publications

Pulled periodically from google scholar

2026

  1. Cancer Cell
    The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapy
    Andrea H Bild, Michelle C Sangar, Jasmine A McQuerry, and 8 more authors
    Cancer Cell, 2026
    Website
  2. Cell
    EcDNA-borne structural variants drive oncogenic fusion transcript amplification
    Hyerim Yi, Shu Zhang, Jason Swinderman, and 8 more authors
    Cell, 2026
    Website

2025

  1. Genome Res.
    OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
    Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, and 8 more authors
    Genome Research, 2025
    Website
  2. Nature Comms.
    Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D
    Biswanath Chowdhury, Kaiyuan Zhu, Chaohui Li, and 8 more authors
    Nature Communications, 2025
    Website
  3. Cancer Discov.
    Extrachromosomal DNA–Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma
    Imran Noorani, Magnus Haughey, Jens Luebeck, and 8 more authors
    Cancer Discovery, 2025
  4. Nature Cell Bio
    Enhancer activation from transposable elements in extrachromosomal DNA
    Katerina Kraft, Sedona E Murphy, Matthew G Jones, and 8 more authors
    Nature cell biology, 2025
  5. Adv. Genetics
    Rare Structural Variants Uncovered by Optical Genome Mapping in Multisystem Inflammatory Syndrome in Children (MIS-C)
    Catherine A Brownstein, Caspar I Made, Kristin Cabral, and 8 more authors
    Advanced Genetics, 2025
  6. Nature Genetics
    Three-dimensional genome landscape of primary human cancers
    Kathryn E Yost, Yanding Zhao, King L Hung, and 8 more authors
    Nature Genetics, 2025
  7. RECOMB
    OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders
    Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, and 8 more authors
    In International Conference on Research in Computational Molecular Biology, 2025
  8. PLOS Comp. Bio.
    Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats
    Sara Javadzadeh, Aaron Adamson, Jonghun Park, and 6 more authors
    PLOS Computational Biology, 2025
  9. Nature Comms.
    Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer
    Takuya Nakagawa, Jens Luebeck, Kaiyuan Zhu, and 8 more authors
    Nature Communications, 2025
  10. Nature Comms.
    Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity
    Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, and 8 more authors
    Nature communications, 2025
  11. Nature
    Engineered extrachromosomal oncogene amplifications promote tumorigenesis
    Davide Pradella, Minsi Zhang, Rui Gao, and 8 more authors
    Nature, 2025
  12. Cancer Discov.
    Spatial–Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment
    Wei Lv, Yuchen Zeng, Conghui Li, and 8 more authors
    Cancer discovery, 2025
  13. Cancer Discov.
    Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair
    John C Rose, Julia A Belk, Ivy Tsz-Lo Wong, and 8 more authors
    Cancer Discovery, 2025

2024

  1. Blood
    A Single Mutation in the SENP1 Region Regulates the Excessive Erythropoiesis in the Andes
    Priti Azad, Ali Akbari, Dan Zhou, and 4 more authors
    Blood, 2024
  2. Nature
    Origins and impact of extrachromosomal DNA
    Chris Bailey, Oriol Pich, Kerstin Thol, and 8 more authors
    Nature, 2024
  3. Nature
    Enhancing transcription–replication conflict targets ecDNA-positive cancers
    Jun Tang, Natasha E Weiser, Guiping Wang, and 8 more authors
    Nature, 2024
  4. Nature
    Coordinated inheritance of extrachromosomal DNAs in cancer cells
    King L Hung, Matthew G Jones, Ivy Tsz-Lo Wong, and 8 more authors
    Nature, 2024
  5. ESMO Open
    111MO Extrachromosomal DNA drives oncogene spatial heterogeneity in IDH-wildtype glioblastomas
    I Noorani, M Haughey, J Luebeck, and 7 more authors
    ESMO Open, 2024
  6. Nature Genetics
    Mapping extrachromosomal DNA amplifications during cancer progression
    Hoon Kim, Soyeon Kim, Taylor Wade, and 8 more authors
    Nature genetics, 2024
  7. JID
    LB1067 Chromosomal structural variants but not extrachromosomal DNAs are common in Merkel cell carcinoma
    JD Bloomstein, J Luebeck, J Rose, and 6 more authors
    Journal of Investigative Dermatology, 2024
  8. Annals Oncol.
    Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomas
    Imran Noorani, Jens Luebeck, Andrew Rowan, and 8 more authors
    Annals of Oncology, 2024
  9. eLife
    Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors
    Miin S Lin, Se-Young Jo, Jens Luebeck, and 4 more authors
    Elife, 2024
  10. Genome Res.
    CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
    Kaiyuan Zhu, Matthew G Jones, Jens Luebeck, and 8 more authors
    Genome Research, 2024

2023

  1. DNA Barcoding
    Analyses of nuclear reads obtained using genome skimming
    Siavash Mirarab and Vineet Bafna
    In DNA Barcoding: Methods and Protocols, 2023
  2. Environ. Intl.
    Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species
    MS Lin, Madhushri Shrikant Varunjikar, Kai Kristoffer Lie, and 8 more authors
    Environment International, 2023
  3. Nature Genetics
    Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma
    Owen S Chapman, Jens Luebeck, Sunita Sridhar, and 8 more authors
    Nature genetics, 2023
  4. Eur. J. Hum. Genet.
    Variable number tandem repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG
    Yuan Chun Ding, Aaron W Adamson, Mehrdad Bakhtiari, and 7 more authors
    European Journal of Human Genetics, 2023
  5. Nature
    Epigenetic dysregulation from chromosomal transit in micronuclei
    Albert S Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, and 8 more authors
    Nature, 2023
  6. Bioinf. Advances
    TRviz: a Python library for decomposing and visualizing tandem repeat sequences
    Jonghun Park, Eli Kaufman, Paul N Valdmanis, and 1 more author
    Bioinformatics Advances, 2023
  7. Nature
    Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus
    Jens Luebeck, Alvin Wei Tian Ng, Patricia C Galipeau, and 8 more authors
    Nature, 2023
  8. PNAS
    Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity
    Ramya Raviram, Anugraha Raman, Sebastian Preissl, and 8 more authors
    Proceedings of the National Academy of Sciences, 2023
  9. Nature Comms.
    A deep population reference panel of tandem repeat variation
    Helyaneh Ziaei Jam, Yang Li, Ross DeVito, and 8 more authors
    Nature Communications, 2023

