S. Mande

发表

Computational Analysis of the ESX-1 Region of Mycobacterium tuberculosis: Insights into the Mechanism of Type VII Secretion System

C. Das, T. Ghosh, S. Mande, 2011, PloS one.

MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks

S. Mande, S. Nagpal, Rashmi Singh, 2020, Nucleic Acids Res..

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups

T. Ghosh, S. Mande, Deepak Yadav, 2016, Gut Pathogens.

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

Bhusan K. Kuntal, S. Mande, B. Kuntal, 2018, The ISME Journal.

C16S - a Hidden Markov Model based algorithm for taxonomic classification of 16S rRNA gene sequences.

Monzoorul Haque Mohammed, T. Ghosh, S. Mande, 2012, Genomics.

INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms

Sharmila S. Mande, Sakshi Shrivastava, S. Mande, 2010, Journal of Biosciences.

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

Monzoorul Haque Mohammed, Sharmila S Mande, Tarini Shankar Ghosh, 2011, BMC Genomics.

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.

Monzoorul Haque Mohammed, Sharmila S Mande, S. Mande, 2012, Gene.

Title: A compendium of predicted growths and derived symbiotic relationships between 803 1 gut microbes in 13 different diets

Anirban Dutta, S. Mande, Rohan Singh, 2021 .

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques

Mohammed M. Haque, S. Mande, Disha Tandon, 2016, PloS one.

Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling

Anirban Dutta, C. Das, S. Mande, 2013, Gut Pathogens.

Modelling of the regulation of the hilA promoter of type three secretion system of Salmonella enterica serovar Typhimurium

S. Mande, R. Maithreye, 2007, Systems and Synthetic Biology.

Xenobiotic Metabolism and Gut Microbiomes

T. Ghosh, S. Mande, Anubhav Das, 2016, PloS one.

A perspective on the benefits of consumption of parboiled rice over brown rice for glycaemic control

Anirban Dutta, S. Mande, T. Bose, 2021, European Journal of Nutrition.

Crosstalk Between Female Gonadal Hormones and Vaginal Microbiota Across Various Phases of Women’s Gynecological Lifecycle

Mohammed M. Haque, S. Mande, Harrisham Kaur, 2020, Frontiers in Microbiology.

Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?

Anirban Dutta, S. Mande, T. Bose, 2021, Virus Research.

Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?

Anirban Dutta, S. Mande, A. Dutta, 2021, Virus Research.

Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses

Anirban Dutta, S. Mande, Sharmistha Banerjee, 2019, Front. Microbiol..

Identification and Functional Characterization of Gene Components of Type VI Secretion System in Bacterial Genomes

S. Mande, Sakshi Shrivastava, 2008, PloS one.

i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets

Monzoorul Haque Mohammed, T. Ghosh, S. Mande, 2011, BMC Genomics.

Lifestyle-Induced Microbial Gradients: An Indian Perspective

Mohammed M. Haque, S. Mande, Rashmi Singh, 2019, Front. Microbiol..

Recto running Title: Detecting eukaryotic sequences in metagenomes Verso running Title: Monzoorul Haque Mohammed et al.

Monzoorul Haque Mohammed, S. Mande, M. H. Mohammed, 2011 .

NetConfer: a web application for comparative analysis of multiple biological networks

S. Mande, B. Kuntal, S. Nagpal, 2020, BMC Biology.

Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?

S. Mande, S. Nagpal, Divyanshu Srivastava, 2022, Journal of Molecular Biology.

Chaperonin Abundance Boosts Bacterial Fitness

Anirban Dutta, S. Mande, P. Lund, 2020, bioRxiv.

Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome

Anirban Dutta, S. Mande, Rashmi Singh, 2022, Applied and Environmental Microbiology.

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

G. Nair, T. Ghosh, S. Mande, 2013, PloS one.

In silico dissection of Type VII Secretion System components across bacteria: New directions towards functional characterization

T. Ghosh, S. Mande, Chandrani Das, 2016, Journal of Biosciences.

Can machines learn the mutation signa- tures of SARS-CoV-2 and enable viral-g-

S. Mande, S. Nagpal, Divyanshu Srivastava, 2022 .

Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome

Anirban Dutta, S. Mande, Rashmi Singh, 2022, Applied and environmental microbiology.

Host-microbiome interactions: Gut-Liver axis and its connection with other organs

S. Mande, S. Anand, 2022, npj Biofilms and Microbiomes.

Système de classification taxinomique

Monzoorul Haque Mohammed, S. Mande, M. H. Mohammed, 2011 .

Understanding the role of interactions between host and Mycobacterium tuberculosis under hypoxic condition: an in silico approach

Anirban Dutta, S. Mande, S. Sadhu, 2018, BMC Genomics.

