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ORCIDVineet Bafna
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- affiliation: University of California, San Diego, USA
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2020 – today
- 2024
[c44]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: 454-457- 2022
- [c43]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: 2:1-2:8 - [c42]Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab:
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. RECOMB 2022: 366-368 - 2021
- [j46]Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna:
FaNDOM: Fast nested distance-based seeding of optical maps. Patterns 2(5): 100248 (2021) - [j45]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) - [c41]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: 35:1-35:7
2010 – 2019
- 2019
- [c40]Shahab Sarmashghi, Vineet Bafna:
A Note on Computing Interval Overlap Statistics. RECOMB 2019: 314-315 - 2018
- [c39]Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna:
Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR. RECOMB 2018: 243-244 - [c38]Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab:
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. RECOMB 2018: 276-277 - 2015
- [j44]Shay Zakov, Vineet Bafna:
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. J. Comput. Biol. 22(6): 577-594 (2015) - [c37]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: 276-280 - 2014
- [j43]Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna:
Using Genome Query Language to uncover genetic variation. Bioinform. 30(1): 1-8 (2014) - [j42]Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker:
Inferring gene ontologies from pairwise similarity data. Bioinform. 30(12): 34-42 (2014) - [c36]Shay Zakov, Vineet Bafna:
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. RECOMB 2014: 400-417 - 2013
- [j41]Sangwoo Kim, Kyowon Jeong, Vineet Bafna:
Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinform. 29(8): 1076-1077 (2013) - [j40]Christine Lo, Sangwoo Kim, Shay Zakov, Vineet Bafna:
Evaluating genome architecture of a complex region via generalized bipartite matching. BMC Bioinform. 14(S-5): S13 (2013) - [j39]Vineet Bafna, Alin Deutsch, Andrew Heiberg, Christos Kozanitis, Lucila Ohno-Machado, George Varghese:
Abstractions for genomics. Commun. ACM 56(1): 83-93 (2013) - [j38]Shay Zakov, Marcus Kinsella, Vineet Bafna:
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc. Natl. Acad. Sci. USA 110(14): 5546-5551 (2013) - [c35]Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna:
Learning Natural Selection from the Site Frequency Spectrum. RECOMB 2013: 230-233 - [c34]Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna:
Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. WABI 2013: 349-363 - 2012
- [j37]Xiaowen Liu, Alessandro Mammana, Vineet Bafna:
Speeding up tandem mass spectral identification using indexes. Bioinform. 28(13): 1692-1697 (2012) - [j36]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:
iDASH: integrating data for analysis, anonymization, and sharing. J. Am. Medical Informatics Assoc. 19(2): 196-201 (2012) - [j35]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): 337-348 (2012) - [j34]Marcus Kinsella, Vineet Bafna:
Combinatorics of the Breakage-Fusion-Bridge Mechanism. J. Comput. Biol. 19(6): 662-678 (2012) - [c33]Marcus Kinsella, Vineet Bafna:
Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. RECOMB 2012: 148-162 - 2011
- [j33]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): 1068-1075 (2011) - [j32]Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna:
Strobe sequence design for haplotype assembly. BMC Bioinform. 12(S-1): S24 (2011) - [j31]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): 209-232 (2011) - [j30]Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese:
Compressing Genomic Sequence Fragments Using SlimGene. J. Comput. Biol. 18(3): 401-413 (2011) - [j29]Vineet Bafna:
Preface: Research in Computational Molecular Biology (RECOMB 2011). J. Comput. Biol. 18(11): 1369 (2011) - [j28]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): 808-818 (2011) - [e2]Vineet Bafna, Süleyman Cenk Sahinalp:
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 [contents] - 2010
- [j27]Dumitru Brinza, Matthew Schultz, Glenn Tesler, Vineet Bafna:
RAPID detection of gene-gene interactions in genome-wide association studies. Bioinform. 26(22): 2856-2862 (2010) - [j26]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): 369-381 (2010) - [j25]Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp:
Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. J. Comput. Biol. 17(5): 669-684 (2010) - [j24]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) - [c32]Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese:
Compressing Genomic Sequence Fragments Using SlimGene. RECOMB 2010: 310-324
2000 – 2009
- 2009
- [j23]Maxim Kalaev, Vineet Bafna, Roded Sharan:
Fast and Accurate Alignment of Multiple Protein Networks. J. Comput. Biol. 16(8): 989-999 (2009) - [c31]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 - [c30]Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna:
Shared Peptides in Mass Spectrometry Based Protein Quantification. RECOMB 2009: 356-371 - 2008
- [j22]Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang:
Structural Alignment of Pseudoknotted RNA. J. Comput. Biol. 15(5): 489-504 (2008) - [j21]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): 913-925 (2008) - [j20]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) - [c29]Vikas Bansal, Vineet Bafna:
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. ECCB 2008: 153-159 - [c28]Maxim Kalaev, Vineet Bafna, Roded Sharan:
Fast and Accurate Alignment of Multiple Protein Networks. RECOMB 2008: 246-256 - [c27]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 - 2007
- [j19]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): 2807-2815 (2007) - [j18]Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song:
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. 14(10): 1247-1272 (2007) - [c26]Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks. RECOMB 2007: 1-15 - [e1]Trey Ideker, Vineet Bafna:
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 [contents] - 2006
- [j17]Vineet Bafna, Haixu Tang, Shaojie Zhang:
Consensus Folding of Unaligned RNA Sequences Revisited. J. Comput. Biol. 13(2): 283-295 (2006) - [j16]Vineet Bafna, Vikas Bansal:
Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots. J. Comput. Biol. 13(2): 501-521 (2006) - [c25]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 - [c24]Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna:
Structural Alignment of Pseudoknotted RNA. RECOMB 2006: 143-158 - 2005
- [j15]Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna:
Searching Genomes for Noncoding RNA Using FastR. IEEE ACM Trans. Comput. Biol. Bioinform. 2(4): 366-379 (2005) - [j14]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) - [c23]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 - [c22]Vineet Bafna, Haixu Tang, Shaojie Zhang:
Consensus Folding of Unaligned RNA Sequences Revisited. RECOMB 2005: 172-187 - [c21]Vineet Bafna, Vikas Bansal:
Improved Recombination Lower Bounds for Haplotype Data. RECOMB 2005: 569-584 - 2004
- [j13]Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph:
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. J. Comput. Biol. 11(5): 858-866 (2004) - [j12]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): 78-90 (2004) - [c20]Vineet Bafna, Shaojie Zhang:
FastR: Fast Database Search Tool for Non-Coding RNA. CSB 2004: 52-61 - 2003
- [j11]Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail:
Robustness of Inference of Haplotype Block Structure. J. Comput. Biol. 10(1): 13-19 (2003) - [j10]Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph:
Haplotyping as Perfect Phylogeny: A Direct Approach. J. Comput. Biol. 10(3/4): 323-340 (2003) - [c19]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 - [c18]Vineet Bafna, Nathan Edwards:
On de novo interpretation of tandem mass spectra for peptide identification. RECOMB 2003: 9-18 - [c17]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 - 2002
- [c16]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 - [c15]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 - 2001
- [c14]Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz:
SNPs Problems, Complexity, and Algorithms. ESA 2001: 182-193 - [c13]Vineet Bafna, Nathan Edwards:
SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. ISMB (Supplement of Bioinformatics) 2001: 13-21 - 2000
- [j9]Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter:
Ligand-Receptor Pairing Via Tree Comparison. J. Comput. Biol. 7(1-2): 59-70 (2000) - [c12]Vineet Bafna, Daniel H. Huson:
The Conserved Exon Method for Gene Finding. ISMB 2000: 3-12
1990 – 1999
- 1999
- [j8]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) - [j7]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) - [j6]Vineet Bafna, Piotr Berman, Toshihiro Fujito:
A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem. SIAM J. Discret. Math. 12(3): 289-297 (1999) - 1998
- [j5]Vineet Bafna, Pavel A. Pevzner:
Sorting by Transpositions. SIAM J. Discret. Math. 11(2): 224-240 (1998) - [c11]Pankaj Agarwal, Vineet Bafna:
The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection. ISMB 1998: 2-7 - [c10]Pankaj Agarwal, Vineet Bafna:
Detecting non-adjoining correlations with signals in DNA. RECOMB 1998: 2-8 - [c9]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 - 1997
- [j4]Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner:
Approximation Algorithms for Multiple Sequence Alignment. Theor. Comput. Sci. 182(1-2): 233-244 (1997) - 1996
- [j3]Vineet Bafna, Babu O. Narayanan, R. Ravi:
Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles). Discret. Appl. Math. 71(1-3): 41-53 (1996) - [j2]Vineet Bafna, Pavel A. Pevzner:
Genome Rearrangements and Sorting by Reversals. SIAM J. Comput. 25(2): 272-289 (1996) - [c8]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 - 1995
- [c7]Vineet Bafna, S. Muthukrishnan, R. Ravi:
Computing Similarity between RNA Strings. CPM 1995: 1-16 - [c6]Vineet Bafna, Piotr Berman, Toshihiro Fujito:
Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs. ISAAC 1995: 142-151 - [c5]Vineet Bafna, Pavel A. Pevzner:
Sorting Permutations by Transpositions. SODA 1995: 614-623 - [c4]Vineet Bafna, Babu O. Narayanan, R. Ravi:
Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles). WADS 1995: 506-517 - 1994
- [j1]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) - [c3]Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner:
Approximation Algorithms for Multiple Sequence Alignment. CPM 1994: 43-53 - 1993
- [c2]Vineet Bafna, Pavel A. Pevzner:
Genome Rearrangements and Sorting by Reversals. FOCS 1993: 148-157 - 1990
- [c1]Amit Gupta, Anindo Banerjea, Vikas Jha, Vineet Bafna, P. C. P. Bhatt:
Parallel Implementation of Logic Languages. CONPAR 1990: 154-165
Coauthor Index
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