publications

Pulled periodically from google scholar

2025

  1. 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
  2. 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
  3. Nature
    Engineered extrachromosomal oncogene amplifications promote tumorigenesis
    Davide Pradella, Minsi Zhang, Rui Gao, and 8 more authors
    Nature, 2025
  4. 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
  5. 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
  6. medRxiv
    OMKar: optical map based automated karyotyping of genomes to identify constitutional abnormalities
    Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, and 8 more authors
    medRxiv, 2025
  7. 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
  8. 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
  9. bioRxiv
    EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs
    Hyerim Yi, Shu Zhang, Jason Swinderman, and 8 more authors
    bioRxiv, 2025
  10. 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
  11. bioRxiv
    Oncogene Silencing via ecDNA Micronucleation
    Lotte Brückner, Robin Xu, Jun Tang, and 8 more authors
    bioRxiv, 2025
  12. Cancer Res.
    AmpliconSuite enables discovery of extrachromosomal DNA in tumor genomes
    Jens Luebeck, Edwin Huang, Ted Liefeld, and 8 more authors
    Cancer Research, 2025
  13. Cancer Res.
    Three-dimensional genome landscape of primary human cancers
    Yanding Zhao, Katie E Yost, King L Hung, and 8 more authors
    Cancer Research, 2025
  14. Cancer Res.
    Engineered extrachromosomal oncogene amplifications promote tumorigenesis
    Melissa A Yao, Davide Pradella, Minsi Zhang, and 8 more authors
    Cancer Research, 2025
  15. 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
  16. 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
  17. bioRxiv
    Accurate Prediction of ecDNA in Interphase Cancer Cells using Deep Neural Networks
    Utkrisht Rajkumar, Gino Prasad, Ellis J Curtis, and 8 more authors
    bioRxiv, 2025
  18. medRxiv
    Extrachromosomal DNA associates with poor survival across a broad spectrum of childhood solid tumors
    Owen S Chapman, Sunita Sridhar, Eugene Yui-Ching Chow, and 8 more authors
    MedRxiv, 2025
  19. Neuro-Oncol. Peds.
    METB-07. Conservation of circular extrachromosomal DNA in xenograft mouse models derived from pediatric brain tumors
    Rishaan Kenkre, Owen Chapman, Jens Luebeck, and 6 more authors
    Neuro-Oncology Pediatrics, 2025
  20. Neuro-Oncol. Peds.
    METB-04. The genomic landscape of extrachromosomal amplifications across pediatric brain tumors
    Owen Chapman, Sunita Sridhar, Eugene Chow, and 8 more authors
    Neuro-Oncology Pediatrics, 2025
  21. bioRxiv
    Preservation and Clonal Behavior of Extrachromosomal DNA in Patient-Derived Xenograft Models of Childhood Cancers
    Rishaan Kenkre, Jon D Larson, Owen S Chapman, and 7 more authors
    bioRxiv, 2025
  22. 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
  23. bioRxiv
    SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation
    bioRxiv, 2025
  24. 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
  25. Cell
    Correction to: Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer (Cell,(2016), 166, 3,(755-765),(S0092867416306730), 10.1016/j. cell. 2016.05. 069)
    Hui Zhang, Tao Liu, Zhen Zhang, and 8 more authors
    Cell, 2025