2022

  1. METHODS AND COMPOSITIONS FOR DETECTING ecDNA
    Paul Mischel, Vineet Bafna, Jens Christian Luebeck, and 1 more author
    Nov 2022
    US Patent App. 17/746,748
  2. Methods of diagnosing and treating cancer targeting extrachromosomal dna
    Paul Mischel, Prashant Mali, Vineet Bafna, and 3 more authors
    Feb 2022
    US Patent App. 17/518,396
  3. Compositions and methods for modulating transcriptional activity of amplified oncogenes contained on extrachromosomal dna
    Paul Mischel, Bing Ren, Kristen Turner, and 4 more authors
    Jan 2022
    US Patent App. 17/311,980
  4. Targeting nad biosynthesis in the treatment of cancer
    Paul S Mischel, Bing Ren, Vineet Bafna, and 1 more author
    May 2022
    US Patent App. 17/438,610
  5. Cell Syst.
    Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling
    Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, and 1 more author
    Cell systems, 2022
  6. Nature Cancer
    Form follows function in cancer genomes
    Paul S Mischel and Vineet Bafna
    Nature Cancer, 2022
  7. Nature Genetics
    Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH
    King L Hung, Jens Luebeck, Siavash R Dehkordi, and 8 more authors
    Nature genetics, 2022
  8. iScience
    Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19
    Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, and 8 more authors
    Iscience, 2022
  9. iScience
    Detecting tandem repeat variants in coding regions using code-adVNTR
    Jonghun Park, Mehrdad Bakhtiari, Bernt Popp, and 2 more authors
    Iscience, 2022
  10. Eur. J. Hum. Genet.
    Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study
    Bernt Popp, Arif B Ekici, Karl X Knaup, and 8 more authors
    European Journal of Human Genetics, 2022
  11. ACM-BCB
    DeepViFi: detecting oncoviral infections in cancer genomes using transformers
    Utkrisht Rajkumar, Sara Javadzadeh, Mihir Bafna, and 4 more authors
    In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 2022
  12. Nature
    Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA
    Erik N Bergstrom, Jens Luebeck, Mia Petljak, and 8 more authors
    Nature, 2022
  13. RECOMB
    Uncertainty quantification using subsampling for assembly-free estimates of genomic distance and phylogenetic relationships
    Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, and 1 more author
    In International Conference on Research in Computational Molecular Biology, 2022
  14. Ann. Rev. Path
    Extrachromosomal DNA: an emerging hallmark in human cancer
    Sihan Wu, Vineet Bafna, Howard Y Chang, and 1 more author
    Annual Review of Pathology: Mechanisms of Disease, 2022
  15. Nature Genetics
    The evolutionary dynamics of extrachromosomal DNA in human cancers
    Joshua T Lange, John C Rose, Celine Y Chen, and 8 more authors
    Nature genetics, 2022
  16. Neuro-Oncology
    INTEGRATED ANALYSIS OF SINGLE CELL CHROMATIN ACCESSIBILITY AND RNA EXPRESSION IDENTIFIED COMMON VULNERABILITY DESPITE GLIOBLASTOMA HETEROGENEITY
    Ramya Raviram, Anugraha Raman, Sebastian Preissl, and 8 more authors
    In NEURO-ONCOLOGY, 2022
  17. NAR Genomics
    FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA
    Sara Javadzadeh, Utkrisht Rajkumar, Nam Nguyen, and 4 more authors
    NAR genomics and bioinformatics, 2022
  18. Ann. Rev. GHG
    Extrachromosomal DNA in cancer
    Vineet Bafna and Paul S Mischel
    Annual review of genomics and human genetics, 2022
  19. Hum. Mol. Genetics
    Heterozygous Tropomodulin 3 mice have improved lung vascularization after chronic hypoxia
    Tsering Stobdan, Pritesh P Jain, Mingmei Xiong, and 3 more authors
    Human Molecular Genetics, 2022
  20. Cancer Discov.
    Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challenges
    Kai Song, Jenna K Minami, Arthur Huang, and 8 more authors
    Cancer discovery, 2022
  21. ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge’s disease
    Priti Azad, Andrew B Caldwell, Srinivasan Ramachandran, and 8 more authors
    Experimental & molecular medicine, 2022

2021

  1. Methods of diagnosing and treating cancer targeting extrachromosomal DNA
    Paul Mischel, Prashant Mali, Vineet Bafna, and 3 more authors
    Dec 2021
    US Patent 11,193,164
  2. PLOS Comp. Bio.
    Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT
    Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, and 3 more authors
    PLoS computational biology, 2021
  3. Extrachromosomal DNA (ecDNA) in cancer pathogenesis
    Sihan Wu, Vineet Bafna, and Paul S Mischel
    Current opinion in genetics & development, 2021
  4. Nature Comms.
    Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster
    Arya Iranmehr, Tsering Stobdan, Dan Zhou, and 4 more authors
    Nature communications, 2021
  5. Clin Cancer Res
    Extrachromosomal DNA in HPV-mediated oropharyngeal cancer drives diverse oncogene transcription
    John Pang, Nam Nguyen, Jens Luebeck, and 8 more authors
    Clinical Cancer Research, 2021
  6. Nature
    ecDNA hubs drive cooperative intermolecular oncogene expression
    King L Hung, Kathryn E Yost, Liangqi Xie, and 8 more authors
    Nature, 2021
  7. ACM-BCB
    A CNN-based cell tracking method for multi-slice intravital imaging data
    Kenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, and 6 more authors
    In Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2021
  8. Nature Comms.
    Variable number tandem repeats mediate the expression of proximal genes
    Mehrdad Bakhtiari, Jonghun Park, Yuan-Chun Ding, and 6 more authors
    Nature communications, 2021
  9. NAR Genomics
    CONSULT: accurate contamination removal using locality-sensitive hashing
    Eleonora Rachtman, Vineet Bafna, and Siavash Mirarab
    NAR Genomics and Bioinformatics, 2021
  10. Patterns
    FaNDOM: Fast nested distance-based seeding of optical maps
    Siavash Raeisi Dehkordi, Jens Luebeck, and Vineet Bafna
    Patterns, 2021

