S. Kumar

A role for keratins in supporting mitochondrial organization and function in skin keratinocytes

This study shows that keratins K6 and K16 regulate mitochondrial structure, function, and dynamics in keratinocytes, contributing to oxidative stress in pachyonychia congenita.

Phosphorylation by Aurora B kinase regulates caspase-2 activity and function

This study identifies Aurora B kinase-mediated phosphorylation of caspase-2 at S384, which inhibits its catalytic activity and apoptosis function during mitotic catastrophe.

The influence of peptide context on signalling and trafficking of glucagon-like peptide-1 receptor biased agonists

The paper evaluates how peptide context affects GLP-1R signaling and trafficking, showing differences in agonist-mediated responses based on sequence homology and structural features.

The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection

This study uses single-cell RNA sequencing to analyze the host and viral RNA dynamics during VEEV infection, identifying superproducer cells and candidate antiviral targets.

Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

This study compares simple and complex substitution models for divergence time estimation, finding that simple models can produce similar results to complex ones in many datasets.

Molecular control of interfacial protein structure on graphene-based substrates steers cell fate

This study shows how altering graphene substrates' surface chemistry affects fibronectin structure, which in turn influences stem cell behavior and bone differentiation.

Broadly neutralizing plasma antibodies effective against diverse autologous circulating viruses in infants with multivariant HIV-1 infection.

The paper identifies viral factors associated with early broadly neutralizing antibody (bnAb) responses in HIV-1-infected infants and suggests implications for polyvalent vaccination strategies.

Nucleotide Analogues as Inhibitors of Viral Polymerases

The paper investigates the potential of nucleotide analogues, specifically EPCLUSA, as inhibitors of viral polymerases in coronaviruses like 2019-nCoV, SARS, and MERS.

Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes

This paper identifies H1t's association with repressed repeat-element chromatin domains in pachytene spermatocytes through ChIP-sequencing and mass spectrometry.

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

The paper introduces a new method to calculate reliable confidence intervals for divergence times estimated using the RelTime method, showing good coverage probabilities in simulations.

Designing of a mini-core that effectively represents 3004 diverse accessions of rice

The paper designs a mini-core of 520 rice accessions that effectively represents the genetic diversity of 3004 rice accessions, capturing SNPs, phenotypes, and geographical regions.

Ecological and evolutionary insights into pathogenic and non-pathogenic rice associated Xanthomonas

This study compares pathogenic and non-pathogenic Xanthomonas strains to reveal evolutionary differences and genomic factors contributing to pathogenicity and host adaptation.

Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India

This study describes a new bacterial species, Xanthomonas sontii, isolated from healthy rice seeds, which is non-pathogenic to rice plants.

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

This study evaluates seven computational methods for inferring clone phylogenies from bulk sequencing data, finding significant variation in their accuracy for mutation order and clone grouping.

Siliplant1 (Slp1) protein precipitates silica in sorghum silica cells

This study identifies Siliplant1 (Slp1) as a protein that precipitates silica in sorghum silica cells through in vitro and in vivo experiments.

Biophysical principles of choanoflagellate self-organization

The paper quantifies biophysical processes in choanoflagellate rosette morphogenesis, showing ECM constraints drive 3D growth and shape colony morphospace.

A new method for inferring timetrees from temporally sampled molecular sequences

This paper introduces RTDT, a new method for inferring timetrees from temporally sampled molecular sequences, which is more accurate and computationally efficient than existing Bayesian methods.

Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle

The paper identifies genetic determinants of Plasmodium falciparum fitness across its life cycle using bulk segregant analysis and experimental crosses.

Molecular dating for phylogenies containing a mix of populations and species

This study evaluates molecular dating methods for phylogenies with mixed populations and species, finding that RelTime performs well compared to Bayesian approaches.

On estimating evolutionary probabilities of population variants

This paper introduces a modified evolutionary probability (EP) method that infers phylogeny and divergence times from sequence alignments, enabling reliable EP estimates without prior knowledge of species relationships.

Physicochemical and microbiological profile of the potable water of Eastern Himalayan State Sikkim: An Indication of Severe Fecal Contamination and Immediate Health Risk

This study evaluates the physicochemical and microbiological quality of spring water in Sikkim, revealing severe fecal contamination and heavy metal exceedances, posing immediate health risks.

Silent crickets reveal the genomic footprint of recent adaptive trait loss

The paper examines the genomic effects of recent sexual signal loss in crickets, finding pleiotropy, hitchhiking, and regulatory disruption associated with the trait loss.

Genomic architecture and introgression shape a butterfly radiation

The paper uses a low-cost genome assembly strategy to study Heliconius butterfly evolution, finding that introgression, not incomplete lineage sorting, explains most non-canonical genetic histories.

Viral characteristics associated with sustenance of elite neutralizing activity in chronically HIV-1C infected monozygotic pediatric twins

This study compares viral characteristics in two HIV-1C infected monozygotic twins with differing elite neutralizing antibody profiles, identifying viral mutations associated with neutralization resistance and susceptibility.

Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis

This study identifies P152Lp53 as a gain-of-function mutant that promotes cell mobility, proliferation, invasion, and tumorigenesis through upregulated signalling pathways.

Quantitative mapping of triacylglycerol chain length and saturation using broadband CARS microscopy

This paper introduces a method to quantitatively analyze triacylglycerol composition in lipid droplets using broadband CARS microscopy, enabling rapid and accurate in situ analysis.

A new method for detecting autocorrelation of evolutionary rates in large phylogenies

This paper introduces a machine learning method to detect evolutionary rate autocorrelation in large phylogenies, finding it common across multiple taxa.

An HIV-1 broadly neutralizing antibody from a clade C infected pediatric elite neutralizer potently neutralizes the contemporaneous and autologous evolving viruses

This study isolates and characterizes an HIV-1 broadly neutralizing antibody from a pediatric elite neutralizer, showing potent neutralization of cross-clade and autologous viruses.

Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius

The paper examines gene expression and molecular evolution in the Z sex chromosome of Heliconius butterflies, finding mixed evidence for a fast-Z effect.

Towards personalized computer simulation of breast cancer treatment: a multi-scale pharmacokinetic and pharmacodynamic model informed by multi-type patient data

This study develops a multi-scale pharmacokinetic and pharmacodynamic model of breast cancer treatment, personalized with patient data to simulate and improve treatment outcomes.