2024

  1. 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
  2. Cancer Res.
    Chromosomal instability causes epigenetic aberrations in cancer
    Albert S Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, and 8 more authors
    Cancer Research, 2024
  3. 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
  4. Cancer Res.
    The origins and clinical impact of extrachromosomal DNA across 39 cancers
    Chris Bailey, Oriol Pich, Kerstin Thol, and 8 more authors
    Cancer Research, 2024
  5. bioRxiv
    Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers
    Jun Tang, Natasha E Weiser, Guiping Wang, and 8 more authors
    bioRxiv, 2024
  6. 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
  7. Neuro-Oncology
    STEM-07. CONSERVATION AND FAITHFUL REPRESENTATION OF CIRCULAR EXTRACHROMOSOMAL DNA IN ORTHOTOPIC PATIENT-DERIVED MEDULLOBLASTOMA XENOGRAFTS
    Rishaan Kenkre, Owen Chapman, Jens Luebeck, and 4 more authors
    Neuro-Oncology, 2024
  8. bioRxiv
    AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
    Jens Luebeck, Edwin Huang, Forrest Kim, and 8 more authors
    bioRxiv, 2024
  9. Neuro-Oncology
    METB-08. CIRCULAR EXTRACHROMOSOMAL DNA IS ASSOCIATED WITH POOR SURVIVAL IN CHILDHOOD CANCER TYPES
    Sunita Sridhar, Owen Chapman, Aditi Dutta, and 6 more authors
    Neuro-Oncology, 2024
  10. 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
  11. Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer
    Joseph Califano, Takuya Nakagawa, Jens Luebeck, and 8 more authors
    2024
  12. Cancer Gen.
    13. AmpliconSuite: Analyzing focal amplifications in cancer genomes
    Jens Luebeck, Edwin Huang, Bhargavi Dameracharla, and 8 more authors
    Cancer Genetics, 2024
  13. Research Square
    Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer
    Takuya Nakagawa, Jens Luebeck, Kaiyuan Zhu, and 8 more authors
    Research Square, 2024
  14. Nature Genetics
    Mapping extrachromosomal DNA amplifications during cancer progression
    Hoon Kim, Soyeon Kim, Taylor Wade, and 8 more authors
    Nature genetics, 2024
  15. 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
  16. bioRxiv
    Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma
    Imran Noorani, Magnus Haughey, Jens Luebeck, and 8 more authors
    bioRxiv, 2024
  17. 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
  18. Nature
    Enhancing transcription–replication conflict targets ecDNA-positive cancers
    Jun Tang, Natasha E Weiser, Guiping Wang, and 8 more authors
    Nature, 2024
  19. Nature
    Origins and impact of extrachromosomal DNA
    Chris Bailey, Oriol Pich, Kerstin Thol, and 8 more authors
    Nature, 2024
  20. 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
  21. Cancer Sci.
    Contribution of human-viral hybrid ecDNA accumulation to the cancer life cycle and potential for novel targeted therapy
    Takuya Nakagawa, Jens Luebeck, Joshua Lange, and 5 more authors
    In CANCER SCIENCE, 2024

2023

  1. bioRxiv
    Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change
    Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, and 8 more authors
    bioRxiv, 2023
  2. bioRxiv
    Immortalization and transformation of primary cells mediated by engineered ecDNAs
    Davide Pradella, Minsi Zhang, Rui Gao, and 8 more authors
    bioRxiv, 2023
  3. 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
  4. 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
  5. 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
  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. bioRxiv
    Coordinated inheritance of extrachromosomal DNA species in human cancer cells
    King L Hung, Matthew G Jones, Ivy Tsz-Lo Wong, and 8 more authors
    bioRxiv, 2023
  8. Nature
    Epigenetic dysregulation from chromosomal transit in micronuclei
    Albert S Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, and 8 more authors
    Nature, 2023
  9. 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
  10. 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
  11. 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
  12. DNA Barcoding
    Analyses of nuclear reads obtained using genome skimming
    Siavash Mirarab and Vineet Bafna
    In DNA Barcoding: Methods and Protocols, 2023

2022

  1. 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
  2. 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
  3. 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
  4. Ann. Rev. GHG
    Extrachromosomal DNA in cancer
    Vineet Bafna and Paul S Mischel
    Annual review of genomics and human genetics, 2022
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. Nature
    Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA
    Erik N Bergstrom, Jens Luebeck, Mia Petljak, and 8 more authors
    Nature, 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. 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
  13. iScience
    Detecting tandem repeat variants in coding regions using code-adVNTR
    Jonghun Park, Mehrdad Bakhtiari, Bernt Popp, and 2 more authors
    Iscience, 2022
  14. 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
  15. bioRxiv
    Extrachromosomal DNA in the cancerous transformation of Barrett’s esophagus
    Jens Luebeck, Alvin Wei Tian Ng, Patricia C Galipeau, and 8 more authors
    bioRxiv, 2022
  16. bioRxiv
    Epigenetic dysregulation from chromosomal transit in micronuclei
    Albert Agustinus, Ramya Raviram, Bhargavi Dameracharla, and 8 more authors
    BioRxiv, 2022
  17. 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
  18. Nature Cancer
    Form follows function in cancer genomes
    Paul S Mischel and Vineet Bafna
    Nature Cancer, 2022
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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