2020

  1. Nature Comms.
    Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
    Tomoyuki Koga, Isaac A Chaim, Jorge A Benitez, and 8 more authors
    Nature communications, 2020
  2. Nature Comms.
    AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications
    Jens Luebeck, Ceyda Coruh, Siavash R Dehkordi, and 8 more authors
    Nature communications, 2020
  3. Mol. Ecol. Res.
    The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters
    Eleonora Rachtman, Metin Balaban, Vineet Bafna, and 1 more author
    Molecular Ecology Resources, 2020
  4. FASEB
    Identification of Candidate Genes Involved in the Survival of Drosophila in Extreme O2 Environments
    Tsering Stobdan, Huiwen W Zhao, Dan Zhou, and 4 more authors
    The FASEB Journal, 2020
  5. Extrachromosomal DNA (ecDNA) carrying amplified oncogenes as a biomarker for insensitivity to pembrolizumab treatment in gastric cancer patients.
    Jason H Christiansen, Nam-phuong Nguyen, Roel Verhaak, and 4 more authors
    2020
  6. Nature Genetics
    Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
    Hoon Kim, Nam-Phuong Nguyen, Kristen Turner, and 8 more authors
    Nature genetics, 2020
  7. FASEB
    Oxygen-Directed Laboratory Evolution and Conserved Mechanisms Underlying Hypoxia Tolerance
    Dan Zhou, Arya Iranmehr, Helen Zhao, and 3 more authors
    The FASEB Journal, 2020
  8. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification
    Kristine Bohmann, Siavash Mirarab, Vineet Bafna, and 1 more author
    2020
  9. IJROBP
    Long-read RNA-Seq of human papillomavirus-associated head and neck cancer reveals novel alternatively spliced viral RNA isoforms
    John Pang, Nam Nguyen, Audrey Finegersh, and 6 more authors
    International Journal of Radiation Oncology, Biology, Physics, 2020
  10. Nature Comms.
    Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
    Tomoyuki Koga, Isaac A Chaim, Jorge A Benitez, and 8 more authors
    Nature communications, 2020

2019

  1. Methods of treating extrachromosomal dna expressing cancers
    Paul Mischel, Vineet Bafna, Junho Ko, and 2 more authors
    2019
  2. Eur. J. Hum. Genet.
    Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders
    Arya Iranmehr, Tsering Stobdan, Dan Zhou, and 8 more authors
    European Journal of Human Genetics, 2019
  3. iScience
    EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA
    Utkrisht Rajkumar, Kristen Turner, Jens Luebeck, and 4 more authors
    Iscience, 2019
  4. Nature Comms.
    Exploring the landscape of focal amplifications in cancer using AmpliconArchitect
    Viraj Deshpande, Jens Luebeck, Nam-Phuong D Nguyen, and 6 more authors
    Nature communications, 2019
  5. Genome Bio.
    Skmer: assembly-free and alignment-free sample identification using genome skims
    Shahab Sarmashghi, Kristine Bohmann, M Thomas P. Gilbert, and 2 more authors
    Genome biology, 2019
  6. Nature
    Circular ecDNA promotes accessible chromatin and high oncogene expression
    Sihan Wu, Kristen M Turner, Nam Nguyen, and 8 more authors
    Nature, 2019
  7. Nature Rev. Cancer
    Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
    Roel GW Verhaak, Vineet Bafna, and Paul S Mischel
    Nature Reviews Cancer, 2019
  8. Nature
    NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling
    Sudhir Chowdhry, Ciro Zanca, Utkrisht Rajkumar, and 8 more authors
    Nature, 2019
  9. JPR
    Proteogenomic annotation of Chinese hamsters reveals extensive novel translation events and endogenous retroviral elements
    Shangzhong Li, Seong Won Cha, Kelly Heffner, and 8 more authors
    Journal of proteome research, 2019
  10. Cell Syst
    Computing the statistical significance of overlap between genome annotations with iStat
    Shahab Sarmashghi and Vineet Bafna
    Cell systems, 2019

2018

  1. Whole-Genome-Sequencing Reveals Involvement of Mitochondria-Dependent Apoptotic Genes in High Altitude Pulmonary Hypertension
    T Stobdan, A Iranmehr, D Zhou, and 8 more authors
    In B108. PULMONARY HYPERTENSION: THE LATEST FINDINGS, 2018
  2. Genome Res.
    Targeted genotyping of variable number tandem repeats with adVNTR
    Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, and 2 more authors
    Genome research, 2018
  3. RECOMB
    Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR
    Vikas Bansal and Vineet Bafna
    In Research in Computational Molecular Biology, 2018
  4. JP
    MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection
    Dmitri V Rozanov, Nikita D Rozanov, Kami E Chiotti, and 8 more authors
    Journal of proteomics, 2018
  5. Nuc. Acids. Res
    ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer
    Nam-Phuong D Nguyen, Viraj Deshpande, Jens Luebeck, and 2 more authors
    Nucleic acids research, 2018
  6. Nature Methods
    Identifying the favored mutation in a positive selective sweep
    Ali Akbari, Joseph J Vitti, Arya Iranmehr, and 4 more authors
    Nature methods, 2018
  7. Cell Syst.
    Proteostorm: An ultrafast metaproteomics database search framework
    Doruk Beyter, Miin S Lin, Yanbao Yu, and 2 more authors
    Cell systems, 2018

2017

  1. Nature
    Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity
    Kristen M Turner, Viraj Deshpande, Doruk Beyter, and 8 more authors
    Nature, 2017
  2. The antibody repertoire of colorectal cancer
    Seong Won Cha, Stefano Bonissone, Seungjin Na, and 2 more authors
    Molecular & Cellular Proteomics, 2017
  3. Blood
    Molecular basis of hypoxia-induced excessive erythrocytosis: critical role of SENP1 gene regulation
    Priti Azad, Ali Akbari, Dan Zhou, and 3 more authors
    Blood, 2017
  4. Genome Res.
    HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
    Peter Edge, Vineet Bafna, and Vikas Bansal
    Genome research, 2017
  5. JMM
    High-altitude adaptation in humans: from genomics to integrative physiology
    Priti Azad, Tsering Stobdan, Dan Zhou, and 4 more authors
    Journal of Molecular Medicine, 2017
  6. PNAS
    Ultraaccurate genome sequencing and haplotyping of single human cells
    Wai Keung Chu, Peter Edge, Ho Suk Lee, and 4 more authors
    Proceedings of the National Academy of Sciences, 2017
  7. Mol Biol. Evol.
    New insights into the genetic basis of Monge’s disease and adaptation to high-altitude
    Tsering Stobdan, Ali Akbari, Priti Azad, and 8 more authors
    Molecular biology and evolution, 2017
  8. Genetics
    CLEAR: Composition of likelihoods for evolve and resequence experiments
    Arya Iranmehr, Ali Akbari, Christian Schlötterer, and 1 more author
    Genetics, 2017

