List of works by Vineet Bafna

A Note on Computing Interval Overlap Statistics

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

scientific article

A decomposition theory for phylogenetic networks and incompatible characters

scientific article published on December 2007

A multidimensional chromatography technology for in-depth phosphoproteome analysis

scientific article published on 11 April 2008

A note on efficient computation of haplotypes via perfect phylogeny.

scientific article

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

scientific article published in July 2006

AMASS: algorithm for MSI analysis by semi-supervised segmentation

scientific article

Abstractions for Genomics

scientific article

Accurate annotation of peptide modifications through unrestrictive database search

scientific article published on 23 November 2007

Accurate mass spectrometry based protein quantification via shared peptides

scientific article published on 13 March 2012

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer

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

Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations

scientific article published on 04 December 2013

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

scientific article

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes

scientific article

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

scientific article published on 18 October 2013

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

scientific article

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

scientific article

Assembly-free and alignment-free sample identification using genome skims

Automated querying and identification of novel peptides using MALDI mass spectrometric imaging

scientific article

Clear: Composition of Likelihoods for Evolve and Resequence Experiments.

scientific article

Combinatorics of the breakage-fusion-bridge mechanism

scientific article

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

scientific article

Compressing genomic sequence fragments using SlimGene

scientific article (publication date: March 2011)

Consensus folding of unaligned RNA sequences revisited

scientific article published in March 2006

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

scientific article

Correction: Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele

scientific article published on 30 November 2016

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

scientific article

Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants.

scientific article published on 11 October 2010

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

scientific article

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

scientific article

Discovery and revision of Arabidopsis genes by proteogenomics

scholarly article

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

scientific article published on 19 February 2016

Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice

scientific article

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

scientific article published on 15 November 2021

Evaluating genome architecture of a complex region via generalized bipartite matching

scientific article

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

scientific article

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

scientific article

Exome sequencing can improve diagnosis and alter patient management

scientific article published on June 2012

Expansion of the mycobacterial "PUPylome"

scientific article

Experimental selection of hypoxia-tolerant Drosophila melanogaster

scientific article

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

scientific article published in Nature Communications

Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription

scientific article published on 21 September 2021

Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers

scientific article published on 17 August 2020

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

scientific article published on 8 February 2017

Extrachromosomal oncogene amplification in tumour pathogenesis and evolution

scientific article published on 01 May 2019

Fast and accurate alignment of multiple protein networks.

scientific article published in August 2009

FastR: fast database search tool for non-coding RNA.

scientific article published in January 2004

Fine-mapping the Favored Mutation in a Positive Selective Sweep

Form follows function in cancer genomes

scientific article published in 2022

Genetic simulation tools for post-genome wide association studies of complex diseases

scientific article

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

scientific article published on 7 December 2011

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

scientific article published on 9 December 2016

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

scientific article

Haplotyping as perfect phylogeny: a direct approach

scientific article (publication date: 2003)

High-altitude adaptation in humans: from genomics to integrative physiology

scientific article published on 26 September 2017

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

scientific article

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

scientific article

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

scientific article published on 27 November 2005

Identification of post-translational modifications via blind search of mass-spectra

scientific article published on January 2005

Identifying the favored mutation in a positive selective sweep.

scientific article published on 19 February 2018

Improving gene annotation using peptide mass spectrometry

scientific article published on 22 December 2006

InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms

scientific article

Inference about recombination from haplotype data: lower bounds and recombination hotspots

scientific article

Inferring gene ontologies from pairwise similarity data

scientific article

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

scientific article

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

scientific article published on 28 June 2016

Integrating scientific cultures

scientific article published on 17 April 2007

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

scientific article

Juvenile granulosa cell tumor associated with Ollier disease

scientific article published on October 2016

Learning natural selection from the site frequency spectrum

scientific article published on 14 June 2013

Ligand-receptor pairing via tree comparison.