2021

  1. Patterns
    FaNDOM: Fast nested distance-based seeding of optical maps
    Siavash Raeisi Dehkordi, Jens Luebeck, and Vineet Bafna
    Patterns, 2021
  2. NAR Genomics
    CONSULT: accurate contamination removal using locality-sensitive hashing
    Eleonora Rachtman, Vineet Bafna, and Siavash Mirarab
    NAR Genomics and Bioinformatics, 2021
  3. bioRxiv
    Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA
    Erik N Bergstrom, Jens Luebeck, Mia Petljak, and 4 more authors
    bioRxiv, 2021
  4. 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
  5. 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
  6. bioRxiv
    Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers
    Joshua T Lange, Celine Y Chen, Yuriy Pichugin, and 8 more authors
    BioRxiv, 2021
  7. Neuro-Oncology
    OMIC-01. THE LANDSCAPE OF EXTRACHROMOSOMAL CIRCULAR DNA IN MEDULLOBLASTOMA SUBGROUPS
    Owen Chapman, Jens Luebeck, Shanqing Wang, and 8 more authors
    Neuro-Oncology, 2021
  8. medRxiv
    Host genome analysis of structural variations by optical genome mapping provides clinically valuable insights into genes implicated in critical immune, viral infection, and viral replication pathways in patients with severe COVID-19
    Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, and 8 more authors
    medRxiv, 2021
  9. Nature
    ecDNA hubs drive cooperative intermolecular oncogene expression
    King L Hung, Kathryn E Yost, Liangqi Xie, and 8 more authors
    Nature, 2021
  10. 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
  11. 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
  12. Extrachromosomal DNA (ecDNA) in cancer pathogenesis
    Sihan Wu, Vineet Bafna, and Paul S Mischel
    Current opinion in genetics & development, 2021
  13. 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
  14. bioRxiv
    The landscape of extrachromosomal circular DNA in medulloblastoma
    Owen S Chapman, Jens Luebeck, Sameena Wani, and 8 more authors
    bioRxiv, 2021
  15. 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

2020

  1. 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
  2. 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
  3. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification
    Kristine Bohmann, Siavash Mirarab, Vineet Bafna, and 1 more author
    2020
  4. 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
  5. 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
  6. bioRxiv
    AmpliconReconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer
    Jens Luebeck, Ceyda Coruh, Siavash R Dehkordi, and 8 more authors
    bioRxiv, 2020
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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

2019

  1. Cell Syst
    Computing the statistical significance of overlap between genome annotations with iStat
    Shahab Sarmashghi and Vineet Bafna
    Cell systems, 2019
  2. bioRxiv
    A Note on Computing Interval Overlap Statistics
    Shahab Sarmashghi and Vineet Bafna
    bioRxiv, 2019
  3. 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
  4. 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
  5. Nature Rev. Cancer
    Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
    Roel GW Verhaak, Vineet Bafna, and Paul S Mischel
    Nature Reviews Cancer, 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. 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
  8. bioRxiv
    Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development
    Tomoyuki Koga, Isaac A Chaim, Jorge A Benitez, and 8 more authors
    bioRxiv, 2019
  9. 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
  10. bioRxiv
    Frequent extrachromosomal oncogene amplification drives aggressive tumors
    Hoon Kim, Nam Nguyen, Kristen Turner, and 8 more authors
    bioRxiv, 2019
  11. iScience
    EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA
    Utkrisht Rajkumar, Kristen Turner, Jens Luebeck, and 4 more authors
    Iscience, 2019
  12. 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
  13. bioRxiv
    Glioblastomas derived from genetically modified pluripotent stem cells recapitulate pathobiology
    Tomoyuki Koga, Jorge A Benitez, Isaac A Chaim, and 8 more authors
    BioRxiv, 2019
  14. Methods of treating extrachromosomal dna expressing cancers
    Paul Mischel, Vineet Bafna, Junho Ko, and 2 more authors
    2019

