Vineet Bafna

Publication Activity (10 Years)

Years Active: 1990-2024
Publications (10 Years): 11

Top Topics

Genetic Variation

Top Venues

J. Comput. Biol.

Publications

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
CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing. RECOMB (2024)
Utkrisht Rajkumar, Sara Javadzadeh, Mihir Bafna, Dongxia Wu, Rose Yu, Jingbo Shang, Vineet Bafna
DeepViFi: detecting oncoviral infections in cancer genomes using transformers. BCB (2022)
Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. RECOMB (2022)
Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PLoS Comput. Biol. 17 (11) (2021)
Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna
FaNDOM: Fast nested distance-based seeding of optical maps. Patterns 2 (5) (2021)
Kenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Vineet Bafna, Hideo Matsuda
A CNN-based cell tracking method for multi-slice intravital imaging data. BCB (2021)
Shahab Sarmashghi, Vineet Bafna
A Note on Computing Interval Overlap Statistics. RECOMB (2019)
Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna
Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR. RECOMB (2018)
Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. RECOMB (2018)
Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, Vineet Bafna
Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele. RECOMB (2015)
Shay Zakov, Vineet Bafna
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. J. Comput. Biol. 22 (6) (2015)
Shay Zakov, Vineet Bafna
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. RECOMB (2014)
Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna
Using Genome Query Language to uncover genetic variation. Bioinform. 30 (1) (2014)
Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker
Inferring gene ontologies from pairwise similarity data. Bioinform. 30 (12) (2014)
Sangwoo Kim, Kyowon Jeong, Vineet Bafna
exome capture. Bioinform. 29 (8) (2013)
Shay Zakov, Marcus Kinsella, Vineet Bafna
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc. Natl. Acad. Sci. USA 110 (14) (2013)
Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna
Learning Natural Selection from the Site Frequency Spectrum. RECOMB (2013)
Vineet Bafna, Alin Deutsch, Andrew Heiberg, Christos Kozanitis, Lucila Ohno-Machado, George Varghese
Abstractions for genomics. Commun. ACM 56 (1) (2013)
Christine Lo, Sangwoo Kim, Shay Zakov, Vineet Bafna
Evaluating genome architecture of a complex region via generalized bipartite matching. BMC Bioinform. 14 (S-5) (2013)
Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna
Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. WABI (2013)
Marcus Kinsella, Vineet Bafna
Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. RECOMB (2012)
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 A. Vinterbo
iDASH: integrating data for analysis, anonymization, and sharing. J. Am. Medical Informatics Assoc. 19 (2) (2012)
Xiaowen Liu, Alessandro Mammana, Vineet Bafna
Speeding up tandem mass spectral identification using indexes. Bioinform. 28 (13) (2012)
Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna
Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. J. Comput. Biol. 19 (4) (2012)
Marcus Kinsella, Vineet Bafna
Combinatorics of the Breakage-Fusion-Bridge Mechanism. J. Comput. Biol. 19 (6) (2012)
Vineet Bafna
Preface: Research in Computational Molecular Biology (RECOMB 2011). J. Comput. Biol. 18 (11) (2011)
Michael Elberfeld, Vineet Bafna, Iftah Gamzu, Alexander Medvedovsky, Danny Segev, Dana Silverbush, Uri Zwick, Roded Sharan
On the Approximability of Reachability-Preserving Network Orientations. Internet Math. 7 (4) (2011)
Banu Dost, Chunlei Wu, Andrew I. Su, Vineet Bafna
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna
Strobe sequence design for haplotype assembly. BMC Bioinform. 12 (S-1) (2011)
Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinform. 27 (8) (2011)
Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese
Compressing Genomic Sequence Fragments Using SlimGene. J. Comput. Biol. 18 (3) (2011)
Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese
Compressing Genomic Sequence Fragments Using SlimGene. RECOMB (2010)
Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp
Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. J. Comput. Biol. 17 (5) (2010)
Dumitru Brinza, Matthew Schultz, Glenn Tesler, Vineet Bafna
RAPID detection of gene-gene interactions in genome-wide association studies. Bioinform. 26 (22) (2010)
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
Optimizing PCR Assays for DNA-Based Cancer Diagnostics. J. Comput. Biol. 17 (3) (2010)
Gaurav Bhatia, Vikas Bansal, Olivier Harismendy, Nicholas J. Schork, Eric J. Topol, Kelly A. Frazer, Vineet Bafna
A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes. PLoS Comput. Biol. 6 (10) (2010)
Maxim Kalaev, Vineet Bafna, Roded Sharan
Fast and Accurate Alignment of Multiple Protein Networks. J. Comput. Biol. 16 (8) (2009)
Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna
Shared Peptides in Mass Spectrometry Based Protein Quantification. RECOMB (2009)
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
Optimizing PCR Assays for DNA Based Cancer Diagnostics. RECOMB (2009)
Maxim Kalaev, Vineet Bafna, Roded Sharan
Fast and Accurate Alignment of Multiple Protein Networks. RECOMB (2008)
Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. WABI (2008)
Vikas Bansal, Vineet Bafna
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. ECCB (2008)
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
QNet: A Tool for Querying Protein Interaction Networks. J. Comput. Biol. 15 (7) (2008)
Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLoS Comput. Biol. 4 (4) (2008)
Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang
Structural Alignment of Pseudoknotted RNA. J. Comput. Biol. 15 (5) (2008)
Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. 14 (10) (2007)
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
QNet: A Tool for Querying Protein Interaction Networks. RECOMB (2007)
Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna
Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinform. 23 (21) (2007)
Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. ISMB (Supplement of Bioinformatics) (2006)
Vineet Bafna, Haixu Tang, Shaojie Zhang
Consensus Folding of Unaligned RNA Sequences Revisited. J. Comput. Biol. 13 (2) (2006)
Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna
Structural Alignment of Pseudoknotted RNA. RECOMB (2006)
Vineet Bafna, Vikas Bansal
Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots. J. Comput. Biol. 13 (2) (2006)
Vineet Bafna, Vikas Bansal
Improved Recombination Lower Bounds for Haplotype Data. RECOMB (2005)
Vineet Bafna, Sorin Istrail, Giuseppe Lancia, Romeo Rizzi
Polynomial and APX-hard cases of the individual haplotyping problem. Theor. Comput. Sci. 335 (1) (2005)
Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna
Searching Genomes for Noncoding RNA Using FastR. IEEE ACM Trans. Comput. Biol. Bioinform. 2 (4) (2005)
Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner
Identification of Post-Translational Modifications via Blind Search of Mass-Spectra. CSB (2005)
Vineet Bafna, Haixu Tang, Shaojie Zhang
Consensus Folding of Unaligned RNA Sequences Revisited. RECOMB (2005)
Vineet Bafna, Vikas Bansal
The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (2) (2004)
Vineet Bafna, Shaojie Zhang
FastR: Fast Database Search Tool for Non-Coding RNA. CSB (2004)
Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. J. Comput. Biol. 11 (5) (2004)
Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph
Haplotyping as Perfect Phylogeny: A Direct Approach. J. Comput. Biol. 10 (3/4) (2003)
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
Combinatorial Problems Arising in SNP and Haplotype Analysis. DMTCS (2003)
Vineet Bafna, Bjarni V. Halldórsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail
Haplotypes and informative SNP selection algorithms: don't block out information. RECOMB (2003)
Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail
Robustness of Inference of Haplotype Block Structure. J. Comput. Biol. 10 (1) (2003)
Vineet Bafna, Nathan Edwards
On de novo interpretation of tandem mass spectra for peptide identification. RECOMB (2003)
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
A Survey of Computational Methods for Determining Haplotypes. Computational Methods for SNPs and Haplotype Inference (2002)
Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia
Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. WABI (2002)
Vineet Bafna, Nathan Edwards
SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. ISMB (Supplement of Bioinformatics) (2001)
Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz
SNPs Problems, Complexity, and Algorithms. ESA (2001)
Vineet Bafna, Daniel H. Huson
The Conserved Exon Method for Gene Finding. ISMB (2000)
Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter
Ligand-Receptor Pairing Via Tree Comparison. J. Comput. Biol. 7 (1-2) (2000)
Vineet Bafna, Piotr Berman, Toshihiro Fujito
A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem. SIAM J. Discret. Math. 12 (3) (1999)
Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, Kun-Mao Chao, R. Ravi, Chuan Yi Tang
A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees. SIAM J. Comput. 29 (3) (1999)
Richa Agarwala, Vineet Bafna, Martin Farach, Mike Paterson, Mikkel Thorup
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). SIAM J. Comput. 28 (3) (1999)
Vineet Bafna, Pavel A. Pevzner
Sorting by Transpositions. SIAM J. Discret. Math. 11 (2) (1998)
Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, Kun-Mao Chao, R. Ravi, Chuan Yi Tang
A Polynomial Time Approximation Scheme for Minimum Routing Cost Spanning Trees. SODA (1998)
Pankaj Agarwal, Vineet Bafna
The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection. ISMB (1998)
Pankaj Agarwal, Vineet Bafna
Detecting non-adjoining correlations with signals in DNA. RECOMB (1998)
Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner
Approximation Algorithms for Multiple Sequence Alignment. Theor. Comput. Sci. 182 (1-2) (1997)
Richa Agarwala, Vineet Bafna, Martin Farach, Babu O. Narayanan, Mike Paterson, Mikkel Thorup
On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). SODA (1996)
Vineet Bafna, Pavel A. Pevzner
Genome Rearrangements and Sorting by Reversals. SIAM J. Comput. 25 (2) (1996)
Vineet Bafna, Babu O. Narayanan, R. Ravi
Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles). Discret. Appl. Math. 71 (1-3) (1996)
Vineet Bafna, Piotr Berman, Toshihiro Fujito
Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs. ISAAC (1995)
Vineet Bafna, S. Muthukrishnan, R. Ravi
Computing Similarity between RNA Strings. CPM (1995)
Vineet Bafna, Babu O. Narayanan, R. Ravi
Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles). WADS (1995)
Vineet Bafna, Pavel A. Pevzner
Sorting Permutations by Transpositions. SODA (1995)
Vineet Bafna, Bala Kalyanasundaram, Kirk Pruhs
Not All Insertion Methods Yield Constant Approximate Tours in the Euclidean Plane. Theor. Comput. Sci. 125 (2) (1994)
Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner
Approximation Algorithms for Multiple Sequence Alignment. CPM (1994)
Vineet Bafna, Pavel A. Pevzner
Genome Rearrangements and Sorting by Reversals FOCS (1993)
Amit Gupta, Anindo Banerjea, Vikas Jha, Vineet Bafna, P. C. P. Bhatt
Parallel Implementation of Logic Languages. CONPAR (1990)