Vineet Bafna

According to our database, Vineet Bafna authored at least 80 papers between 1990 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing.

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

Proceedings of the Research in Computational Molecular Biology, 2024

2022

Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships.

Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab

Proceedings of the Research in Computational Molecular Biology, 2022

DeepViFi: detecting oncoviral infections in cancer genomes using transformers.

Utkrisht Rajkumar, Sara Javadzadeh, Mihir Bafna, Dongxia Wu, Rose Yu, Jingbo Shang, Vineet Bafna

Proceedings of the BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Northbrook, Illinois, USA, August 7, 2022

2021

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.

Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna

PLoS Comput. Biol., 2021

FaNDOM: Fast nested distance-based seeding of optical maps.

Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna

Patterns, 2021

A CNN-based cell tracking method for multi-slice intravital imaging data.

Kenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Vineet Bafna, Hideo Matsuda

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

2019

A Note on Computing Interval Overlap Statistics.

Shahab Sarmashghi, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2019

2018

Assembly-Free and Alignment-Free Sample Identification Using Genome Skims.

Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab

Proceedings of the Research in Computational Molecular Biology, 2018

Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR.

Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2018

2015

Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.

Shay Zakov, Vineet Bafna

J. Comput. Biol., 2015

Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele.

Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2015

2014

Inferring gene ontologies from pairwise similarity data.

Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker

Bioinform., 2014

Using Genome Query Language to uncover genetic variation.

Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna

Bioinform., 2014

2013

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes.

Shay Zakov, Marcus Kinsella, Vineet Bafna

Proc. Natl. Acad. Sci. USA, 2013

Abstractions for genomics.

Vineet Bafna, Alin Deutsch, Andrew Heiberg, Christos Kozanitis, Lucila Ohno-Machado, George Varghese

Commun. ACM, 2013

Evaluating genome architecture of a complex region via generalized bipartite matching.

Christine Lo, Sangwoo Kim, Shay Zakov, Vineet Bafna

BMC Bioinform., 2013

Wessim: a whole-exome sequencing simulator based on <i>in silico</i> exome capture.

Sangwoo Kim, Kyowon Jeong, Vineet Bafna

Bioinform., 2013

Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads.

Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Learning Natural Selection from the Site Frequency Spectrum.

Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2013

2012

Combinatorics of the Breakage-Fusion-Bridge Mechanism.

Marcus Kinsella, Vineet Bafna

J. Comput. Biol., 2012

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides.

Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna

J. Comput. Biol., 2012

iDASH: integrating data for analysis, anonymization, and sharing.

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

J. Am. Medical Informatics Assoc., 2012

Speeding up tandem mass spectral identification using indexes.

Xiaowen Liu, Alessandro Mammana, Vineet Bafna

Bioinform., 2012

Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics.

Marcus Kinsella, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2012

2011

TCLUST: A Fast Method for Clustering Genome-Scale Expression Data.

Banu Dost, Chunlei Wu, Andrew I. Su, Vineet Bafna

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Compressing Genomic Sequence Fragments Using SlimGene.

Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese

J. Comput. Biol., 2011

Preface: Research in Computational Molecular Biology (RECOMB 2011).

Vineet Bafna

J. Comput. Biol., 2011

On the Approximability of Reachability-Preserving Network Orientations.

Michael Elberfeld, Vineet Bafna, Iftah Gamzu, Alexander Medvedovsky, Danny Segev, Dana Silverbush, Uri Zwick, Roded Sharan

Internet Math., 2011

Strobe sequence design for haplotype assembly.

Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna

BMC Bioinform., 2011

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna

Bioinform., 2011

2010

A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes.

Gaurav Bhatia, Vikas Bansal, Olivier Harismendy, Nicholas J. Schork, Eric J. Topol, Kelly A. Frazer, Vineet Bafna

PLoS Comput. Biol., 2010

Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets.

Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp

J. Comput. Biol., 2010

Optimizing PCR Assays for DNA-Based Cancer Diagnostics.

Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna

J. Comput. Biol., 2010

RAPID detection of gene-gene interactions in genome-wide association studies.

Dumitru Brinza, Matthew Schultz, Glenn Tesler, Vineet Bafna

Bioinform., 2010

2009

Fast and Accurate Alignment of Multiple Protein Networks.

Maxim Kalaev, Vineet Bafna, Roded Sharan

J. Comput. Biol., 2009

Shared Peptides in Mass Spectrometry Based Protein Quantification.

Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2009

2008

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.

Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael

PLoS Comput. Biol., 2008

Structural Alignment of Pseudoknotted RNA.

Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang

J. Comput. Biol., 2008

QNet: A Tool for Querying Protein Interaction Networks.

Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan

J. Comput. Biol., 2008

An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks.

Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.

Vikas Bansal, Vineet Bafna

Proceedings of the ECCB'08 Proceedings, 2008

2007

A Decomposition Theory for Phylogenetic Networks and Incompatible Characters.

Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song

J. Comput. Biol., 2007

Optimization of primer design for the detection of variable genomic lesions in cancer.

Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna

Bioinform., 2007

2006

Consensus Folding of Unaligned RNA Sequences Revisited.

Vineet Bafna, Haixu Tang, Shaojie Zhang

J. Comput. Biol., 2006

Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots.

Vineet Bafna, Vikas Bansal

J. Comput. Biol., 2006

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Polynomial and APX-hard cases of the individual haplotyping problem.

Vineet Bafna, Sorin Istrail, Giuseppe Lancia, Romeo Rizzi

Theor. Comput. Sci., 2005

Searching Genomes for Noncoding RNA Using FastR.

Shaojie Zhang, Brian Haas, Eleazar Eskin, Vineet Bafna

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

Improved Recombination Lower Bounds for Haplotype Data.

Vineet Bafna, Vikas Bansal

Proceedings of the Research in Computational Molecular Biology, 2005

Identification of Post-Translational Modifications via Blind Search of Mass-Spectra.

Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004

The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds.

Vineet Bafna, Vikas Bansal

IEEE ACM Trans. Comput. Biol. Bioinform., 2004

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny.

Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph

J. Comput. Biol., 2004

FastR: Fast Database Search Tool for Non-Coding RNA.

Vineet Bafna, Shaojie Zhang

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003

Robustness of Inference of Haplotype Block Structure.

Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail

J. Comput. Biol., 2003

Haplotyping as Perfect Phylogeny: A Direct Approach.

Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph

J. Comput. Biol., 2003

Haplotypes and informative SNP selection algorithms: don't block out information.

Vineet Bafna, Bjarni V. Halldórsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

On de novo interpretation of tandem mass spectra for peptide identification.

Vineet Bafna, Nathan Edwards

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

Combinatorial Problems Arising in SNP and Haplotype Analysis.

Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail

Proceedings of the Discrete Mathematics and Theoretical Computer Science, 2003

2002

Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem.

Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

A Survey of Computational Methods for Determining Haplotypes.

Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail

Proceedings of the Computational Methods for SNPs and Haplotype Inference, 2002

2001

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.

Vineet Bafna, Nathan Edwards

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

SNPs Problems, Complexity, and Algorithms.

Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz

Proceedings of the Algorithms, 2001

2000

Ligand-Receptor Pairing Via Tree Comparison.

Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter

J. Comput. Biol., 2000

The Conserved Exon Method for Gene Finding.

Vineet Bafna, Daniel H. Huson

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999

A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem.

Vineet Bafna, Piotr Berman, Toshihiro Fujito

SIAM J. Discret. Math., 1999

A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees.

Bang Ye Wu, Giuseppe Lancia, Vineet Bafna, Kun-Mao Chao, R. Ravi, Chuan Yi Tang

SIAM J. Comput., 1999

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics).

Richa Agarwala, Vineet Bafna, Martin Farach, Mike Paterson, Mikkel Thorup

SIAM J. Comput., 1999

1998

Sorting by Transpositions.

Vineet Bafna, Pavel A. Pevzner

SIAM J. Discret. Math., 1998

Detecting non-adjoining correlations with signals in DNA.

Pankaj Agarwal, Vineet Bafna

Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection.

Pankaj Agarwal, Vineet Bafna

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

1997

Approximation Algorithms for Multiple Sequence Alignment.

Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner

Theor. Comput. Sci., 1997

1996

Genome Rearrangements and Sorting by Reversals.

Vineet Bafna, Pavel A. Pevzner

SIAM J. Comput., 1996

Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles).

Vineet Bafna, Babu O. Narayanan, R. Ravi

Discret. Appl. Math., 1996

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics).

Richa Agarwala, Vineet Bafna, Martin Farach, Babu O. Narayanan, Mike Paterson, Mikkel Thorup

Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, 1996

1995

Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles).

Vineet Bafna, Babu O. Narayanan, R. Ravi

Proceedings of the Algorithms and Data Structures, 4th International Workshop, 1995

Sorting Permutations by Transpositions.

Vineet Bafna, Pavel A. Pevzner

Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 1995

Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs.

Vineet Bafna, Piotr Berman, Toshihiro Fujito

Proceedings of the Algorithms and Computation, 6th International Symposium, 1995

Computing Similarity between RNA Strings.

Vineet Bafna, S. Muthukrishnan, R. Ravi

Proceedings of the Combinatorial Pattern Matching, 6th Annual Symposium, 1995

1994

Not All Insertion Methods Yield Constant Approximate Tours in the Euclidean Plane.

Vineet Bafna, Bala Kalyanasundaram, Kirk Pruhs

Theor. Comput. Sci., 1994

1990

Parallel Implementation of Logic Languages.

Amit Gupta, Anindo Banerjea, Vikas Jha, Vineet Bafna, P. C. P. Bhatt

Proceedings of the CONPAR 90, 1990