Title: Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?

Anirban Dutta, S. Mande, T. Bose, 2021 .

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences

Anirban Dutta, S. Mande, T. Bose, 2014, PloS one.

In silico dissection of Type VII Secretion System components across bacteria: New directions towards functional characterization

T. Ghosh, S. Mande, Chandrani Das, 2016, Journal of Biosciences.

Homology Model of a Novel Xylanase: Molecular Basis for High-Thermostability and Alkaline Stability

Amit Ghosh, S. Mande, S. Mande, 2000, Journal of biomolecular structure & dynamics.

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly

Varun Mehra, Sharmila S. Mande, Tarini Shankar Ghosh, 2015, J. Bioinform. Comput. Biol..

HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences

Monzoorul Haque Mohammed, Sharmila S. Mande, Tarini Shankar Ghosh, 2011, BMC Bioinformatics.

Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets

Monzoorul Haque Mohammed, Sharmila S Mande, Tarini Shankar Ghosh, 2011, Journal of Biosciences.

SPHINX - an algorithm for taxonomic binning of metagenomic sequences

Monzoorul Haque Mohammed, Sharmila S. Mande, Tarini Shankar Ghosh, 2011, Bioinform..

Influence of acetyl and bromine substitutions on stacking. Crystal and molecular structures of 8-bromo-2',3',5'-triacetyl adenosine and 8-bromo 2',3',5'-triacetyl guanosine

S. Ramakumar, M. Viswamitra, S. Mande, 1992 .

A prospective randomized, double-blind, placebo-controlled, dose-response relationship study to investigate efficacy of fructo-oligosaccharides (FOS) on human gut microflora

Mohammed M. Haque, S. Mande, A. Dubey, 2019, Scientific Reports.

Gut bacterial diversity of the tribes of India and comparison with the worldwide data

N. Reddy, R. Talukdar, S. Mande, 2015, Scientific Reports.

Alterations in the gut bacterial microbiome in fungal Keratitis patients

Anirban Dutta, Savitri Sharma, K. Ranjith, 2018, PloS one.

iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities

Rashmi Singh, Sharmila S. Mande, Mohammed Monzoorul Haque, 2019, Front. Microbiol..

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects

Monzoorul Haque Mohammed, Vivek T. Natarajan, R. Pandey, 2016, Scientific Reports.

Metagenome of the gut of a malnourished child

Monzoorul Haque Mohammed, Sharmila S Mande, Tarini Shankar Ghosh, 2011, Gut pathogens.

Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis

S. Mande, Harrisham Kaur, Chandra Bose, 2019, Front. Neurosci..

In Silico Analysis of Putrefaction Pathways in Bacteria and Its Implication in Colorectal Cancer

S. Mande, Harrisham Kaur, Chandrani Das, 2017, Front. Microbiol..

Conformational Variability in Modified Nucleosides. Crystal and Molecular Structure of 2',3'-O-Isopropylidene Inosine

M. Viswamitra, S. Mande, T. Seshadri, 1992 .

Structure of 6,5'-anhydro-6-hydroxy-2',3'-O-isopropylideneuridine

M. Viswamitra, S. Mande, T. Seshadri, 1988 .

Igloo-Plot: a tool for visualization of multidimensional datasets.

Sharmila S Mande, Tarini Shankar Ghosh, Bhusan K Kuntal, 2014, Genomics.

Computational Analysis of Host–Pathogen Protein Interactions between Humans and Different Strains of Enterohemorrhagic Escherichia coli

K. Venkatesh, S. Mande, Tungadri Bose, 2017, Front. Cell. Infect. Microbiol..

Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark

M. Arumugam, T. Nielsen, O. Pedersen, 2021, Genome Medicine.

ReFDash - A Repository of Functional Dashboards providing comprehensive functional insights inferred from 16S microbiome data sets

Sharmila S. Mande, Mohammed Monzoorul Haque, Mohammed M. Haque, 2019 .

A snapshot of gut microbiota of an adult urban population from Western region of India

Mohammed M. Haque, S. Mande, A. Dubey, 2018, PloS one.

Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome

T. Ghosh, S. Mande, Tanudeep Bhattacharya, 2015, PloS one.

Gut Microbiomes of Indian Children of Varying Nutritional Status

Sharmila S. Mande, Tarini Shankar Ghosh, G. Nair, 2014, PloS one.

Diet, Microbiota and Gut-Lung Connection

S. Mande, S. Anand, 2018, Front. Microbiol..

Chaperonin Abundance Enhances Bacterial Fitness

Anirban Dutta, S. Mande, P. Lund, 2021, Frontiers in Molecular Biosciences.

