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List of works by Sudhir Kumar

A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla

scientific article

A bag-of-words approach for Drosophila gene expression pattern annotation

scientific article

A genomic timescale for the origin of eukaryotes

scientific article

A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis

scientific article

A new method for inferring timetrees from temporally sampled molecular sequences

scientific article published on 17 January 2020

Advances in Time Estimation Methods for Molecular Data

scientific article

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

scientific article published on 01 July 2021

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

scientific article published on 24 September 2020

Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster

scientific article published on December 2009

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary

scientific article published on 16 July 2008

Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression

scientific article

Automatic annotation techniques for gene expression images of the fruit fly embryo

article

BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development

scientific article

Bioinformatics software for biologists in the genomics era.

scientific article published on 07 May 2007

Classification and indexing of gene expression images

article

Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence

2012 scientific article

Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association.

scientific article

Constraining fossil calibrations for molecular clocks

scientific article published in July 2006

Constraint and turnover in sex-biased gene expression in the genus Drosophila

scientific article published on November 2007

Continental breakup and the ordinal diversification of birds and mammals

scientific article

Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions

scientific article

Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning ⬇️

scientific article published on January 1, 2009

Drosophila gene expression pattern annotation through multi-instance multi-label learning

2012 scientific article

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants

scientific article published on 07 April 2022

Estimating divergence times in large molecular phylogenies

scientific article (publication date: 20 November 2012)

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders

scientific article

Evolutionary Diagnosis of non-synonymous variants involved in differential drug response

scientific article

Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome

scientific article

Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants

scientific article published on 5 March 2013

Evolutionary diagnosis method for variants in personal exomes

scientific article published on September 2012

Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery

scientific article

Evolutionary relationships of eukaryotic kingdoms

scientific article published on February 1996

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat.

scientific article

Exploring spatial patterns of gene expression from fruit fly embryogenesis on the iPhone

2012 scientific article

Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times

scientific article (publication date: September 2011)

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis

2011 scientific article

GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes.

scientific article

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome

scientific article

Genome-wide profiling of human cap-independent translation-enhancing elements

scientific article

Genomic clocks and evolutionary timescales

scientific article published in April 2003

Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America

scientific article

Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference

scientific article published on 2 April 2003

Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates

scientific article

Human genomic disease variants: a neutral evolutionary explanation

scientific article

Human origins and analysis of mitochondrial DNA sequences

scientific article published in February 1992

Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations

scientific article

Image-level and group-level models for Drosophila gene expression pattern annotation

scientific article

Incomplete taxon sampling is not a problem for phylogenetic inference

scientific article

Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

article

Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval

scientific article

Lower bounds on multiple sequence alignment using exact 3-way alignment

scientific article

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

article

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

scientific article

MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation

scientific article published on 11 January 2014

MEGA2: molecular evolutionary genetics analysis software

scientific article (publication date: December 2001)

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

scientific article (publication date: June 2004)

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

scientific article

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

scientific article (publication date: October 2011)

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

scientific article

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers

scientific article (publication date: April 1994)

MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences

scientific article (publication date: July 2008)

Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous

article by Sudhindra R. Gadagkar & Sudhir Kumar published 13 July 2005 in Molecular Biology and Evolution

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome

scientific article published on 01 August 2002

Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level

scientific article published on 06 July 2009

Molecular and morphological clocks for estimating evolutionary divergence times

scientific article published on 12 May 2021

Molecular clocks: four decades of evolution

scientific article

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

scientific article published on 02 September 2020

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

scientific article (publication date: 27 October 2010)

Multiple sequence alignment: in pursuit of homologous DNA positions

scientific article published on February 2007

Mutation rates in mammalian genomes

scientific article

Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes ⬇️

scientific article published on May 1, 2003

No Positive Selection for G Allele in a p53 Response Element in Europeans

Nullomers: really a matter of natural selection?

scientific article published in 2007

Obituary: Masatoshi Nei (1931–2023) ⬇️

scholarly article published in 2023

On estimating evolutionary probabilities of population variants

scientific article published on 25 June 2019

Patterns of transitional mutation biases within and among mammalian genomes.

scientific article published on 25 April 2003

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations

scientific article

Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals

scientific article (publication date: June 2010)

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

scientific article

Phylogenetic placement of metagenomic reads using the minimum evolution principle

scientific article

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

scientific article

Placing confidence limits on the molecular age of the human-chimpanzee divergence

scientific article

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

scientific article

Precision of molecular time estimates

scientific article published on May 2004

Prediction of Human Epileptic Seizures based on Optimization and Phase Changes of Brain Electrical Activity

Prospects for building large timetrees using molecular data with incomplete gene coverage among species

scientific article

Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms

scientific article

Pushing Back the Expansion of Introns in Animal Genomes

Quantifying the intragenic distribution of human disease mutations

scientific article

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials

scientific article

Rampant purifying selection conserves positions with posttranslational modifications in human proteins

scientific article

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster

scientific article published on 24 July 2009

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

scientific article (publication date: 22 October 2012)

Signatures of ecological resource availability in the animal and plant proteomes

scientific article published on 26 July 2006

Signatures of natural selection on mutations of residues with multiple posttranslational modifications

scientific article

Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus.

scientific article published on 15 April 2009

Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees.

scientific article published in February 2000

Statistics and truth in phylogenomics

scientific article published on 26 August 2011

Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition

scientific article

Structural dynamics flexibility informs function and evolution at a proteome scale

scientific article

Taxon sampling, bioinformatics, and phylogenomics

scientific article published on February 2003

Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks

scientific article published on 29 August 2003

The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data

scientific article

The evolutionary history of amino acid variations mediating increased resistance of S. aureus identifies reversion mutations in metabolic regulators

scientific article

The origin of Metazoa: a transition from temporal to spatial cell differentiation.

scientific article published on July 2009

The spectrum of human rhodopsin disease mutations through the lens of interspecific variation*1

TimeTree2: species divergence times on the iPhone

scientific article (publication date: 15 July 2011)

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

scientific article

Tree of life reveals clock-like speciation and diversification

scientific article

Understanding human disease mutations through the use of interspecific genetic variation

scientific article published in October 2001

Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence?

scientific article published in 2022

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.

scientific article

myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos

scientific article published on 09 January 2014

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