Sudhir Kumar

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 53

Top Topics

Machine Learning

Respiratory Syndrome Coronavirus

Angiotensin Converting Enzyme

Genetic Diversity

Top Venues

Molecular biology and evolution

bioRxiv : the preprint server for biology

Bioinformatics (Oxford, England)

This page only lists publications with an associated author ORCID identifier.

Publications

Jack M Craig, Glenn S Gerhard, Sudip Sharma, Anastasia Yankovskiy, Sayaka Miura, Sudhir Kumar
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Molecular biology and evolution 41 (1) (2024)
Sudip Sharma, Sudhir Kumar
Discovering fragile clades and causal sequences in phylogenomics by evolutionary sparse learning. Molecular biology and evolution (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning. bioRxiv : the preprint server for biology (2024)
Jack M Craig, Glenn S Gerhard, Sudip Sharma, Anastasia Yankovskiy, Sayaka Miura, Sudhir Kumar
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Molecular biology and evolution 41 (1) (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning. Molecular biology and evolution 41 (7) (2024)
Nicholas James Ose, Paul Campitelli, Tushar Modi, I Can Kazan, Sudhir Kumar, Sefika Banu Ozkan
Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 12 (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning. Molecular biology and evolution 41 (7) (2024)
Sudip Sharma, Sudhir Kumar
Discovering fragile clades and causal sequences in phylogenomics by evolutionary sparse learning. Molecular biology and evolution (2024)
Sudip Sharma, Sudhir Kumar
Discovering fragile clades and causal sequences in phylogenomics by evolutionary sparse learning. Molecular biology and evolution (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning. Molecular biology and evolution 41 (7) (2024)
Nicholas James Ose, Paul Campitelli, Tushar Modi, I Can Kazan, Sudhir Kumar, Sefika Banu Ozkan
Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 12 (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning. bioRxiv : the preprint server for biology (2024)
Nicholas James Ose, Paul Campitelli, Tushar Modi, I Can Kazan, Sudhir Kumar, Sefika Banu Ozkan
Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 12 (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning. bioRxiv : the preprint server for biology (2024)
Jose Barba-Montoya, Jack M Craig, Sudhir Kumar
Integrating Phylogenies with Chronology to Assemble the Tree of Life. bioRxiv : the preprint server for biology (2024)
Nicholas James Ose, Paul Campitelli, Tushar Modi, I Can Kazan, Sudhir Kumar, Sefika Banu Ozkan
Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 12 (2024)
Jose Barba-Montoya, Jack M Craig, Sudhir Kumar
Integrating Phylogenies with Chronology to Assemble the Tree of Life. bioRxiv : the preprint server for biology (2024)
Sudip Sharma, Sudhir Kumar
Discovering Fragile Clades And Causal Sequences In Phylogenomics By Evolutionary Sparse Learning. bioRxiv : the preprint server for biology (2024)
Nicholas James Ose, Paul Campitelli, Tushar Modi, I Can Kazan, Sudhir Kumar, Sefika Banu Ozkan
Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 12 (2024)
Sudhir Kumar, Takashi Gojobori
Obituary: Masatoshi Nei (1931-2023). Molecular biology and evolution 40 (6) (2023)
Jack M Craig, Glenn S Gerhard, Sudip Sharma, Anastasia Yankovskiy, Sayaka Miura, Sudhir Kumar
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Molecular biology and evolution (2023)
Jianzhi Zhang, Sudhir Kumar
Masatoshi Nei (1931-2023). Nature ecology & evolution (2023)
Sudhir Kumar, Qiqing Tao, Alessandra P Lamarca, Koichiro Tamura
Computational reproducibility of molecular phylogenies. Molecular biology and evolution (2023)
Alyssa M Pivirotto, Alexander Platt, Ravi Patel, Sudhir Kumar, Jody Hey
Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls. bioRxiv : the preprint server for biology (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. Bioinformatics (Oxford, England) 39 (1) (2023)
Nicholas James Ose, Paul Campitelli, Tushar Modi, I Can Kazan, Sudhir Kumar, S Banu Ozkan
Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. bioRxiv : the preprint server for biology (2023)
Jack M Craig, Glenn S Gerhard, Sudip Sharma, Anastasia Yankovskiy, Sayaka Miura, Sudhir Kumar
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Molecular biology and evolution (2023)