2018

  1. Cell Syst.
    Proteostorm: An ultrafast metaproteomics database search framework
    Doruk Beyter, Miin S Lin, Yanbao Yu, and 2 more authors
    Cell systems, 2018
  2. 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
  3. 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
  4. bioRxiv
    Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect
    Viraj Deshpande, Jens Luebeck, Mehrdad Bakhtiari, and 6 more authors
    bioRxiv, 2018
  5. 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
  6. RECOMB
    Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR
    Vikas Bansal and Vineet Bafna
    In Research in Computational Molecular Biology, 2018
  7. 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
  8. 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

2017

  1. Genetics
    CLEAR: Composition of likelihoods for evolve and resequence experiments
    Arya Iranmehr, Ali Akbari, Christian Schlötterer, and 1 more author
    Genetics, 2017
  2. 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
  3. 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
  4. 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
  5. bioRxiv
    Fine-mapping the favored mutation in a positive selective sweep
    Ali Akbari, Joseph J Vitti, Arya Iranmehr, and 4 more authors
    bioRxiv, 2017
  6. Research in Computational Molecular Biology
    S Cenk Sahinalp
    2017
  7. Genome Res.
    HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
    Peter Edge, Vineet Bafna, and Vikas Bansal
    Genome research, 2017
  8. 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
  9. The antibody repertoire of colorectal cancer
    Seong Won Cha, Stefano Bonissone, Seungjin Na, and 2 more authors
    Molecular & Cellular Proteomics, 2017
  10. Nature
    Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity
    Kristen M Turner, Viraj Deshpande, Doruk Beyter, and 8 more authors
    Nature, 2017

2016

  1. 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
  2. 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
  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. 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
  5. Cell
    Integrated proteogenomic characterization of human high-grade serous ovarian cancer
    Hui Zhang, Tao Liu, Zhen Zhang, and 8 more authors
    Cell, 2016

2015

  1. 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
  2. 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
  3. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer
    Woo Sunghee, Cha Seong Won, Bonissone Stefano, and 3 more authors
    2015
  4. 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
  5. 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
  6. 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
  7. 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
  8. JCB
    Reconstructing breakage fusion bridge architectures using noisy copy numbers
    Shay Zakov and Vineet Bafna
    Journal of Computational Biology, 2015
  9. 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
  10. 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
  11. Collaborative Research: ABI Innovation: Computational population-genetic analysis for detection of soft selective sweeps
    Vineet Bafna
    NSF Award Number 1458557. Directorate for Biological Sciences, 2015

2014

  1. Bioinformatics
    Using Genome Query Language to uncover genetic variation
    Christos Kozanitis, Andrew Heiberg, George Varghese, and 1 more author
    Bioinformatics, 2014
  2. 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
  3. Bioinformatics
    Inferring gene ontologies from pairwise similarity data
    Michael Kramer, Janusz Dutkowski, Michael Yu, and 2 more authors
    Bioinformatics, 2014
  4. Phys.
    The genetic basis of chronic mountain sickness
    Roy Ronen, Dan Zhou, Vineet Bafna, and 1 more author
    Physiology, 2014
  5. 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
  6. 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
  7. Nuc. Acids. Res
    The elusive evidence for chromothripsis
    Marcus Kinsella, Anand Patel, and Vineet Bafna
    Nucleic acids research, 2014
  8. 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
  9. 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
  10. 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

2013

  1. 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
  2. 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
  3. Using Genome Query Language (GQL) to uncover genetic variation
    Christos Kozanitis, Andrew Heiberg, George Varghese, and 1 more author
    2013
  4. 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
  5. 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
  6. Genetics
    Learning natural selection from the site frequency spectrum
    Roy Ronen, Nitin Udpa, Eran Halperin, and 1 more author
    Genetics, 2013
  7. 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
  8. CACM
    Abstractions for genomics
    Vineet Bafna, Alin Deutsch, Andrew Heiberg, and 3 more authors
    Communications of the ACM, 2013
  9. Genome Bio.
    On the design of clone-based haplotyping
    Christine Lo, Rui Liu, Jehyuk Lee, and 7 more authors
    Genome biology, 2013
  10. Bioinformatics
    Wessim: a whole-exome sequencing simulator based on in silico exome capture
    Sangwoo Kim, Kyowon Jeong, and Vineet Bafna
    Bioinformatics, 2013
  11. arXiv
    Detecting Breakage Fusion Bridge cycles in tumor genomes–an algorithmic approach
    Shay Zakov, Marcus Kinsella, and Vineet Bafna
    arXiv preprint arXiv:1301.2610, 2013
  12. 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