2016

  1. Cell
    Integrated proteogenomic characterization of human high-grade serous ovarian cancer
    Hui Zhang, Tao Liu, Zhen Zhang, and 8 more authors
    Cell, 2016
  2. Nuc. Acids. Res
    InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms
    Anand Patel, Peter Edge, Siddarth Selvaraj, and 2 more authors
    Nucleic acids research, 2016
  3. PLOS Genet.
    Correction: Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele
    Roy Ronen, Glenn Tesler, Ali Akbari, and 3 more authors
    PLoS genetics, 2016
  4. JED
    Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge’s disease
    Priti Azad, Huiwen W Zhao, Pedro J Cabrales, and 7 more authors
    Journal of Experimental Medicine, 2016
  5. Appl. Environ. Microbiol.
    Diversity, productivity, and stability of an industrial microbial ecosystem
    Doruk Beyter, Pei-Zhong Tang, Scott Becker, and 8 more authors
    Applied and environmental microbiology, 2016

2015

  1. ACS Infect. Dis.
    Next-generation sequencing of Plasmodium vivax patient samples shows evidence of direct evolution in drug-resistance genes
    Erika L Flannery, Tina Wang, Ali Akbari, and 8 more authors
    ACS infectious diseases, 2015
  2. Genet. Epidem.
    Genetic simulation tools for post-genome wide association studies of complex diseases
    Huann-Sheng Chen, Carolyn M Hutter, Leah E Mechanic, and 8 more authors
    Genetic epidemiology, 2015
  3. JCB
    Reconstructing breakage fusion bridge architectures using noisy copy numbers
    Shay Zakov and Vineet Bafna
    Journal of Computational Biology, 2015
  4. PNAS
    Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice
    Tsering Stobdan, Dan Zhou, Eilleen Ao-Ieong, and 8 more authors
    Proceedings of the National Academy of Sciences, 2015
  5. PLOS Genet.
    Predicting carriers of ongoing selective sweeps without knowledge of the favored allele
    Roy Ronen, Glenn Tesler, Ali Akbari, and 3 more authors
    PLoS genetics, 2015
  6. Circulation
    Heterozygous Endothelin Receptor Type B Knockout Confers Cardiac Resistance to Extreme Hypoxia in Mice
    Tsering Stobdan, Dan Zhou, Eilleen Ao-Ieong, and 5 more authors
    Circulation, 2015
  7. PLOS One
    The TGF\beta1 promoter SNP C-509T and food sensitization promote esophageal remodeling in pediatric eosinophilic esophagitis
    Renee Rawson, Arjun Anilkumar, Robert O Newbury, and 8 more authors
    PloS one, 2015
  8. JPR
    Advanced proteogenomic analysis reveals multiple peptide mutations and complex immunoglobulin peptides in colon cancer
    Sunghee Woo, Seong Won Cha, Stefano Bonissone, and 4 more authors
    Journal of proteome research, 2015
  9. RECOMB
    Haplotype Allele Frequency (HAF) score: predicting carriers of ongoing selective sweeps without knowledge of the adaptive allele
    Roy Ronen, Glenn Tesler, Ali Akbari, and 3 more authors
    In International Conference on Research in Computational Molecular Biology, 2015

2014

  1. Proteomics
    Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data
    Sunghee Woo, Seong Won Cha, Seungjin Na, and 6 more authors
    Proteomics, 2014
  2. Genome Bio.
    Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes
    Nitin Udpa, Roy Ronen, Dan Zhou, and 8 more authors
    Genome biology, 2014
  3. Genome Res.
    Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
    Anand Patel, Richard Schwab, Yu-Tsueng Liu, and 1 more author
    Genome Research, 2014
  4. Nuc. Acids. Res
    The elusive evidence for chromothripsis
    Marcus Kinsella, Anand Patel, and Vineet Bafna
    Nucleic acids research, 2014
  5. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis
    Dhanashree S Kelkar, Elayne Provost, Raghothama Chaerkady, and 8 more authors
    Molecular & cellular proteomics, 2014
  6. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays
    Natalie E Castellana, Zhouxin Shen, Yupeng He, and 4 more authors
    Molecular & Cellular Proteomics, 2014
  7. Phys.
    The genetic basis of chronic mountain sickness
    Roy Ronen, Dan Zhou, Vineet Bafna, and 1 more author
    Physiology, 2014
  8. Bioinformatics
    Inferring gene ontologies from pairwise similarity data
    Michael Kramer, Janusz Dutkowski, Michael Yu, and 2 more authors
    Bioinformatics, 2014
  9. JPR
    Proteogenomic database construction driven from large scale RNA-seq data
    Sunghee Woo, Seong Won Cha, Gennifer Merrihew, and 5 more authors
    Journal of proteome research, 2014
  10. Bioinformatics
    Using Genome Query Language to uncover genetic variation
    Christos Kozanitis, Andrew Heiberg, George Varghese, and 1 more author
    Bioinformatics, 2014

2013

  1. AJHG
    Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders
    Dan Zhou, Nitin Udpa, Roy Ronen, and 8 more authors
    The American Journal of Human Genetics, 2013
  2. Bioinformatics
    Wessim: a whole-exome sequencing simulator based on in silico exome capture
    Sangwoo Kim, Kyowon Jeong, and Vineet Bafna
    Bioinformatics, 2013
  3. Genome Bio.
    On the design of clone-based haplotyping
    Christine Lo, Rui Liu, Jehyuk Lee, and 7 more authors
    Genome biology, 2013
  4. CACM
    Abstractions for genomics
    Vineet Bafna, Alin Deutsch, Andrew Heiberg, and 3 more authors
    Communications of the ACM, 2013
  5. Nuc. Acids. Res
    Reprever: resolving low-copy duplicated sequences using template driven assembly
    Sangwoo Kim, Paul Medvedev, Tara A Paton, and 1 more author
    Nucleic acids research, 2013
  6. Genetics
    Learning natural selection from the site frequency spectrum
    Roy Ronen, Nitin Udpa, Eran Halperin, and 1 more author
    Genetics, 2013
  7. PNAS
    An algorithmic approach for breakage-fusion-bridge detection in tumor genomes
    Shay Zakov, Marcus Kinsella, and Vineet Bafna
    Proceedings of the National Academy of Sciences, 2013
  8. BMC Bioinform.
    Evaluating genome architecture of a complex region via generalized bipartite matching
    Christine Lo, Sangwoo Kim, Shay Zakov, and 1 more author
    BMC bioinformatics, 2013
  9. Genome Bio.
    Virmid: accurate detection of somatic mutations with sample impurity inference
    Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, and 7 more authors
    Genome biology, 2013
  10. WABI
    Cerulean: a hybrid assembly using high throughput short and long reads
    Viraj Deshpande, Eric DK Fung, Son Pham, and 1 more author
    In International workshop on algorithms in bioinformatics, 2013

