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ORCIDSudhir Kumar 0001
Person information
- affiliation: Arizona State University, Tempe, AZ, USA
- affiliation: King Abdulaziz University, Jeddah, Saudi Arabia
Other persons with the same name
- Sudhir Kumar — disambiguation page
- Sudhir Kumar 0002
![[0000-0002-4052-7099]](https://dblp.uni-trier.de/img/orcid-mark.12x12.png "0000-0002-4052-7099")
— Indian Institute of Technology Patna, India (and 1 more) - Sudhir Kumar 0003 — ICAR-Indian Agricultural Research Institute, New Delhi, India
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Journal Articles
- 2023
[j41]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)- [j40]Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar:
Molecular timetrees using relaxed clocks and uncertain phylogenies. Frontiers Bioinform. 3 (2023) - [j39]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) - [j38]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) - [j37]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) - [j36]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): 2528-2538 (2023) - 2022
- [j35]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): 2719-2726 (2022) - [j34]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) - 2021
- [j33]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): 1125-1134 (2021) - [j32]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): 102-110 (2021) - [j31]Sudip Sharma, Sudhir Kumar:
Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. Nat. Comput. Sci. 1(9): 573-577 (2021) - 2020
- [j30]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): 1712-1717 (2020) - [j29]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) - [j28]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): 322-333 (2020) - 2018
- [j27]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): i917-i926 (2018) - [j26]Sayaka Miura, Karen Gomez, Oscar D. Murillo, Louise A. Huuki, Tracy Vu, Tiffany Buturla, Sudhir Kumar:
Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinform. 34(23): 4017-4026 (2018) - 2014
- [j25]Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye:
Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. Bioinform. 30(2): 266-273 (2014) - [j24]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): 1305-1307 (2014) - [j23]Ivan Montiel, Charlotte Konikoff, Bremen L. Braun, Mary Packard, L. Sian Gramates, Qian Sun, Jieping Ye, Sudhir Kumar:
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos. Bioinform. 30(9): 1319-1321 (2014) - 2013
- [j22]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: 350 (2013) - [j21]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: 372 (2013) - 2012
- [j20]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): 2093-2096 (2012) - [j19]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): 2685-2686 (2012) - [j18]Sudhir Kumar, Kelly Boccia, Michael McCutchan, Jieping Ye:
Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone. Bioinform. 28(21): 2847-2848 (2012) - [j17]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: 107 (2012) - [j16]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): 98-112 (2012) - 2011
- [j15]Sudhir Kumar, S. Blair Hedges:
TimeTree2: species divergence times on the iPhone. Bioinform. 27(14): 2023-2024 (2011) - [j14]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:
FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinform. 27(23): 3319-3320 (2011) - 2009
- [j13]Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar:
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinform. 25(19): 2473-2477 (2009) - [j12]Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye:
A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinform. 10 (2009) - 2008
- [j11]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): 299-306 (2008) - [j10]Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, Jieping Ye:
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinform. 24(17): 1881-1888 (2008) - [j9]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): 4:1-4:21 (2008) - 2007
- [j8]Sudhir Kumar, Joel Dudley:
Bioinformatics software for biologists in the genomics era. Bioinform. 23(14): 1713-1717 (2007) - [j7]Charles J. Colbourn, Sudhir Kumar:
Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinform. 8 (2007) - 2006
- [j6]S. Blair Hedges, Joel Dudley, Sudhir Kumar:
TimeTree: a public knowledge-base of divergence times among organisms. Bioinform. 22(23): 2971-2972 (2006) - 2004
- [j5]Sudhir Kumar, Koichiro Tamura, Masatoshi Nei:
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings Bioinform. 5(2): 150-163 (2004) - [j4]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: 202 (2004) - 2001
- [j3]Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei:
MEGA2: molecular evolutionary genetics analysis software. Bioinform. 17(12): 1244-1245 (2001) - 2000
- [j2]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): 140-151 (2000) - 1994
- [j1]Sudhir Kumar, Koichiro Tamura, Masatoshi Nei:
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput. Appl. Biosci. 10(2): 189-191 (1994)
Conference and Workshop Papers
- 2015
- [c3]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: 1475-1484 - 2009
- [c2]Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou:
DrosophilaGene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IJCAI 2009: 1445-1450 - [c1]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: 407-416
Reference Works
- 2009
- [r1]Jieping Ye, Ravi Janardan, Sudhir Kumar:
Biological Image Analysis via Matrix Approximation. Encyclopedia of Data Warehousing and Mining 2009: 166-170
Informal and Other Publications
- 2020
- [i1]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 abs/2010.10050 (2020)
Coauthor Index
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