Vineet Bafna

Sangwoo Kim, Kyowon Jeong, Vineet Bafna: Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics 29(8): 1076-1077 (2013)

Vineet Bafna, Alin Deutsch, Andrew Heiberg, Christos Kozanitis, Lucila Ohno-Machado, George Varghese: Abstractions for genomics. Commun. ACM 56(1): 83-93 (2013)

Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna: Learning Natural Selection from the Site Frequency Spectrum. RECOMB 2013: 230-233

Xiaowen Liu, Alessandro Mammana, Vineet Bafna: Speeding up tandem mass spectral identification using indexes. Bioinformatics 28(13): 1692-1697 (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. JAMIA 19(2): 196-201 (2012)

Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna: Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. Journal of Computational Biology 19(4): 337-348 (2012)

Marcus Kinsella, Vineet Bafna: Combinatorics of the Breakage-Fusion-Bridge Mechanism. Journal of Computational Biology 19(6): 662-678 (2012)

Marcus Kinsella, Vineet Bafna: Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. RECOMB 2012: 148-162

Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna: Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics 27(8): 1068-1075 (2011)

Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna: Strobe sequence design for haplotype assembly. BMC Bioinformatics 12(S-1): S24 (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 Mathematics 7(4): 209-232 (2011)

Christos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese: Compressing Genomic Sequence Fragments Using SlimGene. Journal of Computational Biology 18(3): 401-413 (2011)

Vineet Bafna: Preface: Research in Computational Molecular Biology (RECOMB 2011). Journal of Computational Biology 18(11): 1369 (2011)

Banu Dost, Chunlei Wu, Andrew I. Su, Vineet Bafna: TCLUST: A Fast Method for Clustering Genome-Scale Expression Data. IEEE/ACM Trans. Comput. Biology Bioinform. 8(3): 808-818 (2011)

Vineet Bafna, Süleyman Cenk Sahinalp (Eds.): Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings. Lecture Notes in Computer Science 6577, Springer 2011, isbn 978-3-642-20035-9

Dumitru Brinza, Matthew Schultz, Glenn Tesler, Vineet Bafna: RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics 26(22): 2856-2862 (2010)

Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna: Optimizing PCR Assays for DNA-Based Cancer Diagnostics. Journal of Computational Biology 17(3): 369-381 (2010)

Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp: Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. Journal of Computational Biology 17(5): 669-684 (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 Computational Biology 6(10) (2010)

Christos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese: Compressing Genomic Sequence Fragments Using SlimGene. RECOMB 2010: 310-324

Maxim Kalaev, Vineet Bafna, Roded Sharan: Fast and Accurate Alignment of Multiple Protein Networks. Journal of Computational Biology 16(8): 989-999 (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: 220-235

Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna: Shared Peptides in Mass Spectrometry Based Protein Quantification. RECOMB 2009: 356-371

Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang: Structural Alignment of Pseudoknotted RNA. Journal of Computational Biology 15(5): 489-504 (2008)

Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan: QNet: A Tool for Querying Protein Interaction Networks. Journal of Computational Biology 15(7): 913-925 (2008)

Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, Benjamin J. Raphael: Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLoS Computational Biology 4(4) (2008)

Vikas Bansal, Vineet Bafna: HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. ECCB 2008: 153-159

Maxim Kalaev, Vineet Bafna, Roded Sharan: Fast and Accurate Alignment of Multiple Protein Networks. RECOMB 2008: 246-256

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: 222-232

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. Bioinformatics 23(21): 2807-2815 (2007)

Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song: A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. Journal of Computational Biology 14(10): 1247-1272 (2007)

Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan: QNet: A Tool for Querying Protein Interaction Networks. RECOMB 2007: 1-15

Trey Ideker, Vineet Bafna (Eds.): 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. Lecture Notes in Computer Science 4532, Springer 2007, isbn 978-3-540-73059-0

Vineet Bafna, Haixu Tang, Shaojie Zhang: Consensus Folding of Unaligned RNA Sequences Revisited. Journal of Computational Biology 13(2): 283-295 (2006)

Vineet Bafna, Vikas Bansal: Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots. Journal of Computational Biology 13(2): 501-521 (2006)

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: 557-565

Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna: Structural Alignment of Pseudoknotted RNA. RECOMB 2006: 143-158

Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna: Searching Genomes for Noncoding RNA Using FastR. IEEE/ACM Trans. Comput. Biology Bioinform. 2(4): 366-379 (2005)

Vineet Bafna, Sorin Istrail, Giuseppe Lancia, Romeo Rizzi: Polynomial and APX-hard cases of the individual haplotyping problem. Theor. Comput. Sci. 335(1): 109-125 (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: 157-166

Vineet Bafna, Haixu Tang, Shaojie Zhang: Consensus Folding of Unaligned RNA Sequences Revisited. RECOMB 2005: 172-187

Vineet Bafna, Vikas Bansal: Improved Recombination Lower Bounds for Haplotype Data. RECOMB 2005: 569-584

Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph: A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. Journal of Computational Biology 11(5): 858-866 (2004)

Vineet Bafna, Vikas Bansal: The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. IEEE/ACM Trans. Comput. Biology Bioinform. 1(2): 78-90 (2004)

Vineet Bafna, Shaojie Zhang: FastR: Fast Database Search Tool for Non-Coding RNA. CSB 2004: 52-61

Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail: Robustness of Inference of Haplotype Block Structure. Journal of Computational Biology 10(1): 13-19 (2003)

Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph: Haplotyping as Perfect Phylogeny: A Direct Approach. Journal of Computational Biology 10(3/4): 323-340 (2003)

Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail: Combinatorial Problems Arising in SNP and Haplotype Analysis. DMTCS 2003: 26-47

Vineet Bafna, Nathan Edwards: On de novo interpretation of tandem mass spectra for peptide identification. RECOMB 2003: 9-18

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: 19-27

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: 26-47

Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia: Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. WABI 2002: 29-43

Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz: SNPs Problems, Complexity, and Algorithms. ESA 2001: 182-193

Vineet Bafna, Nathan Edwards: SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. ISMB (Supplement of Bioinformatics) 2001: 13-21

Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter: Ligand-Receptor Pairing Via Tree Comparison. Journal of Computational Biology 7(1-2): 59-70 (2000)

Vineet Bafna, Daniel H. Huson: The Conserved Exon Method for Gene Finding. ISMB 2000: 3-12

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): 1073-1085 (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): 761-778 (1999)

Vineet Bafna, Piotr Berman, Toshihiro Fujito: A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem. SIAM J. Discrete Math. 12(3): 289-297 (1999)

Vineet Bafna, Pavel A. Pevzner: Sorting by Transpositions. SIAM J. Discrete Math. 11(2): 224-240 (1998)

Pankaj Agarwal, Vineet Bafna: The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection. ISMB 1998: 2-7

Pankaj Agarwal, Vineet Bafna: Detecting non-adjoining correlations with signals in DNA. RECOMB 1998: 2-8

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: 21-32

Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner: Approximation Algorithms for Multiple Sequence Alignment. Theor. Comput. Sci. 182(1-2): 233-244 (1997)

Vineet Bafna, Babu O. Narayanan, R. Ravi: Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles). Discrete Applied Mathematics 71(1-3): 41-53 (1996)

Vineet Bafna, Pavel A. Pevzner: Genome Rearrangements and Sorting by Reversals. SIAM J. Comput. 25(2): 272-289 (1996)

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: 365-372

Vineet Bafna, S. Muthukrishnan, R. Ravi: Computing Similarity between RNA Strings. CPM 1995: 1-16

Vineet Bafna, Piotr Berman, Toshihiro Fujito: Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs. ISAAC 1995: 142-151

Vineet Bafna, Pavel A. Pevzner: Sorting Permutations by Transpositions. SODA 1995: 614-623

Vineet Bafna, Babu O. Narayanan, R. Ravi: Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles). WADS 1995: 506-517

Vineet Bafna, Bala Kalyanasundaram, Kirk Pruhs: Not All Insertion Methods Yield Constant Approximate Tours in the Euclidean Plane. Theor. Comput. Sci. 125(2): 345-360 (1994)

Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner: Approximation Algorithms for Multiple Sequence Alignment. CPM 1994: 43-53

Vineet Bafna, Pavel A. Pevzner: Genome Rearrangements and Sorting by Reversals. FOCS 1993: 148-157

Amit Gupta, Anindo Banerjea, Vikas Jha, Vineet Bafna, P. C. P. Bhatt: Parallel Implementation of Logic Languages. CONPAR 1990: 154-165