Jack M Craig, Glenn S Gerhard, Sudip Sharma, Anastasia Yankovskiy, Sayaka Miura, Sudhir Kumar
Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells. Molecular biology and evolution (2023)
Sudhir Kumar, Takashi Gojobori
Obituary: Masatoshi Nei (1931-2023). Molecular biology and evolution 40 (6) (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. Bioinformatics (Oxford, England) 39 (1) (2023)
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating. Genome biology and evolution 13 (11) (2022)
Ravi Patel, Vincenzo Carnevale, Sudhir Kumar
Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution. Molecular biology and evolution 39 (5) (2022)
Sudhir Kumar, Sudip Sharma
Evolutionary Sparse Learning for Phylogenomics. Molecular biology and evolution 38 (11) (2022)
Sayaka Miura, Tracy Vu, Jiyeong Choi, Jeffrey P Townsend, Sajjad Karim, Sudhir Kumar
A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications biology 5 (1) (2022)
Sudhir Kumar
A Report by the Editor-in-Chief for Molecular Biology and Evolution (MBE), Volume 38. Molecular biology and evolution 39 (12) (2022)
Sudhir Kumar, Michael Suleski, Jack M Craig, Adrienne E Kasprowicz, Maxwell Sanderford, Michael Li, Glen Stecher, S Blair Hedges
TimeTree 5: An Expanded Resource for Species Divergence Times. Molecular biology and evolution (2022)
Sudip Sharma, Sudhir Kumar
Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling. Molecular biology and evolution 39 (11) (2022)
Nicholas James Ose, Brandon M Butler, Avishek Kumar, I Can Kazan, Maxwell Sanderford, Sudhir Kumar, Sefika Banu Ozkan
Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. PLoS computational biology 18 (4) (2022)
Marcos A Caraballo-Ortiz, Sayaka Miura, Maxwell Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L K Pond, Sudhir Kumar
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics (Oxford, England) 38 (10) (2022)
Sudhir Kumar
A Report by the Editor-in-Chief for Molecular Biology and Evolution (MBE), Volume 38. Molecular biology and evolution 39 (12) (2022)
Marta Canuti, Silvia Bianchi, Otto Kolbl, Sergei L Kosakovsky Pond, Sudhir Kumar, Maria Gori, Clara Fappani, Daniela Colzani, Elisa Borghi, Gian Vincenzo Zuccotti, Mario C Raviglione, Elisabetta Tanzi, Antonella Amendola
Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence? BMJ global health 7 (3) (2022)
Antonia Chroni, Sayaka Miura, Lauren Hamilton, Tracy Vu, Stephen G Gaffney, Vivian Aly, Sajjad Karim, Maxwell Sanderford, Jeffrey P Townsend, Sudhir Kumar
Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers 14 (17) (2022)
Jack M Craig, Sudhir Kumar, S Blair Hedges
Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts. Molecular biology and evolution 39 (3) (2022)
Sudhir Kumar
Embracing Green Computing in Molecular Phylogenetics. Molecular biology and evolution 39 (3) (2022)
Sudhir Kumar
A Report by the Editor-in-Chief for Molecular Biology and Evolution (MBE), Volume 38. Molecular biology and evolution 39 (12) (2022)
Ravi Patel, Sudhir Kumar
Epistasis produces an excess of invariant sites in neutral molecular evolution. Proceedings of the National Academy of Sciences of the United States of America 118 (18) (2021)
Sudhir Kumar, Qiqing Tao, Steven Weaver, Maxwell Sanderford, Marcos A Caraballo-Ortiz, Sudip Sharma, Sergei L K Pond, Sayaka Miura
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic. Molecular biology and evolution 38 (8) (2021)
Laura B Scheinfeldt, Andrew Brangan, Dara M Kusic, Sudhir Kumar, Neda Gharani
Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants. Journal of personalized medicine 11 (2) (2021)
Koichiro Tamura, Glen Stecher, Sudhir Kumar
MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular biology and evolution 38 (7) (2021)
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
Molecular and morphological clocks for estimating evolutionary divergence times. BMC ecology and evolution 21 (1) (2021)
Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A Huuki, Sergei L Kosakovsky Pond, Jessica M Priest, Jiamin Deng, Sudhir Kumar
A new method for inferring timetrees from temporally sampled molecular sequences. PLoS computational biology 16 (1) (2020)
Beatriz Mello, Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Molecular ecology resources 21 (1) (2020)
Ravi Patel, Sudhir Kumar
On estimating evolutionary probabilities of population variants. BMC evolutionary biology 19 (1) (2019)