List of works - Vineet Bafna

The Sequence of the Human Genome

scientific article; Venter et al (2001)

An integrated map of genetic variation from 1,092 human genomes

scientific article

The variant call format and VCFtools

scientific article (publication date: August 2011)

The diploid genome sequence of an individual human

scientific article published on 4 September 2007

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

scientific article published in March 2007

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

scientific article

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

scientific article

De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly

scientific article

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

scientific article published on 7 December 2011

A multidimensional chromatography technology for in-depth phosphoproteome analysis

scientific article published on 11 April 2008

Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung

scientific article

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

scientific article published on 28 June 2016

The dog genome: survey sequencing and comparative analysis

scientific article

Discovery and revision of Arabidopsis genes by proteogenomics

scholarly article

Exome sequencing can improve diagnosis and alter patient management

scientific article published on June 2012

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

scientific article

Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?

scientific article published on October 2006

Identification of post-translational modifications by blind search of mass spectra.

scientific article published on 27 November 2005

Improving gene annotation using peptide mass spectrometry

scientific article published on 22 December 2006

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

scientific article

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

scientific article

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

scientific article published on 8 February 2017

Experimental selection of hypoxia-tolerant Drosophila melanogaster

scientific article

Proteogenomics to discover the full coding content of genomes: a computational perspective

scientific article

Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach

scientific article

iDASH: integrating data for analysis, anonymization, and sharing

scientific article (publication date: 2012)

Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes

scientific article

A covering method for detecting genetic associations between rare variants and common phenotypes

scientific article

Protein identification using top-down.

scientific article

Peptide sequence tags for fast database search in mass-spectrometry.

scientific article published in July 2005

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.

scientific article

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

scientific article published on 9 December 2016

Proteogenomic database construction driven from large scale RNA-seq data

scientific article

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer

scientific article

Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders

scientific article

Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes

scientific article

An MCMC algorithm for haplotype assembly from whole-genome sequence data

scientific article

Compressing genomic sequence fragments using SlimGene

scientific article (publication date: March 2011)

Expansion of the mycobacterial "PUPylome"

scientific article

Evidence for large inversion polymorphisms in the human genome from HapMap data

scientific article

Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis

scientific article published on 19 June 2008

Learning natural selection from the site frequency spectrum

scientific article published on 14 June 2013

An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays

scientific article published on 18 October 2013

Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies

scientific article

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

scientific article

Virmid: accurate detection of somatic mutations with sample impurity inference

scientific article

Robustness of inference of haplotype block structure

scientific article published in January 2003

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

scientific article

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

scientific article

QNet: a tool for querying protein interaction networks

scientific article

List of works by Vineet Bafna

The Sequence of the Human Genome

An integrated map of genetic variation from 1,092 human genomes

The variant call format and VCFtools

The diploid genome sequence of an individual human

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

A multidimensional chromatography technology for in-depth phosphoproteome analysis

Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

The dog genome: survey sequencing and comparative analysis

Discovery and revision of Arabidopsis genes by proteogenomics

Exome sequencing can improve diagnosis and alter patient management

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?

Identification of post-translational modifications by blind search of mass spectra.

Improving gene annotation using peptide mass spectrometry

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

Experimental selection of hypoxia-tolerant Drosophila melanogaster

Proteogenomics to discover the full coding content of genomes: a computational perspective

Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach

iDASH: integrating data for analysis, anonymization, and sharing

Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes

A covering method for detecting genetic associations between rare variants and common phenotypes

Protein identification using top-down.

Peptide sequence tags for fast database search in mass-spectrometry.

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Proteogenomic database construction driven from large scale RNA-seq data

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer

Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders

Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes

An MCMC algorithm for haplotype assembly from whole-genome sequence data

Compressing genomic sequence fragments using SlimGene

Expansion of the mycobacterial "PUPylome"

Evidence for large inversion polymorphisms in the human genome from HapMap data

Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis

Learning natural selection from the site frequency spectrum

An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays

Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

Virmid: accurate detection of somatic mutations with sample impurity inference

Robustness of inference of haplotype block structure

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

QNet: a tool for querying protein interaction networks