Vineet Bafna

94 papers A* 4A 3B 26C 4Journal 47Unranked 9
YearRankTypeTitle / Venue / Authors
2025 J jnl
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.
PLoS Comput. Biol.
Sara Javadzadeh, Aaron Adamson, Jonghun Park, Se-Young Jo, Yuan-Chun Ding, Mehrdad Bakhtiari, Vikas Bansal, Susan L. Neuhausen, Vineet Bafna
2025 B conf
OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders.
RECOMB
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
2024 B conf
CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing.
RECOMB
Kaiyuan Zhu, Matthew G. Jones, Jens Luebeck, Xinxin Bu, Hyerim Yi, King L. Hung, Ivy Tsz-Lo Wong, Shu Zhang, Paul S. Mischel, Howard Y. Chang, Vineet Bafna
2022 — conf
DeepViFi: detecting oncoviral infections in cancer genomes using transformers.
BCB
Utkrisht Rajkumar, Sara Javadzadeh, Mihir Bafna, Dongxia Wu, Rose Yu, Jingbo Shang, Vineet Bafna
2022 B conf
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships.
RECOMB
Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab
2021 — conf
A CNN-based cell tracking method for multi-slice intravital imaging data.
BCB
Kenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Vineet Bafna, Hideo Matsuda
2021 J jnl
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.
PLoS Comput. Biol.
Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna
2021 J jnl
FaNDOM: Fast nested distance-based seeding of optical maps.
Patterns
Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna
2019 B conf
A Note on Computing Interval Overlap Statistics.
RECOMB
Shahab Sarmashghi, Vineet Bafna
2018 B conf
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims.
RECOMB
Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab
2018 B conf
Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR.
RECOMB
Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna
2015 B conf
Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele.
RECOMB
Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, Vineet Bafna
2015 J jnl
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.
J. Comput. Biol.
Shay Zakov, Vineet Bafna
2014 J jnl
Inferring gene ontologies from pairwise similarity data.
Bioinform.
Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker
2014 B conf
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.
RECOMB
Shay Zakov, Vineet Bafna
2014 J jnl
Using Genome Query Language to uncover genetic variation.
Bioinform.
Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna
2013 J jnl
Abstractions for genomics.
Commun. ACM
Vineet Bafna, Alin Deutsch, Andrew Heiberg, Christos Kozanitis, Lucila Ohno-Machado, George Varghese
2013 J jnl
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes.
Proc. Natl. Acad. Sci. USA
Shay Zakov, Marcus Kinsella, Vineet Bafna
2013 C conf
Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads.
WABI
Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna
2013 J jnl
Evaluating genome architecture of a complex region via generalized bipartite matching.
BMC Bioinform.
Christine Lo, Sangwoo Kim, Shay Zakov, Vineet Bafna
2013 B conf
Learning Natural Selection from the Site Frequency Spectrum.
RECOMB
Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna
2013 J jnl
Wessim: a whole-exome sequencing simulator based on
Bioinform.
Sangwoo Kim, Kyowon Jeong, Vineet Bafna
2012 J jnl
Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides.
J. Comput. Biol.
Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna
2012 J jnl
Combinatorics of the Breakage-Fusion-Bridge Mechanism.
J. Comput. Biol.
Marcus Kinsella, Vineet Bafna
2012 B conf
Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics.
RECOMB
Marcus Kinsella, Vineet Bafna
2012 J jnl
Speeding up tandem mass spectral identification using indexes.
Bioinform.
Xiaowen Liu, Alessandro Mammana, Vineet Bafna
2012 J jnl
iDASH: integrating data for analysis, anonymization, and sharing.
J. Am. Medical Informatics Assoc.
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, Michael E. Matheny, Frederic S. Resnic, Staal Amund Vinterbo
2011 J jnl
Compressing Genomic Sequence Fragments Using SlimGene.
J. Comput. Biol.
Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese
2011 J jnl
On the Approximability of Reachability-Preserving Network Orientations.
Internet Math.
Michael Elberfeld, Vineet Bafna, Iftah Gamzu, Alexander Medvedovsky, Danny Segev, Dana Silverbush, Uri Zwick, Roded Sharan
2011 J jnl
Preface: Research in Computational Molecular Biology (RECOMB 2011).