2012

  1. Bioinformatics
    Speeding up tandem mass spectral identification using indexes
    Xiaowen Liu, Alessandro Mammana, and Vineet Bafna
    Bioinformatics, 2012
  2. Genome Res.
    Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
    Gary C Hon, R David Hawkins, Otavia L Caballero, and 8 more authors
    Genome research, 2012
  3. JCB
    Combinatorics of the breakage-fusion-bridge mechanism
    Marcus Kinsella and Vineet Bafna
    Journal of Computational Biology, 2012
  4. JCB
    Accurate mass spectrometry based protein quantification via shared peptides
    Banu Dost, Nuno Bandeira, Xiangqian Li, and 3 more authors
    Journal of Computational Biology, 2012
  5. Nature Genetics
    De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly
    Jeong Ho Lee, My Huynh, Jennifer L Silhavy, and 8 more authors
    Nature genetics, 2012
  6. RECOMB
    Modeling the breakage-fusion-bridge mechanism: combinatorics and cancer genomics
    Marcus Kinsella and Vineet Bafna
    In Annual International Conference on Research in Computational Molecular Biology, 2012
  7. PLOS One
    Sample reproducibility of genetic association using different multimarker TDTs in genome-wide association studies: characterization and a new approach
    Mara M Abad-Grau, Nuria Medina-Medina, Rosana Montes-Soldado, and 2 more authors
    PLoS One, 2012
  8. JAMIA
    iDASH: integrating data for analysis, anonymization, and sharing
    Lucila Ohno-Machado, Vineet Bafna, Aziz A Boxwala, and 8 more authors
    Journal of the American Medical Informatics Association, 2012
  9. Sci. Trans. Med
    Exome sequencing can improve diagnosis and alter patient management
    Tracy J Dixon-Salazar, Jennifer L Silhavy, Nitin Udpa, and 8 more authors
    Science translational medicine, 2012

2011

  1. AF: Small: Algorithms for Genetics: Epistatic Interactions, Haplotype Assembly, and Selection Signatures
    Vineet Bafna
    NSF Award Number 1115206. Directorate for Computer and Information Science and Engineering, 2011
  2. JPR
    Automated querying and identification of novel peptides using MALDI mass spectrometric imaging
    Jocelyne Bruand, Srinivas Sistla, Céline Mériaux, and 8 more authors
    Journal of proteome research, 2011
  3. JCB
    Preface: satellite workshop on comparative genomics, research in computational molecular biology (RECOMB-CG 2010) preface
    Vineet Bafna
    Journal of Computational Biology, 2011
  4. ACM-BCB
    2011 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 8
    Christopher Abdul-Wahid, Sarah Abdul-Wahid, Andre Aberer, and 8 more authors
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011
  5. On the approximability of reachability-preserving network orientations
    Michael Elberfeld, Vineet Bafna, Iftah Gamzu, and 5 more authors
    Internet Mathematics, 2011
  6. Visualization of the MS-Align algorithm results for the protein spectrum matches
    Yakov Sirotkin, Xiaowen Liu, Yufeng Shen, and 7 more authors
    Department of Bioengineering and Bioinformatics of MV Lomonosov Moscow State University, 2011
  7. JPR
    AMASS: algorithm for MSI analysis by semi-supervised segmentation
    Jocelyne Bruand, Theodore Alexandrov, Srinivas Sistla, and 7 more authors
    Journal of proteome research, 2011
  8. JPR
    Practical 4-phosphopantetheine active site discovery from proteomic samples
    Jordan L Meier, Anand D Patel, Sherry Niessen, and 8 more authors
    Journal of proteome research, 2011
  9. Front. Genet.
    Tests of selection in pooled case-control data: an empirical study
    Nitin Udpa, Dan Zhou, Gabriel G Haddad, and 1 more author
    Frontiers in Genetics, 2011
  10. PNAS
    Experimental selection of hypoxia-tolerant Drosophila melanogaster
    Dan Zhou, Nitin Udpa, Merril Gersten, and 8 more authors
    Proceedings of the National Academy of Sciences, 2011
  11. On the Approximability of Reachability-Preserving Network Orientations
    Iftah Gamzu, Michael Elberfeld, Vineet Bafna, and 5 more authors
    Internet Mathematics, 2011
  12. Metabolic Network Analysis Demystified. Ed. Vineet Bafna, S. Cenk Shinalp. LNCS Sublibrary: SL 8-Bioinformatics
    Leonid Chindelevitch, Aviv Regev, and Bonnie Berger
    2011
  13. Bioinformatics
    Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
    Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, and 2 more authors
    Bioinformatics, 2011
  14. Research in Computational Molecular Biology: 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings
    Vineet Bafna and S Cenk Sahinalp
    2011
  15. BMC Bioinform.
    Strobe sequence design for haplotype assembly
    Christine Lo, Ali Bashir, Vikas Bansal, and 1 more author
    BMC bioinformatics, 2011
  16. JCB
    Compressing genomic sequence fragments using SlimGene
    Christos Kozanitis, Chris Saunders, Semyon Kruglyak, and 2 more authors
    Journal of Computational Biology, 2011
  17. Proteomics
    Resurrection of a clinical antibody: Template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-αantibody
    Natalie E Castellana, Krista McCutcheon, Victoria C Pham, and 8 more authors
    Proteomics, 2011