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

S. Mande, B. Kuntal, Pranjal Chandrakar, 2018, The ISME Journal.

Classification of metagenomic sequences: methods and challenges

Monzoorul Haque Mohammed, Sharmila S. Mande, Tarini Shankar Ghosh, 2012, Briefings Bioinform..

Towards Engineering an Ecosystem: A Review of Computational Approaches to Explore and Exploit the Human Microbiome for Healthcare

Sharmila S. Mande, Anirban Dutta, Anirban Dutta, 2021, Transactions of the Indian National Academy of Engineering.

Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations

Sharmila S. Mande, Bhusan K. Kuntal, Chetan Gadgil, 2019, Front. Microbiol..

A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets

Anirban Dutta, S. Mande, Rohan Singh, 2021, bioRxiv.

First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk

Mohammed M. Haque, Anirban Dutta, S. Mande, 2017, Scientific Reports.

MarkerML - Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning.

S. Mande, S. Nagpal, Rohan Singh, 2022, Journal of molecular biology.

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

Monzoorul Haque Mohammed, S. Mande, Rachamalla Maheedhar Reddy, 2014, Genomics.

An L40C mutation converts the cysteine-sulfenic acid redox center in enterococcal NADH peroxidase to a disulfide.

W. Hol, S. Mande, D. Parsonage, 1995, Biochemistry.

Crystallographic analyses of NADH peroxidase Cys42Ala and Cys42Ser mutants: active site structures, mechanistic implications, and an unusual environment of Arg 303.

W. Hol, S. Mande, D. Parsonage, 1995, Biochemistry.

Can Targeting Non-Contiguous V-Regions With Paired-End Sequencing Improve 16S rRNA-Based Taxonomic Resolution of Microbiomes?: An In Silico Evaluation

Anirban Dutta, S. Mande, Nishal Kumar Pinna, 2019, Front. Genet..

16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India

Mohammed M. Haque, S. Mande, S. Mande, 2019, Scientific Data.

16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India

Mohammed M. Haque, S. Mande, S. Mande, 2019, Scientific Data.

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks

G. Nair, B. Das, T. Ghosh, 2017, Scientific Reports.

What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes

Sharmila S. Mande, Sunil Nagpal, Divyanshu Srivastava, 2020, bioRxiv.

Can Pathogenic and Nonpathogenic Bacteria Be Distinguished by Sensory Protein Abundance?

S. Mande, S. Bhar, Tungadri Bose, 2020, Applied and Environmental Microbiology.

Comparative analysis of tandem repeats in the 44 outer membrane proteins of non-pathogenic (K12) and two pathogenic (O157) strains of E. coli

V. R. Rao, S. Mande, 2006 .

DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

Monzoorul Haque Mohammed, Sharmila S. Mande, Tarini Shankar Ghosh, 2010, BMC Bioinformatics.

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

Monzoorul Haque Mohammed, Sharmila S. Mande, Tarini Shankar Ghosh, 2009, Bioinform..

Investigating host-bacterial interactions among enteric pathogens

K. Venkatesh, S. Mande, Tungadri Bose, 2019, BMC Genomics.

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

Tungadri Bose, Sharmila S. Mande, Mohammed Monzoorul Haque, 2015, PloS one.

Comparative In silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens

S. Mande, S. Anand, Harrisham Kaur, 2016, Front. Microbiol..

Decoding the microbiome for the development of translational applications: Overview, challenges and pitfalls

Sharmila S Mande, Mohammed Monzoorul Haque, Mohammed M. Haque, 2019, Journal of Biosciences.

‘GutFeel’: an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome

S. Mande, S. Anand, Harrisham Kaur, 2021, FEBS letters.

Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India

M. Arumugam, T. Nielsen, O. Pedersen, 2021, Genome Medicine.

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes

Anirban Dutta, S. Mande, Deepak Yadav, 2019, DNA research : an international journal for rapid publication of reports on genes and genomes.

Dynamics and Control of Flagella Assembly in Salmonella typhimurium

S. Saini, S. Mande, Chandrani Das, 2018, Front. Cell. Infect. Microbiol..

Structural aspects of lesional and non-lesional skin microbiota reveal key community changes in leprosy patients from India

Mohammed M. Haque, S. Mande, S. Mande, 2021, Scientific Reports.

FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information

Sharmila S Mande, Swadha Anand, Bhusan K Kuntal, 2019, Bioinform..

Gut Microbiota of the Asian-Indian Type 2 Diabetes Phenotype: How Different It Is from the Rest of the World?

Anirban Dutta, S. Mande, Nishal Kumar Pinna, 2023, Journal of the Indian Institute of Science.

Antibiotic stewardship in premature infants: a systematic review

Anirban Dutta, G. Greisen, S. Mande, 2020, medRxiv.

Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase.

