li Liu, Maxwell D. Sanderford, Daniel Peterson, Koichiro Tamura, Sudhir Kumar
2014 J jnl
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in
Bioinform.
Ivan Montiel, Charlotte Konikoff, Bremen L. Braun, Mary Packard, L. Sian Gramates, Qian Sun, Jieping Ye, Sudhir Kumar
2013 J jnl
A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis.
BMC Bioinform.
Wenlu Zhang, Daming Feng, Rongjian Li, Andrey N. Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart J. Newfeld, Sudhir Kumar, Shuiwang Ji
2013 J jnl
Image-level and group-level models for Drosophila gene expression pattern annotation.
BMC Bioinform.
Qian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye
2012 J jnl
Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou
2012 J jnl
Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone.
Bioinform.
Sudhir Kumar, Kelly Boccia, Michael McCutchan, Jieping Ye
2012 J jnl
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval.
BMC Bioinform.
Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye
2012 J jnl
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.
Bioinform.
Sudhir Kumar, Glen Stecher, Daniel Peterson, Koichiro Tamura
2012 J jnl
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations.
Bioinform.
Vanessa E. Gray, Kimberly R. Kukurba, Sudhir Kumar
2011 J jnl
FlyExpress: visual mining of spatiotemporal patterns for genes and publications in
Bioinform.
Sudhir Kumar, 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, Kristyn Gerold, Michael McCutchan, Stuart J. Newfeld
2011 J jnl
TimeTree2: species divergence times on the iPhone.
Bioinform.
Sudhir Kumar, S. Blair Hedges
2009 J jnl
A bag-of-words approach for
BMC Bioinform.
Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye
2009 — ch.
Biological Image Analysis via Matrix Approximation.
Encyclopedia of Data Warehousing and Mining
Jieping Ye, Ravi Janardan, Sudhir Kumar
2009 A* conf
Drosophila gene expression pattern annotation using sparse features and term-term interactions.
KDD
Shuiwang Ji, Lei Yuan, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye
2009 A* conf
DrosophilaGene Expression Pattern Annotation through Multi-Instance Multi-Label Learning.
IJCAI
Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou
2009 J jnl
Relationship between gene co-expression and sharing of transcription factor binding sites in
Bioinform.
Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar
2008 J jnl
Automated annotation of
Bioinform.
Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, Jieping Ye
2008 J jnl
Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA.
ACM Trans. Knowl. Discov. Data
Jieping Ye, Jianhui Chen, Ravi Janardan, Sudhir Kumar
2008 J jnl
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences.
Briefings Bioinform.
Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura
2007 J jnl
Bioinformatics software for biologists in the genomics era.
Bioinform.
Sudhir Kumar, Joel Dudley
2007 J jnl
Lower bounds on multiple sequence alignment using exact 3-way alignment.
BMC Bioinform.
Charles J. Colbourn, Sudhir Kumar
2006 J jnl
TimeTree: a public knowledge-base of divergence times among organisms.
Bioinform.
S. Blair Hedges, Joel Dudley, Sudhir Kumar
2004 J jnl
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations.
BMC Bioinform.
Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan, Sudhir Kumar
2004 J jnl
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.
Briefings Bioinform.
Sudhir Kumar, Koichiro Tamura, Masatoshi Nei
2001 J jnl
MEGA2: molecular evolutionary genetics analysis software.
Bioinform.
Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei
2000 J jnl
Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees.
Bioinform.
Paul Walton Purdom Jr., Phillip G. Bradford, Koichiro Tamura, Sudhir Kumar
1994 J jnl
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers.
Comput. Appl. Biosci.
Sudhir Kumar, Koichiro Tamura, Masatoshi Nei