J. Comput. Biol.
Vineet Bafna
2011 B ed.
Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings
RECOMB
Vineet Bafna, Süleyman Cenk Sahinalp
2011 J jnl
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Bioinform.
Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna
2011 J jnl
Strobe sequence design for haplotype assembly.
BMC Bioinform.
Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna
2011 J jnl
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Banu Dost, Chunlei Wu, Andrew I. Su, Vineet Bafna
2010 J jnl
A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes.
PLoS Comput. Biol.
Gaurav Bhatia, Vikas Bansal, Olivier Harismendy, Nicholas J. Schork, Eric J. Topol, Kelly A. Frazer, Vineet Bafna
2010 B conf
Compressing Genomic Sequence Fragments Using SlimGene.
RECOMB
Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese
2010 J jnl
Optimizing PCR Assays for DNA-Based Cancer Diagnostics.
J. Comput. Biol.
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
2010 J jnl
Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets.
J. Comput. Biol.
Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp
2010 J jnl
RAPID detection of gene-gene interactions in genome-wide association studies.
Bioinform.
Dumitru Brinza, Matthew Schultz, Glenn Tesler, Vineet Bafna
2009 J jnl
Fast and Accurate Alignment of Multiple Protein Networks.
J. Comput. Biol.
Maxim Kalaev, Vineet Bafna, Roded Sharan
2009 B conf
Optimizing PCR Assays for DNA Based Cancer Diagnostics.
RECOMB
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
2009 B conf
Shared Peptides in Mass Spectrometry Based Protein Quantification.
RECOMB
Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna
2008 C conf
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks.
WABI
Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan
2008 J jnl
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.
PLoS Comput. Biol.
Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael
2008 B conf
Fast and Accurate Alignment of Multiple Protein Networks.
RECOMB
Maxim Kalaev, Vineet Bafna, Roded Sharan
2008 C conf
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.
ECCB
Vikas Bansal, Vineet Bafna
2008 J jnl
QNet: A Tool for Querying Protein Interaction Networks.
J. Comput. Biol.
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
2008 J jnl
Structural Alignment of Pseudoknotted RNA.
J. Comput. Biol.
Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang
2007 J jnl
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters.
J. Comput. Biol.
Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song
2007 J jnl
Optimization of primer design for the detection of variable genomic lesions in cancer.
Bioinform.
Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna
2007 B conf
QNet: A Tool for Querying Protein Interaction Networks.
RECOMB
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
2007 — ed.
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
Systems Biology and Computational Proteomics
Trey Ideker, Vineet Bafna
2006 — conf
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.
ISMB (Supplement of Bioinformatics)
Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna
2006 J jnl
Consensus Folding of Unaligned RNA Sequences Revisited.
J. Comput. Biol.
Vineet Bafna, Haixu Tang, Shaojie Zhang
2006 J jnl
Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots.
J. Comput. Biol.
Vineet Bafna, Vikas Bansal
2006 B conf
Structural Alignment of Pseudoknotted RNA.
RECOMB
Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna
2005 B conf
Consensus Folding of Unaligned RNA Sequences Revisited.
RECOMB
Vineet Bafna, Haixu Tang, Shaojie Zhang
2005 — conf
Identification of Post-Translational Modifications via Blind Search of Mass-Spectra.
CSB
Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner
2005 B conf
Improved Recombination Lower Bounds for Haplotype Data.
RECOMB
Vineet Bafna, Vikas Bansal
2005 J jnl
Polynomial and APX-hard cases of the individual haplotyping problem.
Theor. Comput. Sci.
Vineet Bafna, Sorin Istrail, Giuseppe Lancia, Romeo Rizzi
2005 J jnl
Searching Genomes for Noncoding RNA Using FastR.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna
2004 J jnl
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny.
J. Comput. Biol.
Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph
2004 — conf
FastR: Fast Database Search Tool for Non-Coding RNA.
CSB
Vineet Bafna, Shaojie Zhang
2004 J jnl
The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds.