W. Hol, M. Allen, R. Perham, 1996, Structure.

Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

Sharmila S Mande, Tarini Shankar Ghosh, Bhusan K Kuntal, 2013, Genomics.

FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways

Sharmila S. Mande, Anwesha Mohapatra, Vineet Bhatt, 2018, Front. Microbiol..

Understanding the role of interactions between host and Mycobacterium tuberculosis under hypoxic condition: an in silico approach

Anirban Dutta, S. Mande, Vishnuvardhan Mahamkali, 2018, BMC Genomics.

Composition of nasopharyngeal microbiota in individuals with SARS-CoV-2 infection across three COVID-19 waves in India

Divya Tej Sowpati, Mohammed M. Haque, Anirban Dutta, 2023, bioRxiv.

BactInt: A domain driven transfer learning approach and a corpus for extracting inter-bacterial interactions from biomedical text

Bhusan K. Kuntal, S. Mande, B. Kuntal, 2023, ArXiv.

Utilizing domain-based features to improve classification accuracy of biomedical text having bacterial associations

Sharmila S. Mande, Divyanshu Srivastava, Bhusan K. Kuntal, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

“EviMass”: A Literature Evidence-Based Miner for Human Microbial Associations

Sharmila S. Mande, Divyanshu Srivastava, Bhusan K. Kuntal, 2019, Front. Genet..

CompNet: a GUI based tool for comparison of multiple biological interaction networks

Anirban Dutta, Sharmila S. Mande, Bhusan K. Kuntal, 2016, BMC Bioinformatics.

First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk

Mohammed M. Haque, Anirban Dutta, S. Mande, 2017, Scientific Reports.

Tracking mutational semantics of SARS-CoV-2 genomes

S. Mande, S. Nagpal, Rohan Singh, 2021, Scientific Reports.

Structure of 2',3'-O-isopropylideneguanosine hemihydrate

M. Viswamitra, S. Mande, T. Seshadri, 1989 .

Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

Sharmila S. Mande, Mohammed Monzoorul Haque, Mohammed M. Haque, 2016, PloS one.

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets.

Tungadri Bose, Sharmila S Mande, Mohammed Monzoorul Haque, 2015, Genomics.

A prospective randomized, double-blind, placebo-controlled, dose-response relationship study to investigate efficacy of fructo-oligosaccharides (FOS) on human gut microflora

Mohammed M. Haque, S. Mande, A. Dubey, 2019, Scientific Reports.

NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams

Sharmila S Mande, Sunil Nagpal, Bhusan K Kuntaland, 2020, Bioinform..

Environmental insults and compensative responses: when microbiome meets cancer

S. Mande, Sunil Nagpal, 2023, Discover Oncology.

Identification of compositionally distinct regions in genomes using the centroid method

Sarang Aravamuthan, Sharmila S. Mande, Issaac Rajan, 2007, Bioinform..

Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.

Mohammed M. Haque, S. Mande, S. Nagpal, 2016 .

Investigating host-bacterial interactions among enteric pathogens

K. Venkatesh, S. Mande, Tungadri Bose, 2019, BMC Genomics.

‘TIME’: A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data

Sharmila S. Mande, Bhusan K. Kuntal, Krishanu D. Baksi, 2018, Front. Microbiol..

A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India

Divya Tej Sowpati, Mohammed M. Haque, Anirban Dutta, 2023, Frontiers in Microbiology.

(Machine) Learning the mutation signatures of SARS-CoV-2: a primer for predictive prognosis

S. Mande, S. Nagpal, Divyanshu Srivastava, 2021, bioRxiv.

Correction: Alterations in the gut bacterial microbiome in fungal Keratitis patients

Anirban Dutta, Savitri Sharma, K. Ranjith, 2019, PloS one.

Understanding Communication Signals during Mycobacterial Latency through Predicted Genome-Wide Protein Interactions and Boolean Modeling

Sharmila S. Mande, Chandrani Das, Shekhar C. Mande, 2012, PloS one.

Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

T. Ghosh, S. Mande, B. Kuntal, 2013, Genomics.

FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information

Anirban Dutta, S. Mande, Mohammed Mh, 2015, Journal of Biosciences.

Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework

T. Ghosh, S. Mande, V. Mehra, 2016, Journal of Biosciences.

ProViDE: A software tool for accurate estimation of viral diversity in metagenomic samples

Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Dinakar Komanduri, 2011, Bioinformation.

Visual exploration of microbiome data

Sharmila S. Mande, Bhusan K. Kuntal, S. Mande, 2019, Journal of Biosciences.

BactInt: A domain driven transfer learning approach for extracting inter-bacterial associations from biomedical text.

Bhusan K. Kuntal, S. Mande, Vatsala Pokhrel, 2024, Computational biology and chemistry.