2010

  1. Genome Bio.
    Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants
    Olivier Harismendy
    Genome Biology, 2010
  2. BMC Genomics
    Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
    Eduardo R Macagno, Terry Gaasterland, Lee Edsall, and 8 more authors
    BMC genomics, 2010
  3. PLOS Comp. Bio.
    A covering method for detecting genetic associations between rare variants and common phenotypes
    Gaurav Bhatia, Vikas Bansal, Olivier Harismendy, and 4 more authors
    PLoS computational biology, 2010
  4. FASEB
    Mapping of peptides and proteins in Leech (Hirudo medicinalis) by Mass Spectrometry Imaging
    Srinivas Sistla, Jocelyne Bruand, Majid Ghassemian, and 4 more authors
    The FASEB Journal, 2010
  5. JP
    Proteogenomics to discover the full coding content of genomes: a computational perspective
    Natalie Castellana and Vineet Bafna
    Journal of proteomics, 2010
  6. Bioinformatics
    RAPID detection of gene–gene interactions in genome-wide association studies
    Dumitru Brinza, Matthew Schultz, Glenn Tesler, and 1 more author
    Bioinformatics, 2010
  7. ACM-BCB
    TCLUST: A fast method for clustering genome-scale expression data
    Banu Dost, Chunlei Wu, Andrew Su, and 1 more author
    IEEE/ACM transactions on computational biology and bioinformatics, 2010
  8. Template proteogenomics: sequencing whole proteins using an imperfect database
    Natalie E Castellana, Victoria Pham, David Arnott, and 2 more authors
    Molecular & Cellular Proteomics, 2010
  9. Genome Bio.
    Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level
    Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, and 8 more authors
    Genome biology, 2010
  10. BMC Genomics
    Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance
    Ali Bashir, Vikas Bansal, and Vineet Bafna
    BMC genomics, 2010
  11. MBIO
    Expansion of the mycobacterial “PUPylome”
    Jeramie Watrous, Kristin Burns, Wei-Ting Liu, and 6 more authors
    Molecular bioSystems, 2010
  12. Deconvolution and database search of complex tandem mass spectra of intact proteins
    Xiaowen Liu, Yuval Inbar, Pieter C Dorrestein, and 6 more authors
    Molecular & Cellular Proteomics, 2010
  13. JCB
    Protein-protein interaction network evaluation for identifying potential drug targets
    Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, and 1 more author
    Journal of Computational Biology, 2010
  14. BMC Genomics
    Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
    Eduardo R Macagno, Terry Gaasterland, Lee Edsall, and 8 more authors
    BMC Genomics, 2010
  15. JCB
    Optimizing PCR assays for DNA-based cancer diagnostics
    Ali Bashir, Qing Lu, Dennis Carson, and 3 more authors
    Journal of Computational Biology, 2010
  16. RECOMB
    Compressing genomic sequence fragments using SlimGene
    Christos Kozanitis, Chris Saunders, Semyon Kruglyak, and 2 more authors
    In Annual International Conference on Research in Computational Molecular Biology, 2010

2009

  1. RECOMB
    Shared peptides in mass spectrometry based protein quantification
    Banu Dost, Nuno Bandeira, Xiangqian Li, and 3 more authors
    In Annual International Conference on Research in Computational Molecular Biology, 2009
  2. JCB
    Fast and accurate alignment of multiple protein networks
    Maxim Kalaev, Vineet Bafna, and Roded Sharan
    Journal of computational biology, 2009
  3. Genome Res.
    Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
    Kevin Judd McKernan, Heather E Peckham, Gina L Costa, and 8 more authors
    Genome research, 2009

2008

  1. Bioinformatics
    HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
    Vikas Bansal and Vineet Bafna
    Bioinformatics, 2008
  2. RECOMB
    Qnet: A tool for querying biological networks
    Banu Dost, Tomer Shlomi, Nitin Gupta, and 2 more authors
    RECOMB 2007 and JCB, 2008
  3. RECOMB
    Fast and accurate alignment of multiple protein networks
    Maxim Kalaev, Vineet Bafna, and Roded Sharan
    In Annual International Conference on Research in Computational Molecular Biology, 2008
  4. A multidimensional chromatography technology for in-depth phosphoproteome analysis
    Claudio P Albuquerque, Marcus B Smolka, Samuel H Payne, and 3 more authors
    Molecular & Cellular Proteomics, 2008
  5. Genome Res.
    Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes
    Nitin Gupta, Jamal Benhamida, Vipul Bhargava, and 8 more authors
    Genome research, 2008
  6. PLOS Comp. Bio.
    Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer
    Ali Bashir, Stanislav Volik, Colin Collins, and 2 more authors
    PLoS computational biology, 2008
  7. JCB
    Structural alignment of pseudoknotted RNA
    Buhm Han, Banu Dost, Vineet Bafna, and 1 more author
    Journal of Computational Biology, 2008
  8. PNAS
    Discovery and revision of Arabidopsis genes by proteogenomics
    Natalie E Castellana, Samuel H Payne, Zhouxin Shen, and 3 more authors
    Proceedings of the national academy of sciences, 2008
  9. JPR
    Accurate annotation of peptide modifications through unrestrictive database search
    Stephen Tanner, Samuel H Payne, Surendra Dasari, and 6 more authors
    Journal of proteome research, 2008
  10. WABI
    An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks
    Alexander Medvedovsky, Vineet Bafna, Uri Zwick, and 1 more author
    In International Workshop on Algorithms in Bioinformatics, 2008
  11. JPR
    Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis
    Samuel H Payne, Margaret Yau, Marcus B Smolka, and 3 more authors
    Journal of proteome research, 2008
  12. Genome Res.
    An MCMC algorithm for haplotype assembly from whole-genome sequence data
    Vikas Bansal, Aaron L Halpern, Nelson Axelrod, and 1 more author
    Genome research, 2008