IEEE ACM Trans. Comput. Biol. Bioinform.
Vineet Bafna, Vikas Bansal
2003 — conf
Combinatorial Problems Arising in SNP and Haplotype Analysis.
DMTCS
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
2003 B conf
Haplotypes and informative SNP selection algorithms: don't block out information.
RECOMB
Vineet Bafna, Bjarni V. Halldórsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail
2003 J jnl
Haplotyping as Perfect Phylogeny: A Direct Approach.
J. Comput. Biol.
Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph
2003 B conf
On de novo interpretation of tandem mass spectra for peptide identification.
RECOMB
Vineet Bafna, Nathan Edwards
2003 J jnl
Robustness of Inference of Haplotype Block Structure.
J. Comput. Biol.
Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail
2002 — conf
A Survey of Computational Methods for Determining Haplotypes.
Computational Methods for SNPs and Haplotype Inference
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
2002 C conf
Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem.
WABI
Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia
2001 — conf
SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.
ISMB (Supplement of Bioinformatics)
Vineet Bafna, Nathan Edwards
2001 A conf
SNPs Problems, Complexity, and Algorithms.
ESA
Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz
2000 J jnl
Ligand-Receptor Pairing Via Tree Comparison.
J. Comput. Biol.
Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter
2000 A conf
The Conserved Exon Method for Gene Finding.
ISMB
Vineet Bafna, Daniel H. Huson
1999 J jnl
A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem.
SIAM J. Discret. Math.
Vineet Bafna, Piotr Berman, Toshihiro Fujito
1999 J jnl
A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees.
SIAM J. Comput.
Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, Kun-Mao Chao, R. Ravi, Chuan Yi Tang
1999 J jnl
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics).
SIAM J. Comput.
Richa Agarwala, Vineet Bafna, Martin Farach, Mike Paterson, Mikkel Thorup
1998 A* conf
A Polynomial Time Approximation Scheme for Minimum Routing Cost Spanning Trees.
SODA
Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, Kun-Mao Chao, R. Ravi, Chuan Yi Tang
1998 B conf
Detecting non-adjoining correlations with signals in DNA.
RECOMB
Pankaj Agarwal, Vineet Bafna
1998 J jnl
Sorting by Transpositions.
SIAM J. Discret. Math.
Vineet Bafna, Pavel A. Pevzner
1998 A conf
The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection.
ISMB
Pankaj Agarwal, Vineet Bafna
1997 J jnl
Approximation Algorithms for Multiple Sequence Alignment.
Theor. Comput. Sci.
Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner
1996 J jnl
Genome Rearrangements and Sorting by Reversals.
SIAM J. Comput.
Vineet Bafna, Pavel A. Pevzner
1996 J jnl
Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles).
Discret. Appl. Math.
Vineet Bafna, Babu O. Narayanan, R. Ravi
1996 A* conf
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics).
SODA
Richa Agarwala, Vineet Bafna, Martin Farach, Babu O. Narayanan, Mike Paterson, Mikkel Thorup
1995 B conf
Computing Similarity between RNA Strings.
CPM
Vineet Bafna, S. Muthukrishnan, R. Ravi
1995 B conf
Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs.
ISAAC
Vineet Bafna, Piotr Berman, Toshihiro Fujito
1995 B conf
Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles).
WADS
Vineet Bafna, Babu O. Narayanan, R. Ravi
1995 A* conf
Sorting Permutations by Transpositions.
SODA
Vineet Bafna, Pavel A. Pevzner
1994 B conf
Approximation Algorithms for Multiple Sequence Alignment.
CPM
Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner
1994 J jnl
Not All Insertion Methods Yield Constant Approximate Tours in the Euclidean Plane.
Theor. Comput. Sci.
Vineet Bafna, Bala Kalyanasundaram, Kirk Pruhs
1993 A* conf
Genome Rearrangements and Sorting by Reversals
FOCS
Vineet Bafna, Pavel A. Pevzner
1990 — conf
Parallel Implementation of Logic Languages.
CONPAR
Amit Gupta, Anindo Banerjea, Vikas Jha, Vineet Bafna, P. C. P. Bhatt