2012

  1. 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
  2. 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
  3. 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
  4. 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
  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. 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
  7. JCB
    Combinatorics of the breakage-fusion-bridge mechanism
    Marcus Kinsella and Vineet Bafna
    Journal of Computational Biology, 2012
  8. 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
  9. Bioinformatics
    Speeding up tandem mass spectral identification using indexes
    Xiaowen Liu, Alessandro Mammana, and Vineet Bafna
    Bioinformatics, 2012
  10. Sample Reproducibility of Genetic Association Using Different
    MM Abad-Grau, N Medina-Medina, R Montes-Soldado, and 2 more authors
    2012

2011

  1. 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
  2. JCB
    Compressing genomic sequence fragments using SlimGene
    Christos Kozanitis, Chris Saunders, Semyon Kruglyak, and 2 more authors
    Journal of Computational Biology, 2011
  3. BMC Bioinform.
    Strobe sequence design for haplotype assembly
    Christine Lo, Ali Bashir, Vikas Bansal, and 1 more author
    BMC bioinformatics, 2011
  4. 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
  5. Bioinformatics
    Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
    Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, and 2 more authors
    Bioinformatics, 2011
  6. Metabolic Network Analysis Demystified. Ed. Vineet Bafna, S. Cenk Shinalp. LNCS Sublibrary: SL 8-Bioinformatics
    Leonid Chindelevitch, Aviv Regev, and Bonnie Berger
    2011
  7. On the Approximability of Reachability-Preserving Network Orientations
    Iftah Gamzu, Michael Elberfeld, Vineet Bafna, and 5 more authors
    Internet Mathematics, 2011
  8. 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
  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. 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
  11. 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
  12. 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
  13. On the approximability of reachability-preserving network orientations
    Michael Elberfeld, Vineet Bafna, Iftah Gamzu, and 5 more authors
    Internet Mathematics, 2011
  14. 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
  15. JCB
    Preface: satellite workshop on comparative genomics, research in computational molecular biology (RECOMB-CG 2010) preface
    Vineet Bafna
    Journal of Computational Biology, 2011
  16. 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
  17. 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

2010

  1. 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
  2. JCB
    Optimizing PCR assays for DNA-based cancer diagnostics
    Ali Bashir, Qing Lu, Dennis Carson, and 3 more authors
    Journal of Computational Biology, 2010
  3. Research article 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
    2010
  4. 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
  5. 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
  6. Expansion of the mycobacterial “PUPylome”
    Jeramie Watrous, Kristin Burns, Wei-Ting Liu, and 6 more authors
    Molecular bioSystems, 2010
  7. BMC Genomics
    Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance
    Ali Bashir, Vikas Bansal, and Vineet Bafna
    BMC genomics, 2010
  8. 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
  9. Template proteogenomics: sequencing whole proteins using an imperfect database
    Natalie E Castellana, Victoria Pham, David Arnott, and 2 more authors
    Molecular & Cellular Proteomics, 2010
  10. 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
  11. Bioinformatics
    RAPID detection of gene–gene interactions in genome-wide association studies
    Dumitru Brinza, Matthew Schultz, Glenn Tesler, and 1 more author
    Bioinformatics, 2010
  12. JP
    Proteogenomics to discover the full coding content of genomes: a computational perspective
    Natalie Castellana and Vineet Bafna
    Journal of proteomics, 2010
  13. 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
  14. 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
  15. 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
  16. Genome Bio.
    Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants
    Olivier Harismendy
    Genome Biology, 2010

2009

  1. 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
  2. JCB
    Fast and accurate alignment of multiple protein networks
    Maxim Kalaev, Vineet Bafna, and Roded Sharan
    Journal of computational biology, 2009
  3. 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
  4. CSE280 Class Projects (Suggested)
    Vineet Bafna
    2009

2008

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. JCB
    Structural alignment of pseudoknotted RNA
    Buhm Han, Banu Dost, Vineet Bafna, and 1 more author
    Journal of Computational Biology, 2008
  7. 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
  8. 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
  9. 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
  10. 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
  11. RECOMB
    Qnet: A tool for querying biological networks
    Banu Dost, Tomer Shlomi, Nitin Gupta, and 2 more authors
    RECOMB 2007 and JCB, 2008
  12. Bioinformatics
    HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
    Vikas Bansal and Vineet Bafna
    Bioinformatics, 2008
  13. Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in
    A Bashir, S Volik, C Collins, and 2 more authors
    2008