2007

  1. Phosphorylation-specific MS/MS scoring
    S Payne, M Yau, M Smolka, and 2 more authors
    Molecular & Cellular Proteomics, 2007
  2. Bioinformatics
    Optimization of primer design for the detection of variable genomic lesions in cancer
    Ali Bashir, Yu-Tsueng Liu, Benjamin J Raphael, and 2 more authors
    Bioinformatics, 2007
  3. Systems Biology and Computational Proteomics: Joint RECOMB 2006 Satellite Workshops on Systems Biology, and on Computational Proteomics, San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers
    Trey Ideker and Vineet Bafna
    2007
  4. Genome Res.
    Improving gene annotation using peptide mass spectrometry
    Stephen Tanner, Zhouxin Shen, Julio Ng, and 4 more authors
    Genome research, 2007
  5. PLOS Bio
    The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    Shibu Yooseph, Granger Sutton, Douglas B Rusch, and 8 more authors
    PLoS biology, 2007
  6. PLOS Bio
    The diploid genome sequence of an individual human
    Samuel Levy, Granger Sutton, Pauline C Ng, and 8 more authors
    PLoS biology, 2007
  7. Genome Res.
    Evidence for large inversion polymorphisms in the human genome from HapMap data
    Vikas Bansal, Ali Bashir, and Vineet Bafna
    Genome research, 2007
  8. Genome Res.
    Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
    Nitin Gupta, Stephen Tanner, Navdeep Jaitly, and 8 more authors
    Genome research, 2007
  9. JCB
    A decomposition theory for phylogenetic networks and incompatible characters
    Dan Gusfield, Vikas Bansal, Vineet Bafna, and 1 more author
    Journal of Computational Biology, 2007
  10. Mol. Syst. Bio.
    Integrating scientific cultures
    Trey Ideker, Vineet Bafna, and Thomas Lemberger
    Molecular Systems Biology, 2007
  11. RECOMB
    QNet: a tool for querying protein interaction networks
    Banu Dost, Tomer Shlomi, Nitin Gupta, and 3 more authors
    In Annual International Conference on Research in Computational Molecular Biology, 2007

2006

  1. JCB
    Consensus folding of unaligned RNA sequences revisited
    Vineet Bafna, Haixu Tang, and Shaojie Zhang
    Journal of computational biology, 2006
  2. Identification of informative genetic markers
    Bjarni Halldorsson, Vineet Bafna, Ross Lippert, and 4 more authors
    Mar 2006
    US Patent App. 11/040,652
  3. JPR
    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?
    PA Wilmarth, S Tanner, S Dasari, and 5 more authors
    Journal of proteome research, 2006
  4. Bioinformatics
    A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements
    Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, and 2 more authors
    Bioinformatics, 2006
  5. JCB
    Inference about recombination from haplotype data: lower bounds and recombination hotspots
    Vineet Bafna and Vikas Bansal
    Journal of Computational Biology, 2006
  6. RECOMB
    Structural alignment of pseudoknotted RNA
    Banu Dost, Buhm Han, Shaojie Zhang, and 1 more author
    In Annual International Conference on Research in Computational Molecular Biology, 2006
  7. CSB
    EXPLORING THE OCEAN’S MICROBES: SEQUENCING THE SEVEN SEAS
    Marvin E Frazier, Douglas B Rusch, Aaron L Halpern, and 8 more authors
    In Computational Systems Bioinformatics, 2006
  8. Nature Protocols
    Unrestrictive identification of post-translational modifications through peptide mass spectrometry
    Stephen Tanner, Pavel A Pevzner, and Vineet Bafna
    Nature protocols, 2006

2005

  1. ACM-BCB
    2005 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 2
    MS Alber, J Allali, Au Wai-Ho, and 8 more authors
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2005
  2. JPR
    Peptide sequence tags for fast database search in mass-spectrometry
    Ari Frank, Stephen Tanner, Vineet Bafna, and 1 more author
    Journal of proteome research, 2005
  3. ACM-BCB
    Searching genomes for noncoding RNA using FastR
    Shaojie Zhang, Brian Haas, Eleazar Eskin, and 1 more author
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2005
  4. Genome Res.
    Orthologous repeats and mammalian phylogenetic inference
    Ali Bashir, Chun Ye, Alkes L Price, and 1 more author
    Genome Research, 2005
  5. Identification of post-translational modifications via blind search of mass-spectra
    Dekel Tsur, Stephen Tanner, Ebrahim Zandi, and 2 more authors
    In 2005 IEEE Computational Systems Bioinformatics Conference (CSB’05), 2005
  6. Theor. Comp. Sci.
    Polynomial and APX-hard cases of the individual haplotyping problem
    Vineet Bafna, Sorin Istrail, Giuseppe Lancia, and 1 more author
    Theoretical Computer Science, 2005
  7. RECOMB
    Consensus folding of unaligned RNA sequences revisited
    Vineet Bafna, Haixu Tang, and Shaojie Zhang
    In Annual International Conference on Research in Computational Molecular Biology, 2005
  8. Anal. Chem.
    InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
    Stephen Tanner, Hongjun Shu, Ari Frank, and 5 more authors
    Analytical chemistry, 2005
  9. RECOMB
    Improved recombination lower bounds for haplotype data
    Vineet Bafna and Vikas Bansal
    In Annual International Conference on Research in Computational Molecular Biology, 2005

2004

  1. IEEE CSB
    FastR: Fast database search tool for non-coding RNA
    Vineet Bafna and Shaojie Zhang
    In Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004., 2004
  2. JCB
    A note on efficient computation of haplotypes via perfect phylogeny
    Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, and 1 more author
    Journal of Computational Biology, 2004
  3. ACM-BCB
    The number of recombination events in a sample history: conflict graph and lower bounds
    Vineet Bafna and Vikas Bansal
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004
  4. Genome Res.
    Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies
    Bjarni V Halldorsson, Vineet Bafna, Ross Lippert, and 4 more authors
    Genome research, 2004
  5. Anal. Chem.
    Shotgun protein sequencing by tandem mass spectra assembly
    Nuno Bandeira, Haixu Tang, Vineet Bafna, and 1 more author
    Analytical chemistry, 2004
  6. Mass spectrometry and computational proteomics
    Vineet Bafna and Knut Reinert
    Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2004

2003

  1. RECOMB
    Haplotypes and informative SNP selection algorithms: don’t block out information
    Vineet Bafna, Bjarni V Halldórsson, Russell Schwartz, and 2 more authors
    In Proceedings of the seventh annual international conference on Research in computational molecular biology, 2003
  2. JCB
    Robustness of inference of haplotype block structure
    Russell Schwartz, Bjarni V Halldórsson, Vineet Bafna, and 2 more authors
    Journal of Computational Biology, 2003
  3. Science
    The dog genome: survey sequencing and comparative analysis
    Ewen F Kirkness, Vineet Bafna, Aaron L Halpern, and 8 more authors
    Science, 2003
  4. DMTCS
    Combinatorial problems arising in SNP and haplotype analysis
    Bjarni V Halldórsson, Vineet Bafna, Nathan Edwards, and 3 more authors
    In International Conference on Discrete Mathematics and Theoretical Computer Science, 2003
  5. RECOMB
    On de novo interpretation of tandem mass spectra for peptide identification
    Vineet Bafna and Nathan Edwards
    In Proceedings of the seventh annual international conference on Research in computational molecular biology, 2003
  6. JCB
    Haplotyping as perfect phylogeny: A direct approach
    Vineet Bafna, Dan Gusfield, Giuseppe Lancia, and 1 more author
    Journal of Computational Biology, 2003

