A. Mukhopadhyay

Prognostic relevance of correlated co-expression of coding and noncoding RNAs in cervical cancers

The paper identifies prognostically relevant co-expression patterns between coding and noncoding RNAs in HPV16-positive cervical cancers and links them to patient survival.

Desiccated cyanobacteria serve as efficient plasmid DNA carrier in space flight

The paper demonstrates that desiccated cyanobacteria can safely transport plasmid DNA to and from space without cryogenic storage, preserving DNA integrity for use in synthetic biology.

ZymePackNet: rotamer-sampling free graph neural network method for protein sidechain prediction

ZymePackNet predicts protein sidechain conformations using a graph neural network without requiring rotamer libraries or energy functions, achieving high accuracy in dihedral angle prediction.

Automated Protein Affinity Optimization using a 1D-CNN Deep Learning Model

This paper introduces ZymeSwapNet, a 1D-CNN model for protein sequence prediction that optimizes design objectives like stability and binding specificity in antibody domains.

A 30-Color Full-Spectrum Flow Cytometry Panel to Characterize the Immune Cell Landscape in Spleen and Tumors within a Syngeneic MC-38 Murine Colon Carcinoma Model

A chromosome-scale assembly of Brassica carinata (BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions into B. juncea (AABB)

The paper presents a chromosome-scale genome assembly of B. carinata and assesses introgression potential into B. juncea for disease resistance.

Revealing Pentose Catabolism in Pseudomonas putida

The paper identifies three Pseudomonas putida isolates with diverse pentose catabolism capabilities and characterizes their genes and pathways for xylose and arabinose oxidation.

Differences in durability of PARP inhibition by clinically approved PARP inhibitors: implications for combinations and scheduling

This paper compares the durability of PARP inhibition by five PARP inhibitors in ovarian cancer cells and shows rucaparib provides the longest-lasting inhibition, with implications for combination therapies with ATR inhibitors.

RICTOR Drives ZFX-mediated Ganglioside Biosynthesis to Promote Breast Cancer Progression.

This study identifies RICTOR's role in regulating ganglioside biosynthesis via ZFX and UGCG, promoting breast cancer progression through EGFR signaling.

Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation

This study examines post-translational phosphorylation of Pseudomonas response regulators expressed in E. coli, finding that phosphorylation states are influenced by host factors rather than exogenous phospho-donors.

Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing

This study identifies genes and proteins involved in nitrogen metabolism in Pseudomonas putida using transposon sequencing and provides an interactive visualization tool for the data.

Using Deep Learning to Count Monarch Butterflies in Dense Clusters

This paper develops a deep learning tool to count monarch butterflies in dense clusters, achieving high accuracy and releasing an annotated dataset for conservation use.

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

The paper identifies 41 viral clusters in groundwater plasmidomes, links them to bacterial hosts, and detects novel phage genera and host-specific genes.

Generation of fluorescent HCV pseudoparticles to study early viral entry events- involvement of Rab1a in HCV entry

This study generates fluorescent HCV pseudoparticles to investigate early viral entry, showing Rab1a's role in HCV trafficking and membrane fusion within 15 minutes.

Plasmodium falciparum Kelch13 and its artemisinin-resistant mutants assemble as hexamers in solution: a SAXS data driven shape restoration study.

This study uses SAXS data to show that PfKelch13 forms a stable hexamer with specific domain arrangements, and that resistant mutants have altered spatial configurations.

Nuclear Morphology Optimized Deep Hybrid Learning (NUMODRIL): A novel architecture for accurate diagnosis/prognosis of Ovarian Cancer

This paper introduces a novel deep hybrid learning architecture, NUMODRIL, for classifying ovarian cancer tissues based on nuclear morphology and lamin protein distribution, achieving high accuracy and efficiency.

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq

This study uses RB-TnSeq to functionally analyze fatty acid and alcohol metabolism in Pseudomonas putida, identifying gene roles and catabolic pathways for isoprenol and isopentanol.

REC protein family expansion by the emergence of a new signaling pathways

The paper identifies a mechanism of REC protein family expansion through gene recombination and positive selection, leading to functional divergence in bacterial response regulators.

Optimal inaccuracy: estimating male fitness in the movement-assisted dichogamous species Clerodendrum infortunatum

The paper investigates anther positioning in Clerodendrum infortunatum, finding that despite high pollination inaccuracy, anther dynamics maximize overall male fitness.

Selective Nanotherapeutic Targeting of the Neutrophil Subset Mediating Inflammatory Injury

This study identifies a neutrophil subset responsible for ALI in sepsis and shows that targeting it with nanotherapeutics prevents ALI without harming host defense.

Iron Supplementation Eliminates Antagonistic Interactions Between Root Associated Bacteria

The paper shows iron supplementation eliminates antagonistic interactions between root-associated bacteria by revealing iron limitation drives these interactions.

Fine-tuned spatiotemporal dynamics of sporophylls in movement-assisted dichogamy: a study on Clerodendrum infortunatum

This study examines the spatiotemporal dynamics of sporophylls in movement-assisted dichogamy in Clerodendrum infortunatum, finding that physical and chemical adaptations during the transition phase enhance pollen exclusion.

Chemoinformatic-guided engineering of polyketide synthases

This study uses chemoinformatics to engineer polyketide synthases for producing saturated β-carbon compounds, finding a correlation between chemical similarity and product titers.

Population dynamics analysis of Saccharomyces cerevisiae deletion library during fed-batch cultivation using Bar-seq

The paper uses Bar-seq to analyze population dynamics of a yeast deletion library during fed-batch cultivation, identifying genes associated with stress responses in industrial fermentation.

Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

This study engineers Pseudomonas putida to produce indigoidine with high titer, rate, and yield by coupling product formation with growth through metabolic rewiring and CRISPRi knockdowns.

BjuWRR1, a CC-NB-LRR gene identified in Brassica juncea, confers resistance to white rust caused by Albugo candida

The paper identifies and validates BjuWRR1, a CC-NB-LRR gene in Brassica juncea, as a resistance gene against white rust caused by Albugo candida through genetic transformation.

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids

This study enhances methyl ketone production in Pseudomonas putida using plant-derived amino acids from hydrolysates, achieving a 9-fold increase in titer.

Habitat-Net: Segmentation of habitat images using deep learning

Habitat-Net segments tropical rainforest habitat images using deep learning, achieving higher accuracy and faster processing than manual methods and U-Net.