2007

  1. 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
  2. Integrating scientific cultures
    Trey Ideker, Vineet Bafna, and Thomas Lemberger
    Molecular Systems Biology, 2007
  3. 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
  4. 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
  5. Genome Res.
    Evidence for large inversion polymorphisms in the human genome from HapMap data
    Vikas Bansal, Ali Bashir, and Vineet Bafna
    Genome research, 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. 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
  8. Genome Res.
    Improving gene annotation using peptide mass spectrometry
    Stephen Tanner, Zhouxin Shen, Julio Ng, and 4 more authors
    Genome research, 2007
  9. 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
  10. Integrating scientific cultures
    Vineet Bafna and Thomas Lemberger
    Molecular Systems Biology, 2007
  11. 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
  12. Phosphorylation-specific MS/MS scoring
    S Payne, M Yau, M Smolka, and 2 more authors
    In MOLECULAR & CELLULAR PROTEOMICS, 2007
  13. Systems biology and computational proteomics
    Trey Ideker and Vineet Bafna
    Lecture notes in computer science, 2007

2006

  1. Nature Protocols
    Unrestrictive identification of post-translational modifications through peptide mass spectrometry
    Stephen Tanner, Pavel A Pevzner, and Vineet Bafna
    Nature protocols, 2006
  2. 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
  3. 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
  4. JCB
    Inference about recombination from haplotype data: lower bounds and recombination hotspots
    Vineet Bafna and Vikas Bansal
    Journal of Computational Biology, 2006
  5. 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
  6. 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
  7. Identification of informative genetic markers
    Bjarni Halldorsson, Vineet Bafna, Ross Lippert, and 4 more authors
    Mar 2006
    US Patent App. 11/040,652
  8. JCB
    Consensus folding of unaligned RNA sequences revisited
    Vineet Bafna, Haixu Tang, and Shaojie Zhang
    Journal of computational biology, 2006

2005

  1. RECOMB
    Improved recombination lower bounds for haplotype data
    Vineet Bafna and Vikas Bansal
    In Annual International Conference on Research in Computational Molecular Biology, 2005
  2. 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
  3. 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
  4. 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
  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. Genome Res.
    Orthologous repeats and mammalian phylogenetic inference
    Ali Bashir, Chun Ye, Alkes L Price, and 1 more author
    Genome Research, 2005
  7. Nuc. Acids. Res.
    Orthologous repeats and mammalian phylogenetic inference. Genome Res
    Ali Bashir, Chun Ye, Alkes L Price, and 1 more author
    In Nucleic Acids Res, 2005
  8. 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
  9. 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
  10. 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
  11. Novel Algorithms for NcRNA Discovery and RNA Structure Prediction
    Vineet Bafna
    NSF Award Number 0516440. Directorate for Biological Sciences, 2005

2004

  1. Mass spectrometry and computational proteomics
    Vineet Bafna and Knut Reinert
    Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2004
  2. Anal. Chem.
    Shotgun protein sequencing by tandem mass spectra assembly
    Nuno Bandeira, Haixu Tang, Vineet Bafna, and 1 more author
    Analytical chemistry, 2004
  3. Pattern matching algorithms
    Vineet Bafna
    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. 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
  6. 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
  7. 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

2003

  1. JCB
    Haplotyping as perfect phylogeny: A direct approach
    Vineet Bafna, Dan Gusfield, Giuseppe Lancia, and 1 more author
    Journal of Computational Biology, 2003
  2. 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
  3. 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
  4. Science
    The dog genome: survey sequencing and comparative analysis
    Ewen F Kirkness, Vineet Bafna, Aaron L Halpern, and 8 more authors
    Science, 2003
  5. JCB
    Robustness of inference of haplotype block structure
    Russell Schwartz, Bjarni V Halldórsson, Vineet Bafna, and 2 more authors
    Journal of Computational Biology, 2003
  6. 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

