Sudhir Kumar

Publication Activity (10 Years)

Years Active: 1994-2023
Publications (10 Years): 18

Top Topics

Linkage Disequilibrium

Image Classification

Training Samples

Machine Learning

Top Venues

Frontiers Bioinform.

PLoS Comput. Biol.

Publications

Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar
Molecular timetrees using relaxed clocks and uncertain phylogenies. Frontiers Bioinform. 3 (2023)
Jack M. Craig, Sudhir Kumar, S. Blair Hedges
The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. Frontiers Bioinform. 3 (2023)
Lei Cai, Zhengyang Wang, Rob Kulathinal, Sudhir Kumar, Shuiwang Ji
Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples. IEEE Trans. Neural Networks Learn. Syst. 34 (5) (2023)
Jack M. Craig, Grace L. Bamba, Jose Barba-Montoya, S. Blair Hedges, Sudhir Kumar
Completing a molecular timetree of apes and monkeys. Frontiers Bioinform. 3 (2023)
Jared Huzar, Madelyn Shenoy, Maxwell D. Sanderford, Sudhir Kumar, Sayaka Miura
Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. Frontiers Bioinform. 3 (2023)
Marija Stanojevic, Jovan Andjelkovic, Adrienne Kasprowicz, Louise A. Huuki, Jennifer Chao, S. Blair Hedges, Sudhir Kumar, Zoran Obradovic
Discovering research articles containing evolutionary timetrees by machine learning. Bioinform. 39 (1) (2023)
Nicholas J. Ose, Brandon M. Butler, Avishek Kumar, I. Can Kazan, Maxwell D. Sanderford, Sudhir Kumar, S. Banu Ozkan
Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. PLoS Comput. Biol. 18 (4) (2022)
Marcos A. Caraballo-Ortiz, Sayaka Miura, Maxwell D. Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L. Kosakovsky Pond, Sudhir Kumar
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinform. 38 (10) (2022)
Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies. Bioinform. 37 (Supplement) (2021)
Li Liu, Pramod Chandrashekar, Biao Zeng, Maxwell D. Sanderford, Sudhir Kumar, Greg Gibson
TreeMap: a structured approach to fine mapping of eQTL variants. Bioinform. 37 (8) (2021)
Sudip Sharma, Sudhir Kumar
Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. Nat. Comput. Sci. 1 (9) (2021)
Lei Cai, Zhengyang Wang, Rob Kulathinal, Sudhir Kumar, Shuiwang Ji
Deep Low-Shot Learning for Biological Image Classification and Visualization from Limited Training Samples. CoRR (2020)
Wenlu Zhang, Rongjian Li, Tao Zeng, Qian Sun, Sudhir Kumar, Jieping Ye, Shuiwang Ji
Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis. IEEE Trans. Big Data 6 (2) (2020)
Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar
A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Comput. Biol. 16 (1) (2020)
Pramod Chandrashekar, Navid Ahmadinejad, Junwen Wang, Aleksandar Sekulic, Jan B. Egan, Yan W. Asmann, Sudhir Kumar, Carlo Maley, Li Liu
Somatic selection distinguishes oncogenes and tumor suppressor genes. Bioinform. 36 (6) (2020)
Sayaka Miura, Louise A. Huuki, Tiffany Buturla, Tracy Vu, Karen Gomez, Sudhir Kumar
Computational enhancement of single-cell sequences for inferring tumor evolution. Bioinform. 34 (17) (2018)
Sayaka Miura, Karen Gomez, Oscar Murillo, Louise A. Huuki, Tracy Vu, Tiffany Buturla, Sudhir Kumar
Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinform. 34 (23) (2018)
Wenlu Zhang, Rongjian Li, Tao Zeng, Qian Sun, Sudhir Kumar, Jieping Ye, Shuiwang Ji
Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis. KDD (2015)
Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye
embryos in images containing spatial patterns of expression. Bioinform. 30 (2) (2014)
Glen Stecher, Li Liu, Maxwell D. Sanderford, Daniel Peterson, Koichiro Tamura, Sudhir Kumar
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinform. 30 (9) (2014)
Ivan Montiel, Charlotte Konikoff, Bremen L. Braun, Mary Packard, L. Sian Gramates, Qian Sun, Jieping Ye, Sudhir Kumar
embryos. Bioinform. 30 (9) (2014)
Qian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye
Image-level and group-level models for Drosophila gene expression pattern annotation. BMC Bioinform. 14 (2013)
Wenlu Zhang, Daming Feng, Rongjian Li, Andrey N. Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart J. Newfeld, Sudhir Kumar, Shuiwang Ji
A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. BMC Bioinform. 14 (2013)
Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval. BMC Bioinform. 13 (2012)
Sudhir Kumar, Kelly Boccia, Michael McCutchan, Jieping Ye
Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone. Bioinform. 28 (21) (2012)
Sudhir Kumar, Glen Stecher, Daniel Peterson, Koichiro Tamura
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinform. 28 (20) (2012)
Vanessa E. Gray, Kimberly R. Kukurba, Sudhir Kumar
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. Bioinform. 28 (16) (2012)
Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou
Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (1) (2012)
Sudhir Kumar, S. Blair Hedges
TimeTree2: species divergence times on the iPhone. Bioinform. 27 (14) (2011)
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
embryogenesis. Bioinform. 27 (23) (2011)
Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar
. Bioinform. 25 (19) (2009)
Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye
gene expression pattern annotation. BMC Bioinform. 10 (2009)
Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou
DrosophilaGene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IJCAI (2009)
Shuiwang Ji, Lei Yuan, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye
Drosophila gene expression pattern annotation using sparse features and term-term interactions. KDD (2009)
Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, Jieping Ye
gene expression patterns using a controlled vocabulary. Bioinform. 24 (17) (2008)
Jieping Ye, Jianhui Chen, Ravi Janardan, Sudhir Kumar
Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA. ACM Trans. Knowl. Discov. Data 2 (1) (2008)
Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings Bioinform. 9 (4) (2008)
Sudhir Kumar, Joel Dudley
Bioinformatics software for biologists in the genomics era. Bioinform. 23 (14) (2007)
Charles J. Colbourn, Sudhir Kumar
Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinform. 8 (2007)
S. Blair Hedges, Joel Dudley, Sudhir Kumar
TimeTree: a public knowledge-base of divergence times among organisms. Bioinform. 22 (23) (2006)
Sudhir Kumar, Koichiro Tamura, Masatoshi Nei
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings Bioinform. 5 (2) (2004)
Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan, Sudhir Kumar
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. BMC Bioinform. 5 (2004)
Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei
MEGA2: molecular evolutionary genetics analysis software. Bioinform. 17 (12) (2001)
Paul Walton Purdom Jr., Phillip G. Bradford, Koichiro Tamura, Sudhir Kumar
Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinform. 16 (2) (2000)
Sudhir Kumar, Koichiro Tamura, Masatoshi Nei
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput. Appl. Biosci. 10 (2) (1994)