Shyam Gopalakrishnan

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

Twenty-three new Yersinia pestis genomes from Scandinavia, the Netherlands, Iceland and Armenia extend the Second Plague Pandemic phylogeny, with the first Icelandic plague genome and eastward-spreading pestis secunda strains.

Genomic impact of the second plague pandemic on three human populations

This study analyzes ancient DNA from three European sites to assess the genomic impact of the second plague pandemic, finding no strong positive selection but evidence of reduced long-range immigration post-pandemic.

On the ancestry and evolution of the extinct dire wolf

This study uses paleogenomes of dire wolves to resolve their evolutionary relationships and identify genes under diversifying selection.

Habitat discontinuity and fidelity to migratory routes shape narwhal genetic structure and diversity

This study uses genomic data from narwhals to show that habitat discontinuities and migration fidelity shape population structure, with low genetic diversity and inbreeding in small populations.

The population structure and genetic health of European wolves

The paper analyzes 1,001 wolf genomes to reveal distinct evolutionary lineages and genetic health issues across Europe, highlighting the need for region-specific conservation strategies.

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

The paper uses whole genomes of wolves across Eurasia to study their genetic diversity and evolutionary history, finding major lineage barriers and admixture events shaping their genetic structure.

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

This study imputes ancient dog and wolf genomes to analyze inbreeding history over 10,000 years, finding lower inbreeding in ancient populations and associations between low ROH regions and olfaction/immune genes.

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

The paper estimates effective population size (Ne) of western chimpanzees in Guinea-Bissau using genetic data to inform conservation strategies.

Multi-omics time-series analysis in microbiome research: a systematic review

This paper reviews data science methods for longitudinal multi-omics in microbiome research, highlighting the need for integrated approaches and the lack of widely adopted methods.

Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland

The paper uses ancient environmental DNA to analyze marine biodiversity in pre-industrial Iceland, finding limited human impact compared to climate effects.

The information content of species: formal definitions of pangenome complexity track with bacterial lifestyle

The paper quantifies pangenome complexity as information content, finding that free-living bacteria have higher genomic complexity than host-associated species.

Genomic differentiation among European perch in the western Baltic Sea reflects colonization history and local adaptation

This study uses genomic data to show that brackish water perch in the Baltic Sea have distinct genetic clusters and that salinity tolerance genes are under selection, reflecting colonization history and local adaptation.

Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

The paper analyzes the genomes of Sicilian wolves to reveal their complex history of isolation and admixture with ancient dogs, showing admixture with European dog breeds and signs of inbreeding.

HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph

HaploCart classifies human mtDNA haplogroups using a pangenomic reference graph and Bayesian inference, outperforming existing tools with more accurate and unbiased confidence scores.

Uncovering the hologenomic basis of an extraordinary plant invasion

The paper investigates the genomic basis of invasiveness in Ambrosia artemisiifolia, finding selection signatures in defense genes and reduced pathogen prevalence in invasive populations.

Benchmarking freely available human leukocyte antigen typing algorithms across varying genes, coverages and typing resolutions

This study benchmarks five HLA typing tools across different genes, coverages, and resolutions, finding HLA*LA has highest accuracy for some loci while Optitype performs best for others.

Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem.

The paper presents a desert dingo genome assembly and compares it to domestic dog genomes, identifying structural variants and physiological differences linked to ecological roles.

Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility

The paper combines data from two independent mouse studies to identify genetic loci for traits, finds poor replication rates, and proposes a method to assess confidence in associations.

Genomic analyses of the extinct Sardinian dhole (Cynotherium sardous) reaveal its evolutionary history

The paper sequenced the genome of an extinct Sardinian dhole to determine its evolutionary history and phylogenetic position, finding it diverged from Asian dholes and experienced gene flow before isolation.

Population genomics of the emerging forest pathogen Neonectria neomacrospora

This study uses whole-genome sequencing to analyze the population genetics of Neonectria neomacrospora, revealing clade divergence and gene flow patterns in Europe.

Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats

The paper adapts genotype-by-sequencing for HS rats to call and impute over 3.7 million SNPs with 99% concordance compared to a genotyping array.

Stone Age \"chewing gum\" yields 5,700 year-old human genome and oral microbiome

The paper sequences a 5,700-year-old human genome and oral microbiome from Stone Age chewing gum, revealing genetic and microbial insights.

Plasmodium vivax Malaria viewed through the lens of an eradicated European strain

The paper generates a genome from a historical European Plasmodium vivax strain, revealing its evolutionary relationship to American strains and the presence of drug resistance variants predating their use.

The genetic origins of Saint Helena’s liberated Africans

The paper uses ancient DNA analysis of 20 individuals from St Helena to determine the genetic origins of liberated Africans, finding they came from West Central Africa and were culturally diverse.

Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells

The paper compares chromatin accessibility and transcription factor binding in human and chimpanzee induced pluripotent stem cells, finding widespread conservation and suggesting the pluripotent state is evolutionarily constrained.