2002

  1. 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
  2. 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
  3. UC Davis Computer Science Technical Report CSE-2002-21
    Vineet Bafna, Dan Gusfield, Giuseppe Lancia, and 1 more author
    2002
  4. 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

2001

  1. Bioinformatics
    SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database
    Vineet Bafna and Nathan Edwards
    Bioinformatics, 2001
  2. Science
    The sequence of the human genome
    J Craig Venter, Mark D Adams, Eugene W Myers, and 8 more authors
    science, 2001
  3. SNPs problems, algorithms and complexity
    Giuseppe Lancia, V Bafna, S Istrail, and 2 more authors
    2001
  4. Science
    The sequence of the human genome
    J Craig Venter, Mark D Adams, Eugene W Myers, and 8 more authors
    Science, 2001
  5. Science
    The sequence of the human genome
    Venter J Craig, Mark D Adams, Eugene W Myers, and 8 more authors
    Science, 2001

2000

  1. JCB
    Ligand-receptor pairing via tree comparison
    Vineet Bafna, Sridhar Hannenhalli, Ken Rice, and 1 more author
    Journal of Computational Biology, 2000
  2. 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
  3. SIAM Computing
    A polynomial-time approximation scheme for minimum routing cost spanning trees
    Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, and 3 more authors
    SIAM Journal on Computing, 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
  2. A Polynomial-time Approximation Scheme for the Minimum Routing Cost Tree Problem
    V BAFNA, KM CHAO, R RAVI, and 3 more authors
    1999

1998

  1. SIAM Disc. Math.
    Sorting by transpositions
    Vineet Bafna and Pavel A Pevzner
    SIAM Journal on Discrete Mathematics, 1998
  2. SODA
    A Polynomial Time Approximation Scheme for Minimum Routing Cost Spanning Trees
    Chuan Yi Tang
    In Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, 1998
  3. 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
  4. SIAM Disc. Math.
    Sorting by transpositions
    V Vineet Bafna and PA Pevzner
    SIAM Journal on Discrete Mathematics, 1998
  5. 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
  6. 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
  7. 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

1997

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

1996

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

1995

  1. Sorting by reversals: genome rearrangements in plant organelles and evolutionary history of X chromosome.
    Vineet Bafna and Pavel A Pevzner
    1995
  2. 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
  3. Non-Overlapping Local Alignments
    Vineet Bafna, Babu Narayanan, and R Ravi
    Lecture Notes in Computer Science, 1995
  4. On the approximability of numerical taxonomy
    Richa Agarwala, Vineet Bafna, Martin Farach, and 3 more authors
    1995
  5. CPM
    Computing similarity between RNA strings
    Vineet Bafna, S Muthukrishnan, and R Ravi
    In Annual Symposium on Combinatorial Pattern Matching, 1995
  6. Sorting by Reversals: Genome Rearrangements in Plant Organelles1
    Vineet Bafna
    In Proceedings of Phylogeny Workshop, 1995
  7. 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
  8. Constant Ratio Approximations of the Weighted
    Vineet Bafna and Toshihiro Fujito
    In Algorithms and Computations: 6th International Symposium, ISAAC’95 Cairns, Australia, December 4-6, 1995. Proceedings Proceedings., 1995

1994

  1. 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
  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. Approximation algorithms for multiple alignment and genome rearrangements
    Vineet Bafna
    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

1985

  1. JAM
    13 Comparative RNA analysis
    V Bafna, S Muthukrishnan, R Ravi, and 1 more author
    Journal of Appl. Math, 1985