2002

  1. RECOMB Workshop
    Haplotyping as perfect phylogeny
    Vineet Bafna, Dan Gusfield, Giuseppe Lancia, and 1 more author
    In RECOMB Workshop on Computational Methods for SNPs and Haplotype Inference, 2002
  2. UC Davis Computer Science Technical Report CSE-2002-21
    Vineet Bafna, Dan Gusfield, Giuseppe Lancia, and 1 more author
    2002
  3. RECOMB Workshop
    A survey of computational methods for determining haplotypes
    Bjarni V Halldórsson, Vineet Bafna, Nathan Edwards, and 3 more authors
    In RECOMB Workshop on Computational Methods for SNPs and Haplotype Inference, 2002
  4. WABI
    Practical algorithms and fixed-parameter tractability for the single individual SNP haplotyping problem
    Romeo Rizzi, Vineet Bafna, Sorin Istrail, and 1 more author
    In International Workshop on Algorithms in Bioinformatics, 2002

2001

  1. Science
    The sequence of the human genome
    Venter J Craig, Mark D Adams, Eugene W Myers, and 8 more authors
    Science, 2001
  2. SNPs Problems, Complexity, and Algorithms
    Giuseppe Lancia, Vineet Bafna, Sorin Istrail, and 2 more authors
    In Proceedings of the 9th Annual European Symposium on Algorithms, 2001
    Website
  3. Science
    The sequence of the human genome
    J Craig Venter, Mark D Adams, Eugene W Myers, and 8 more authors
    science, 2001
  4. Bioinformatics
    SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database
    Vineet Bafna and Nathan Edwards
    Bioinformatics, 2001

2000

  1. Comp. Gen.
    Circular permutations and genome shuffling
    Vineet Bafna, Donald Beaver, Martin Fürer, and 1 more author
    In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, 2000
  2. JCB
    Ligand-receptor pairing via tree comparison
    Vineet Bafna, Sridhar Hannenhalli, Ken Rice, and 1 more author
    Journal of Computational Biology, 2000

1999

  1. SIAM Disc. Math.
    A 2-approximation algorithm for the undirected feedback vertex set problem
    Vineet Bafna, Piotr Berman, and Toshihiro Fujito
    SIAM Journal on Discrete Mathematics, 1999

1998

  1. JCI
    Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung.
    Robert Bals, Xiaorong Wang, Zhongren Wu, and 5 more authors
    The Journal of clinical investigation, 1998
  2. RECOMB
    Detecting non-adjoining correlations with signals in DNA
    Pankaj Agarwal and Vineet Bafna
    In Proceedings of the second annual international conference on Computational molecular biology, 1998
  3. ISMB
    The ribosome scanning model for translation initiation: implications for gene prediction and full-length cDNA detection.
    Pankaj Agarwal and Vineet Bafna
    In ISMB, 1998
  4. SODA
    A polynomial time approximation scheme for minimum routing cost spanning trees
    Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, and 3 more authors
    In Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, San Francisco, California, USA, 1998
    Website
  5. SIAM Disc. Math.
    Sorting by transpositions
    Vineet Bafna and Pavel A Pevzner
    SIAM Journal on Discrete Mathematics, 1998
  6. SIAM Computing
    On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics)
    Richa Agarwala, Vineet Bafna, Martin Farach, and 2 more authors
    SIAM Journal on Computing, 1998
    DOI Website

1997

  1. Theor. Comp. Sci.
    with two errors (Mathematical Games)
    V Bafna, EL Lawler, PA Pevzner, and 1 more author
    Theoretical Computer Science, 1997
  2. Theor. Comp. Sci.
    Approximation algorithms for multiple sequence alignment
    Vineet Bafna, Eugene L Lawler, and Pavel A Pevzner
    Theoretical Computer Science, 1997

1996

  1. DAM
    Nonoverlapping local alignments (weighted independent sets of axis-parallel rectangles)
    Vineet Bafna, Babu Narayanan, and R Ravi
    Discrete Applied Mathematics, 1996
  2. SIAM Computing
    Genome rearrangements and sorting by reversals
    Vineet Bafna and Pavel A Pevzner
    SIAM Journal on computing, 1996
  3. Constant ratio approximations of feedback vertex sets in weighted undirected graphs
    Vineet Bafna, Piotr Berman, and Toshihiro Fujito
    1996
  4. Constant Ratio Approximations of Feedback Vertex Sets inWeighted Undirected Graphs
    Vineet Bafna, Piotr Berman, and Toshihiro Fujito
    1996

1995

  1. ISAAC
    Constant ratio approximations of the weighted feedback vertex set problem for undirected graphs
    Vineet Bafna, Piotr Berman, and Toshihiro Fujito
    In International Symposium on Algorithms and Computation, 1995
  2. CPM
    Computing similarity between RNA strings
    Vineet Bafna, S Muthukrishnan, and R Ravi
    In Annual Symposium on Combinatorial Pattern Matching, 1995
  3. WADS
    Nonoverlapping local alignments (weighted independent sets of axis parallel rectangles)
    Vineet Bafna, Babu Narayanan, and Ramamoorthi Ravi
    In Workshop on Algorithms and Data Structures, 1995
  4. Mol Biol. Evol.
    Sorting by Reversals: Genome Rearrangements in Plant Organelles and Evolutionary History of X Chromosome
    V Bafna and PA Pevzner
    Molecular Biology and Evolution, Mar 1995
    DOI Website

1994

  1. Approximation algorithms for multiple alignment and genome rearrangements
    Vineet Bafna
    1994
  2. CPM
    Approximation algorithms for multiple sequence alignment
    Vineet Bafna, Eugene L Lawler, and Pavel A Pevzner
    In Annual Symposium on Combinatorial Pattern Matching, 1994
  3. Theor. Comp. Sci.
    Not all insertion methods yield constant approximate tours in the Euclidean plane
    Vineet Bafna, Bala Kalyanasundaram, and Kirk Pruhs
    Theoretical Computer Science, 1994

1990

  1. VECPAR
    Parallel implementation of logic languages
    Amit Gupta, Anindo Banerjea, Vikas Jha, and 2 more authors
    In International Conference on Vector and Parallel Processing, 1990