Parallel Implementation of Logic Languages. - Amit Gupta; Anindo Banerjea; Vikas Jha; Vineet Bafna; P. C. P. Bhatt (CONPAR, 1990)

Not All Insertion Methods Yield Constant Approximate Tours in the Euclidean Plane. - Vineet Bafna; Bala Kalyanasundaram; Kirk Pruhs (Theor. Comput. Sci., 1994)

Computing Similarity between RNA Strings. - Vineet Bafna; S. Muthukrishnan 001; R. Ravi 001 (CPM, 1995)

Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs. - Vineet Bafna; Piotr Berman; Toshihiro Fujito (ISAAC, 1995)

Sorting Permutations by Transpositions. - Vineet Bafna; Pavel A. Pevzner (SODA, 1995)

Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles). - Vineet Bafna; Babu O. Narayanan; R. Ravi 001 (WADS, 1995)

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). - Richa Agarwala; Vineet Bafna; Martin Farach; Babu O. Narayanan; Mike Paterson; Mikkel Thorup (SODA, 1996)

Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles). - Vineet Bafna; Babu O. Narayanan; R. Ravi 001 (Discret. Appl. Math., 1996)

Genome Rearrangements and Sorting by Reversals. - Vineet Bafna; Pavel A. Pevzner (SIAM J. Comput., 1996)

Approximation Algorithms for Multiple Sequence Alignment. - Vineet Bafna; Eugene L. Lawler; Pavel A. Pevzner (Theor. Comput. Sci., 1997)

The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection. - Pankaj Agarwal; Vineet Bafna (ISMB, 1998)

Detecting non-adjoining correlations with signals in DNA. - Pankaj Agarwal; Vineet Bafna (RECOMB, 1998)

Sorting by Transpositions. - Vineet Bafna; Pavel A. Pevzner (SIAM J. Discret. Math., 1998)

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). - Richa Agarwala; Vineet Bafna; Martin Farach; Mike Paterson; Mikkel Thorup (SIAM J. Comput., 1999)

A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees. - Bang Ye Wu; Giuseppe Lancia; Vineet Bafna; Kun-Mao Chao; R. Ravi 001; Chuan Yi Tang (SIAM J. Comput., 1999)

A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem. - Vineet Bafna; Piotr Berman; Toshihiro Fujito (SIAM J. Discret. Math., 1999)

The Conserved Exon Method for Gene Finding. - Vineet Bafna; Daniel H. Huson (ISMB, 2000)

Ligand-Receptor Pairing Via Tree Comparison. - Vineet Bafna; Sridhar Hannenhalli; Ken Rice; Lisa Vawter (J. Comput. Biol., 2000)

SNPs Problems, Complexity, and Algorithms. - Giuseppe Lancia; Vineet Bafna; Sorin Istrail; Ross Lippert; Russell Schwartz (ESA, 2001)

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. - Vineet Bafna; Nathan Edwards (ISMB (Supplement of Bioinformatics), 2001)

A Survey of Computational Methods for Determining Haplotypes. - Bjarni V. Halldórsson; Vineet Bafna; Nathan Edwards; Ross Lippert; Shibu Yooseph; Sorin Istrail (Computational Methods for SNPs and Haplotype Inference, 2002)

Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. - Romeo Rizzi; Vineet Bafna; Sorin Istrail; Giuseppe Lancia (WABI, 2002)

Combinatorial Problems Arising in SNP and Haplotype Analysis. - Bjarni V. Halldórsson; Vineet Bafna; Nathan Edwards; Ross Lippert; Shibu Yooseph; Sorin Istrail (DMTCS, 2003)

On de novo interpretation of tandem mass spectra for peptide identification. - Vineet Bafna; Nathan Edwards (RECOMB, 2003)

Haplotypes and informative SNP selection algorithms: don't block out information. - Vineet Bafna; Bjarni V. Halldórsson; Russell Schwartz; Andrew G. Clark; Sorin Istrail (RECOMB, 2003)

Haplotyping as Perfect Phylogeny: A Direct Approach. - Vineet Bafna; Dan Gusfield; Giuseppe Lancia; Shibu Yooseph (J. Comput. Biol., 2003)

Robustness of Inference of Haplotype Block Structure. - Russell Schwartz; Bjarni V. Halldórsson; Vineet Bafna; Andrew G. Clark; Sorin Istrail (J. Comput. Biol., 2003)

FastR: Fast Database Search Tool for Non-Coding RNA. - Vineet Bafna; Shaojie Zhang 001 (CSB, 2004)

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. - Vineet Bafna; Dan Gusfield; Sridhar Hannenhalli; Shibu Yooseph (J. Comput. Biol., 2004)

The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. - Vineet Bafna; Vikas Bansal 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Identification of Post-Translational Modifications via Blind Search of Mass-Spectra. - Dekel Tsur; Stephen Tanner; Ebrahim Zandi; Vineet Bafna; Pavel A. Pevzner (CSB, 2005)