scientific article published in February 2000

New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude

scientific article published on 19 September 2017

Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes

scientific article

Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders

scientific article published on 25 September 2018

On the design of clone-based haplotyping

scientific article published on January 2013

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

scientific article

Optimization of primer design for the detection of variable genomic lesions in cancer

scientific article published on 30 August 2007

Optimizing PCR assays for DNA-based cancer diagnostics

scientific article published on March 2010

Orthologous repeats and mammalian phylogenetic inference

scientific article published on July 2005

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

scientific article published in July 2005

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

scientific article published on 19 June 2008

Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level

scientific article

Practical 4'-phosphopantetheine active site discovery from proteomic samples

scientific article

Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele

scientific article

Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study

scientific article

Protein identification using top-down.

scientific article

Protein-protein interaction network evaluation for identifying potential drug targets.

scientific article published in May 2010

ProteoStorm: An Ultrafast Metaproteomics Database Search Framework

article by Doruk Beyter et al published September 2018 in Cell systems

Proteogenomic database construction driven from large scale RNA-seq data

scientific article

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

scientific article

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

scientific article

QNet: a tool for querying protein interaction networks

scientific article

RAPID detection of gene-gene interactions in genome-wide association studies

scientific article

Reconstructing breakage fusion bridge architectures using noisy copy numbers

scientific article

Reprever: resolving low-copy duplicated sequences using template driven assembly

scientific article published on 08 May 2013

Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody

scientific article

Robustness of inference of haplotype block structure

scientific article published in January 2003

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

scientific article

Sample reproducibility of genetic association using different multimarker TDTs in genome-wide association studies: characterization and a new approach.

scientific article

Searching genomes for noncoding RNA using FastR.

scientific article

Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease

scientific article

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

scientific article

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

scientific article

Shotgun protein sequencing by tandem mass spectra assembly

scientific article published in December 2004

Speeding up tandem mass spectral identification using indexes.

scientific article published on 27 April 2012

Strobe sequence design for haplotype assembly

scientific article

Structural alignment of pseudoknotted RNA.

scientific article

TCLUST: a fast method for clustering genome-scale expression data

scientific article

Template proteogenomics: sequencing whole proteins using an imperfect database

scientific article

Tests of selection in pooled case-control data: an empirical study

scientific article

The Sequence of the Human Genome

scientific article

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

scientific article published in March 2007

The TGFβ1 Promoter SNP C-509T and Food Sensitization Promote Esophageal Remodeling in Pediatric Eosinophilic Esophagitis

scientific article published on 14 December 2015

The antibody repertoire of colorectal cancer.

scientific article published on 18 October 2017

The conserved exon method for gene finding

article

The diploid genome sequence of an individual human

scientific article published on 4 September 2007

The dog genome: survey sequencing and comparative analysis

scientific article

The elusive evidence for chromothripsis

scientific article

The genetic basis of chronic mountain sickness

scientific article

The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters

scientific article published on 13 January 2020

The number of recombination events in a sample history: conflict graph and lower bounds

scientific article published in April 2004

The ribosome scanning model for translation initiation: implications for gene prediction and full-length cDNA detection.

scientific article published in January 1998

The variant call format and VCFtools

scientific article (publication date: August 2011)

Ultraaccurate genome sequencing and haplotyping of single human cells.

scientific article

Unrestrictive identification of post-translational modifications through peptide mass spectrometry

scientific article

Using Genome Query Language to uncover genetic variation

scientific article published on 10 June 2013

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.

scientific article published on 20 March 2018

Virmid: accurate detection of somatic mutations with sample impurity inference

scientific article

Wessim: a whole-exome sequencing simulator based on in silico exome capture

scientific article published on 14 February 2013

Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes

scientific article

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

scientific article

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

scientific article

ecDNA hubs drive cooperative intermolecular oncogene expression

scientific article published on 24 November 2021

iDASH: integrating data for analysis, anonymization, and sharing

scientific article (publication date: 2012)

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