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List of works by Raja Mazumder

A Primer for Access to Repositories of Cancer-Related Genomic Big Data

scientific article published on 01 January 2019

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

scientific article

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs

scientific article (publication date: 3 June 2014)

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)

scientific article

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data

scientific article

Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor beta Pathway Short title: Prognostic significance of TGF-β signature in liver cancer.

scientific article published on 14 September 2017

Baseline human gut microbiota profile in healthy people and standard reporting template

scientific article published on 11 September 2019

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery.

scientific article published on 9 October 2017

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.

scientific article

Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.

scientific article published on 14 December 2016

Biocuration Virtual Issue 2012

scientific article published on 20 March 2012

COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases

scientific article published on 10 September 2020

Census-based rapid and accurate metagenome taxonomic profiling

scientific article

Community annotation in biology

scientific article (publication date: 18 February 2010)

Comparisons of gene colinearity in genomes using GeneOrder2.0.

scientific article

Computational clustering for viral reference proteomes.

scientific article published on 26 February 2016

CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes

scientific article

Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily

scientific article

DiMeX: A Text Mining System for Mutation-Disease Association Extraction.

scientific article

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

scientific article published on 31 December 2018

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis

scientific article

Germ line variants of human N-methylpurine DNA glycosylase show impaired DNA repair activity and facilitate 1,N6-ethenoadenine-induced mutations

scientific article

GlyGen data model and processing workflow

scientific article published on 23 April 2020

GlyGen: Computational and Informatics Resources for Glycoscience

scientific article published on 01 January 2020

HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis

scientific article

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

scientific article

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

scientific article

Human germline and pan-cancer variomes and their distinct functional profiles

scientific article

Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis

scientific article published on 22 October 2018

Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins.

scientific article

Impact of germline and somatic missense variations on drug binding sites

scientific article

Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer

scientific article published on 01 April 2019

Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer.

scientific article

MMDB: Entrez's 3D-structure database.

scientific article

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

scientific article

Ongoing and future developments at the Universal Protein Resource

scientific article

Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

scientific article published on 24 February 2013

Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes

scientific article

Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices.

scientific article published on 23 March 2016

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Reorganizing the protein space at the Universal Protein Resource (UniProt)

scientific article (publication date: 2012)

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

scientific article

SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways.

scientific article published on 5 December 2012

Separation and assembly of deep sequencing data into discrete sub-population genomes.

scientific article published on 28 August 2017

Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based biomarker discovery and diagnostics

scientific article

Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes

scientific article

Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2.

scientific article published on 15 October 2014

Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function.

scientific article

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets

scientific article (publication date: 25 September 2009)

The COG database: an updated version includes eukaryotes

scientific article

The Global Cancer Genomics Consortium's Second Annual Symposium: Genomics Medicine in Cancer Research

scientific article published on 17 April 2013

The Universal Protein Resource (UniProt): an expanding universe of protein information

scientific article

Trends in protein evolution inferred from sequence and structure analysis.

scientific article

UniRef: comprehensive and non-redundant UniProt reference clusters

scientific article (publication date: 15 May 2007)

Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes

scientific article published on 12 June 2014

miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines

scientific article published on 17 January 2019

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