S. Tripathi

Intra-DNA k-mer Conservation Patterns Encode Evolutionary Selection of Variants

The paper introduces kGain, a metric quantifying k-mer frequency shifts due to mutations, and shows it predicts adaptive potential across species and experimental systems.

Evaluating Paraspinal Muscle Response and Compensation via Musculoskeletal Modeling in Spinal Stenosis Surgeries

This study compares muscle force changes in different spinal stenosis surgeries using musculoskeletal modeling, finding that laminotomy reduces muscle compensation compared to laminectomy.

Soft Tissue Mechanics in Hip Distraction after Total Knee Arthroplasty: A Finite Element Analysis

This study uses finite element analysis to compare the biomechanical effects of different total knee arthroplasty techniques on hip distraction, finding that ligament-sacrificing procedures increase soft tissue strain and risk of injury.

Biomechanical Implications of Spinopelvic Alignment on Femoral Head Cartilage and the Proximal Femoral Physis in Slipped Capital Femoral Epiphysis: A Theoretical Finite Element Analysis

This study uses finite element analysis to show that posterior pelvic tilt and high pelvic incidence increase shear stress on the growth plate, potentially causing slippage in slipped capital femoral epiphysis.

Regulation of chromatin transcription dynamics by DNA supercoiling

This paper models chromatin torsion and RNAP translocation to show how DNA supercoiling and nucleosome dynamics regulate transcription velocity and gene expression.

Bat RNA viruses employ viral RHIMs orchestrating species-specific cell death programs linked to Z-RNA sensing and ZBP1-RIPK3 signaling

The paper identifies viral RHIMs in bat RNA viruses that regulate host cell death through Z-RNA sensing and ZBP1-RIPK3 signaling, revealing species-specific effects on human and bat cells.

SARS-CoV-2 variants exhibit differential gut tropism and dysbiosis in Syrian golden hamsters.

This study examines SARS-CoV-2 variants' gut tropism and impact on gut microbiota in Syrian golden hamsters, finding Delta's stronger gastrointestinal preference and greater microbial dysbiosis.

Leveraging RAS-mSIN1 Interaction to Selectively Inhibit mTORC2 Employing Competitive RAS Binding Peptide: Implications in Breast Cancer Metastasis

The paper withdraws a manuscript due to incomplete experiments and requests that it not be cited as a reference.

Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1

This study shows that isoform-specific phosphorylation in the C-terminal tail of CK1δ regulates its autoinhibition and affects circadian rhythms.

A broadly protective CHO cell expressed recombinant spike protein subunit based vaccine (IMT-CVAX) against SARS-CoV-2

This paper develops a recombinant spike protein subunit vaccine (IMT-CVAX) against SARS-CoV-2 that elicits broad neutralization against variants and provides protection in animal models.

A prebiotic genetic alphabet as an early Darwinian ancestor for pre-RNA evolution

This study synthesizes a prebiotic genetic alphabet with barbituric acid and demonstrates its enzymatic incorporation into RNA and transfer to DNA, suggesting a pathway for early genetic code evolution.

HuR enhances SARS-CoV-2 non-structural protein translation through the genomic 5'-UTR, by promoting polypyrimidine tract-binding protein binding

This paper identifies HuR's role in enhancing SARS-CoV-2 non-structural protein translation via the 5'-UTR by promoting PTB binding, while suppressing structural protein translation, and shows potential therapeutic targeting of HuR.

ENHANCED RECOMBINATION AMONG SARS-COV-2 OMICRON VARIANTS CONTRIBUTES TO VIRAL IMMUNE ESCAPE.

The paper analyzes SARS-CoV-2 genome sequences to show increased recombination in Omicron variants, leading to immune escape and enhanced viral transmission.

PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period

This study shows that PER phosphorylation inhibits CK1 activity, stabilizing PER and extending circadian period through feedback inhibition.

Structural basis for tunable affinity and specificity of LxCxEdependentprotein interactions with the retinoblastoma protein family

This study presents crystal structures of the p107 pocket domain bound to LxCxE peptides, revealing structural determinants that explain differences in binding affinity between viral and cellular proteins.

ORF6 protein of SARS-CoV-2 inhibits TRIM25 mediated RIG-I ubiquitination to mitigate type I IFN induction.

This study identifies ORF6 as a SARS-CoV-2 protein that inhibits TRIM25-mediated RIG-I ubiquitination, thereby blocking type I IFN induction and signaling.

RadGenNets: Deep Learning-Based Radiogenomics Model For Gene Mutation Prediction In Lung Cancer

The paper develops a deep learning model that predicts gene mutations in NSCLC patients using CT scans and clinical-genomics data, achieving 94% AUC.

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

This study compares infant gut microbiome assembly in Hadza hunter-gatherers and industrialized infants, finding distinct microbial trajectories and functional differences.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

The paper uses ultra-deep metagenomic sequencing to analyze the gut microbiome of Hadza hunter-gatherers, revealing many microbes absent from existing datasets and highlighting differences in microbial dynamics compared to industrialized populations.

A natural broad-spectrum inhibitor of enveloped virus entry, effective against SARS-CoV-2 and Influenza A Virus in preclinical animal models.

This paper identifies picolinic acid as a broad-spectrum antiviral that inhibits enveloped virus entry, showing efficacy against SARS-CoV-2 and Influenza A Virus in animal models.

Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2

This study identifies montelukast sodium hydrate as a potential antiviral drug against SARS-CoV-2 by targeting the Nsp1-ribosomal complex and reducing viral replication in cell cultures.

Bronco T (Shirisadi kasaya), a polyherbal formulation ameliorates LPS induced septicemia in rats

Bronco T, a polyherbal formulation, improves survival and lung function in LPS-induced septicemia in rats, with effects comparable to pentoxifylline.

DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

The paper presents a theoretical model showing DNA supercoiling mediates long-range cooperation between co-transcribing RNA polymerases, affecting transcription elongation rates and orientation-dependent interactions.

Identification of COVID-19 prognostic markers and therapeutic targets through meta-analysis and validation of Omics data from nasopharyngeal samples

This study identifies prognostic markers and therapeutic targets for COVID-19 by analyzing Omics data from nasal and BALF samples, finding S100 family genes and TXN as key factors, and validating Auranofin as a potential treatment.

Immunogenicity and protective efficacy of a highly thermotolerant, trimeric SARS-CoV-2 receptor binding domain derivative

This study designs a thermotolerant trimeric RBD vaccine candidate that elicits strong neutralizing antibodies against multiple SARS-CoV-2 variants in animal models.

A Mechanistic Modeling Framework Reveals the Key Principles Underlying Tumor Metabolism

This paper presents a mechanistic model of tumor metabolism that identifies key principles governing metabolic heterogeneity and plasticity in cancer cells.

Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT

This study identifies two mechanisms—epigenetic feedback in the ZEB1/GRHL2 loop and stochastic partitioning during cell division—that can drive resistance to EMT in cancer cells.

Structural mimicry confers robustness in the cyanobacterial circadian clock

The paper shows SasA regulates circadian clock robustness in cyanobacteria by structurally mimicking KaiB to modulate protein complex assembly.

A Mechanism for Epithelial-Mesenchymal Heterogeneity in a Population of Cancer Cells

The paper shows that epithelial-mesenchymal heterogeneity in cancer cells arises from noise in RNA and protein partitioning during division and models its implications for therapy.

Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum

This study compares three transcriptomics-based metrics for quantifying EMT status across tumor types, finding that MLR-based scoring better distinguishes pure hybrid E/M cells from mixed populations.