  1. Comparative Analysis of Post-Translational Modifications in Young and Aged Lens: Does Deamidation Contribute to Crystallin Insolubility?
    Phillip A Wilmarth, Stephen Tanner, Surendra Dasari, and 5 more authors
  2. Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Favored Allele—Supporting Information
    Roy Ronen, Glenn Tesler, Ali Akbari, and 3 more authors
  3. Exploring the Assembly of an Organism using MALDI Imaging: A Systems Approach to Understanding Embryonic Development
    Maxence Wisztorski, Jocelyne Bruand, Julien Franck, and 6 more authors
  4. Pathophys.
    Arthur L. Delcher, Mihai Pop, Wei Wang, Claire M. Fraser, J. Craig Venter 2
    Ewen F Kirkness, Vineet Bafna, Aaron L Halpern, and 3 more authors
    pathophysiology
  5. RECOMB
    Assembly-Free and Alignment-Free Sample Identification Using Genome Skims
    Vineet Bafna and Siavash Mirarab
    In Research in Computational Molecular Biology
  6. Protein Identification: Algorithmic Challenges
    Vineet Bafna, Ari Frank, Pavel Pevzner, and 2 more authors
  7. ESA
    Novel statistical methods to leverage low-coverage whole-genome sequencing data in biodiversity studies
    Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, and 2 more authors
    In 2020 ESA Annual Meeting (August 3-6)
  8. NSF III-2010 Workshop: PI Reports
    Peggy Agouris, Vassilis Athitsos, Ramazan Aygun, and 8 more authors
  9. Identifying the genetic basis of disease
    Vineet Bafna
    BIOINFORMATICS FOR BIOLOGISTS
  10. Automatic Identification of RNA Structural Motifs
    Cuncong Zhong, Haixu Tang, Vineet Bafna, and 1 more author
  11. Abstractions For Genomics Large genomic databases with interactive access require new, layered abstractions, including separating" evidence" from" inference.
    Vineet Bafna, Alin Deutsch, Andrew Heiberg, and 3 more authors
  12. NSF III-2010 PI Workshop Report on “Future Directions for III”
    Peggy Agouris, Vassilis Athitsos, Ramazan Aygun, and 8 more authors
  13. Algorithms for Genetics: Basics of Wright Fisher Model and Coalescent Theory
    Vineet Bafna, Harish Nagarajan, and Nitin Udpa
  14. FastR: Fast database search tool for structured RNA sequences
    Vineet Bafna and Shaojie Zhang
  15. An emerging toolkit for targeted cancer therapies 177
    Gordon B Mills, James D Brooks, Emily A Vucic, and 8 more authors
  16. Targeted Genotyping of Variable Number Tandem Repeats with
    Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, and 2 more authors
  17. SODA
    Sorting permutations by tanspositions
    Vineet Bafna and Pavel Pevzner
    In Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
  18. A New Approch to Multiple RNA Structure Alignment
    Daniel DeBlasio, Jocelyne Bruand, Vineet Bafna, and 1 more author
  19. Interactive Genomics: Rapidly Querying Genomes in the Cloud
    Christos Kozanitis, Vineet Bafna, Ravi Pandya MSR, and 1 more author
  20. Optimal Haplotype Block-Free Selection of Tagging SNPs for
    Bjarni V Halldórsson, Vineet Bafna, Ross Lippert, and 1 more author
  21. Supporting Information Text S1 to Sample Reproducibility of Genetic Association using Different Multimarker TDTs in Genome-wide Association Studies: Characterization and a New Approach
    Marıa M Abad-Grau, Nuria Medina-Medina, Rosana Montes-Soldado, and 2 more authors
  22. Deconvolution of Complex Tandem Mass Spectra of Intact Proteins: A Combinatorial Approach
    Xiaowen Liu, Yuval Inbar, Pieter C Dorrestein, and 4 more authors
  23. Nonoverlapping Local Alignments, Weighted Independent Sets of Axis
    Vineet Bafna and R Ravi Babu Narayanan
  24. Epigenetic dysregulation from chromosomal transit in micronuclei
    F Bakhoum14, Dan Landau, Vineet Bafna, and 3 more authors
  25. Orthologous Repeats and Phylogenetic Inference
    Ali Bashir, Chun Ye, Alkes Price, and 1 more author
  26. IELSEVIER
    V Bafna, B Narayanan, R Ravi, and 1 more author
  27. Aarts, EHL, and Korst, J.(1989), Simulated Annealing and Boltzmann Ma-chines, John Wiley & Sons, New York. Agarwal, PK, and Procopiuc, CM (1998),“Exact and approximation algo-rithms for clustering”, Proc. 9th Annual ACM-SIAM Symposium on Dis-crete Algorithms, ACM-SIAM, 658–667.(ND53)
    R Agarwala, V Bafna, M Farach, and 8 more authors
  28. DIMACS TR: 96-30 Computing similarity between RNA strings
    V Bafna, S Muthukrishnan, and R Ravi
  29. 1Submit Datasets
    Jeremy Carver, Ian Kaufman, Claudiu Farcas, and 2 more authors