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Vineet Bafna
Person information
- 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
![](https://dblp1.uni-trier.de/img/cog.dark.24x24.png)
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last updated on 2024-06-19 21:48 CEST by the dblp team
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