Improved Recombination Lower Bounds for Haplotype Data. - Vineet Bafna; Vikas Bansal 001 (RECOMB, 2005)

Searching Genomes for Noncoding RNA Using FastR. - Shaojie Zhang 001; Brian Haas; Eleazar Eskin; Vineet Bafna (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

Polynomial and APX-hard cases of the individual haplotyping problem. - Vineet Bafna; Sorin Istrail; Giuseppe Lancia; Romeo Rizzi (Theor. Comput. Sci., 2005)

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. - Shaojie Zhang 001; Ilya Borovok; Yair Aharonowitz; Roded Sharan; Vineet Bafna (ISMB (Supplement of Bioinformatics), 2006)

Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots. - Vineet Bafna; Vikas Bansal 001 (J. Comput. Biol., 2006)

Consensus Folding of Unaligned RNA Sequences Revisited. - Vineet Bafna; Haixu Tang; Shaojie Zhang 001 (J. Comput. Biol., 2006)

Optimization of primer design for the detection of variable genomic lesions in cancer. - Ali Bashir; Yu-Tsueng Liu; Benjamin J. Raphael; Dennis Carson; Vineet Bafna (Bioinform., 2007)

A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. - Dan Gusfield; Vikas Bansal 001; Vineet Bafna; Yun S. Song (J. Comput. Biol., 2007)

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. - Vikas Bansal 001; Vineet Bafna (ECCB, 2008)

An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. - Alexander Medvedovsky; Vineet Bafna; Uri Zwick; Roded Sharan (WABI, 2008)

QNet: A Tool for Querying Protein Interaction Networks. - Banu Dost; Tomer Shlomi; Nitin Gupta 002; Eytan Ruppin; Vineet Bafna; Roded Sharan (J. Comput. Biol., 2008)

Structural Alignment of Pseudoknotted RNA. - Buhm Han; Banu Dost; Vineet Bafna; Shaojie Zhang 001 (J. Comput. Biol., 2008)

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. - Ali Bashir; Stanislav Volik; Colin C. Collins; Vineet Bafna; Benjamin J. Raphael (PLoS Comput. Biol., 2008)

Shared Peptides in Mass Spectrometry Based Protein Quantification. - Banu Dost; Nuno Bandeira; Xiangqian Li; Zhouxin Shen; Steve Briggs; Vineet Bafna (RECOMB, 2009)

Fast and Accurate Alignment of Multiple Protein Networks. - Maxim Kalaev; Vineet Bafna; Roded Sharan (J. Comput. Biol., 2009)

RAPID detection of gene-gene interactions in genome-wide association studies. - Dumitru Brinza; Matthew Schultz; Glenn Tesler; Vineet Bafna (Bioinform., 2010)

Optimizing PCR Assays for DNA-Based Cancer Diagnostics. - Ali Bashir; Qing Lu; Dennis Carson; Benjamin J. Raphael; Yu-Tsueng Liu; Vineet Bafna (J. Comput. Biol., 2010)

Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. - Fereydoun Hormozdiari; Raheleh Salari; Vineet Bafna; Süleyman Cenk Sahinalp (J. Comput. Biol., 2010)

A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes. - Gaurav Bhatia; Vikas Bansal 001; Olivier Harismendy; Nicholas J. Schork; Eric J. Topol; Kelly A. Frazer; Vineet Bafna (PLoS Comput. Biol., 2010)

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. - Marcus Kinsella; Olivier Harismendy; Masakazu Nakano; Kelly A. Frazer; Vineet Bafna (Bioinform., 2011)

Strobe sequence design for haplotype assembly. - Christine Lo; Ali Bashir; Vikas Bansal 001; Vineet Bafna (BMC Bioinform., 2011)

On the Approximability of Reachability-Preserving Network Orientations. - Michael Elberfeld; Vineet Bafna; Iftah Gamzu; Alexander Medvedovsky; Danny Segev; Dana Silverbush; Uri Zwick; Roded Sharan (Internet Math., 2011)

Preface: Research in Computational Molecular Biology (RECOMB 2011). - Vineet Bafna (J. Comput. Biol., 2011)

Compressing Genomic Sequence Fragments Using SlimGene. - Christos Kozanitis; Christopher T. Saunders; Semyon Kruglyak; Vineet Bafna; George Varghese (J. Comput. Biol., 2011)

TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. - Banu Dost; Chunlei Wu; Andrew I. Su; Vineet Bafna (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. - Marcus Kinsella; Vineet Bafna (RECOMB, 2012)

