| 2025 | RECOMB | OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional Disorders. | Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Gleray-Lafci, Jrgen Neesen, Alex Hastie, Andy Wing Chun Pang, Paul Dremsek, Vineet Bafna |
| 2024 | RECOMB | 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 |
| 2022 | RECOMB | Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. | Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab |
| 2019 | RECOMB | A Note on Computing Interval Overlap Statistics. | Shahab Sarmashghi, Vineet Bafna |
| 2018 | RECOMB | Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR. | Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna |
| 2018 | RECOMB | Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. | Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab |
| 2015 | RECOMB | 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 |
| 2014 | RECOMB | Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. | Shay Zakov, Vineet Bafna |
| 2013 | RECOMB | Learning Natural Selection from the Site Frequency Spectrum. | Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna |
| 2013 | WABI | Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. | Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna |
| 2012 | RECOMB | Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. | Marcus Kinsella, Vineet Bafna |
| 2010 | RECOMB | Compressing Genomic Sequence Fragments Using SlimGene. | Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese |
| 2009 | RECOMB | Optimizing PCR Assays for DNA Based Cancer Diagnostics. | Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna |
| 2009 | RECOMB | Shared Peptides in Mass Spectrometry Based Protein Quantification. | Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna |
| 2008 | ECCB | HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. | Vikas Bansal, Vineet Bafna |
| 2008 | RECOMB | Fast and Accurate Alignment of Multiple Protein Networks. | Maxim Kalaev, Vineet Bafna, Roded Sharan |
| 2008 | WABI | 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 |
| 2007 | RECOMB | QNet: A Tool for Querying Protein Interaction Networks. | Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan |
| 2006 | ISMB | 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 |
| 2006 | RECOMB | Structural Alignment of Pseudoknotted RNA. | Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna |
| 2005 | RECOMB | Improved Recombination Lower Bounds for Haplotype Data. | Vineet Bafna, Vikas Bansal |
| 2005 | RECOMB | Consensus Folding of Unaligned RNA Sequences Revisited. | Vineet Bafna, Haixu Tang, Shaojie Zhang |
| 2003 | RECOMB | On de novo interpretation of tandem mass spectra for peptide identification. | Vineet Bafna, Nathan Edwards |
| 2003 | RECOMB | Haplotypes and informative SNP selection algorithms: don't block out information. | Vineet Bafna, Bjarni V. Halldrsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail |
| 2002 | RECOMB | A Survey of Computational Methods for Determining Haplotypes. | Bjarni V. Halldrsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail |
| 2002 | WABI | Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. | Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia |
| 2001 | ESA | SNPs Problems, Complexity, and Algorithms. | Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz |
| 2001 | ISMB | SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. | Vineet Bafna, Nathan Edwards |
| 2000 | ISMB | The Conserved Exon Method for Gene Finding. | Vineet Bafna, Daniel H. Huson |
| 1998 | ISMB | The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection. | Pankaj Agarwal, Vineet Bafna |
| 1998 | RECOMB | Detecting non-adjoining correlations with signals in DNA. | Pankaj Agarwal, Vineet Bafna |
| 1998 | SODA | 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 |
| 1996 | SODA | On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics). | Richa Agarwala, Vineet Bafna, Martin Farach, Babu O. Narayanan, Mike Paterson, Mikkel Thorup |
| 1995 | CPM | Computing Similarity between RNA Strings. | Vineet Bafna, S. Muthukrishnan, R. Ravi |
| 1995 | ISAAC | Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs. | Vineet Bafna, Piotr Berman, Toshihiro Fujito |
| 1995 | SODA | Sorting Permutations by Transpositions. | Vineet Bafna, Pavel A. Pevzner |
| 1995 | WADS | Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles). | Vineet Bafna, Babu O. Narayanan, R. Ravi |
| 1994 | CPM | Approximation Algorithms for Multiple Sequence Alignment. | Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner |
| 1993 | FOCS | Genome Rearrangements and Sorting by Reversals | Vineet Bafna, Pavel A. Pevzner |