Speeding up tandem mass spectral identification using indexes. - Xiaowen Liu; Alessandro Mammana; Vineet Bafna (Bioinform., 2012)

iDASH: integrating data for analysis, anonymization, and sharing. - Lucila Ohno-Machado; Vineet Bafna; Aziz A. Boxwala; Brian E. Chapman; Wendy Webber Chapman; Kamalika Chaudhuri; Michele E. Day; Claudiu Farcas; Nathaniel D. Heintzman; Xiaoqian Jiang; Hyeoneui Kim; Jihoon Kim 001; et al. (J. Am. Medical Informatics Assoc., 2012)

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. - Banu Dost; Nuno Bandeira; Xiangqian Li; Zhouxin Shen; Steve Briggs; Vineet Bafna (J. Comput. Biol., 2012)

Combinatorics of the Breakage-Fusion-Bridge Mechanism. - Marcus Kinsella; Vineet Bafna (J. Comput. Biol., 2012)

Learning Natural Selection from the Site Frequency Spectrum. - Roy Ronen; Nitin Udpa; Eran Halperin; Vineet Bafna (RECOMB, 2013)

Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. - Viraj Deshpande; Eric D. K. Fung; Son Pham; Vineet Bafna (WABI, 2013)

Wessim: a whole-exome sequencing simulator based on in silico exome capture. - Sangwoo Kim; Kyowon Jeong 001; Vineet Bafna (Bioinform., 2013)

Evaluating genome architecture of a complex region via generalized bipartite matching. - Christine Lo; Sangwoo Kim; Shay Zakov; Vineet Bafna (BMC Bioinform., 2013)

Abstractions for genomics. - Vineet Bafna; Alin Deutsch; Andrew Heiberg; Christos Kozanitis; Lucila Ohno-Machado; George Varghese (Commun. ACM, 2013)

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. - Shay Zakov; Marcus Kinsella; Vineet Bafna (Proc. Natl. Acad. Sci. USA, 2013)

Using Genome Query Language to uncover genetic variation. - Christos Kozanitis; Andrew Heiberg; George Varghese; Vineet Bafna (Bioinform., 2014)

Inferring gene ontologies from pairwise similarity data. - Michael Kramer; Janusz Dutkowski; Michael Yu; Vineet Bafna; Trey Ideker (Bioinform., 2014)

Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele. - Roy Ronen; Glenn Tesler; Ali Akbari; Shay Zakov; Noah A. Rosenberg; Vineet Bafna (RECOMB, 2015)

Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. - Shay Zakov; Vineet Bafna (J. Comput. Biol., 2015)

Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR. - Mehrdad Bakhtiari; Sharona Shleizer-Burko; Melissa Gymrek; Vikas Bansal 001; Vineet Bafna (RECOMB, 2018)

Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. - Shahab Sarmashghi; Kristine Bohmann; M. Thomas P. Gilbert; Vineet Bafna; Siavash Mirarab (RECOMB, 2018)

A Note on Computing Interval Overlap Statistics. - Shahab Sarmashghi; Vineet Bafna (RECOMB, 2019)

A CNN-based cell tracking method for multi-slice intravital imaging data. - Kenji Fujimoto; Tsubasa Mizugaki; Utkrisht Rajkumar; Hironori Shigeta; Shigeto Seno; Yutaka Uchida; Masaru Ishii; Vineet Bafna; Hideo Matsuda (BCB, 2021)

FaNDOM: Fast nested distance-based seeding of optical maps. - Siavash Raeisi Dehkordi; Jens Luebeck; Vineet Bafna (Patterns, 2021)

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. - Shahab Sarmashghi; Metin Balaban; Eleonora Rachtman; Behrouz Touri; Siavash Mirarab; Vineet Bafna (PLoS Comput. Biol., 2021)

DeepViFi: detecting oncoviral infections in cancer genomes using transformers. - Utkrisht Rajkumar; Sara Javadzadeh; Mihir Bafna; Dongxia Wu; Rose Yu; Jingbo Shang; Vineet Bafna (BCB, 2022)

Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. - Eleonora Rachtman; Shahab Sarmashghi; Vineet Bafna; Siavash Mirarab (RECOMB, 2022)

CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing. - Kaiyuan Zhu; Matthew G. Jones; Jens Luebeck; Xinxin Bu; Hyerim Yi; King L. Hung; Ivy Tsz-Lo Wong; Shu Zhang 014; Paul S. Mischel; Howard Y. Chang; Vineet Bafna (RECOMB, 2024)

OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders. - Siavash Raeisi Dehkordi; Zhaoyang Jia; Joey Estabrook; Jen Hauenstein; Neil Miller; Naz Güleray-Lafci; Jürgen Neesen; Alex Hastie; Andy Wing Chun Pang; Paul Dremsek; Vineet Bafna (RECOMB, 2025)

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; Se-Young Jo; Yuan-Chun Ding; Mehrdad Bakhtiari; Vikas Bansal 001; Susan L. Neuhausen; Vineet Bafna (PLoS Comput. Biol., 2025)