Vineet Bafna

According to our database1, Vineet Bafna authored at least 82 papers between 1990 and 2018.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

Homepages:

On csauthors.net:

Bibliography

2018
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims.
Proceedings of the Research in Computational Molecular Biology, 2018

Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR.
Proceedings of the Research in Computational Molecular Biology, 2018

2015
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.
Journal of Computational Biology, 2015

Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele.
Proceedings of the Research in Computational Molecular Biology, 2015

2014
Inferring gene ontologies from pairwise similarity data.
Bioinformatics, 2014

Using Genome Query Language to uncover genetic variation.
Bioinformatics, 2014

Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers.
Proceedings of the Research in Computational Molecular Biology, 2014

2013
Abstractions for genomics.
Commun. ACM, 2013

Evaluating genome architecture of a complex region via generalized bipartite matching.
BMC Bioinformatics, 2013

Wessim: a whole-exome sequencing simulator based on in silico exome capture.
Bioinformatics, 2013

Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Learning Natural Selection from the Site Frequency Spectrum.
Proceedings of the Research in Computational Molecular Biology, 2013

2012
Combinatorics of the Breakage-Fusion-Bridge Mechanism.
Journal of Computational Biology, 2012

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides.
Journal of Computational Biology, 2012

iDASH: integrating data for analysis, anonymization, and sharing.
JAMIA, 2012

Speeding up tandem mass spectral identification using indexes.
Bioinformatics, 2012

Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics.
Proceedings of the Research in Computational Molecular Biology, 2012

2011
TCLUST: A Fast Method for Clustering Genome-Scale Expression Data.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Compressing Genomic Sequence Fragments Using SlimGene.
Journal of Computational Biology, 2011

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

On the Approximability of Reachability-Preserving Network Orientations.
Internet Mathematics, 2011

Strobe sequence design for haplotype assembly.
BMC Bioinformatics, 2011

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Bioinformatics, 2011

2010
A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes.
PLoS Computational Biology, 2010

Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets.
Journal of Computational Biology, 2010

Optimizing PCR Assays for DNA-Based Cancer Diagnostics.
Journal of Computational Biology, 2010

RAPID detection of gene-gene interactions in genome-wide association studies.
Bioinformatics, 2010

Compressing Genomic Sequence Fragments Using SlimGene.
Proceedings of the Research in Computational Molecular Biology, 2010

2009
Fast and Accurate Alignment of Multiple Protein Networks.
Journal of Computational Biology, 2009

Shared Peptides in Mass Spectrometry Based Protein Quantification.
Proceedings of the Research in Computational Molecular Biology, 2009

Optimizing PCR Assays for DNA Based Cancer Diagnostics.
Proceedings of the Research in Computational Molecular Biology, 2009

2008
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.
PLoS Computational Biology, 2008

Structural Alignment of Pseudoknotted RNA.
Journal of Computational Biology, 2008

QNet: A Tool for Querying Protein Interaction Networks.
Journal of Computational Biology, 2008

An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Fast and Accurate Alignment of Multiple Protein Networks.
Proceedings of the Research in Computational Molecular Biology, 2008

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.
Proceedings of the ECCB'08 Proceedings, 2008

2007
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters.
Journal of Computational Biology, 2007

Optimization of primer design for the detection of variable genomic lesions in cancer.
Bioinformatics, 2007

QNet: A Tool for Querying Protein Interaction Networks.
Proceedings of the Research in Computational Molecular Biology, 2007

2006
Consensus Folding of Unaligned RNA Sequences Revisited.
Journal of Computational Biology, 2006

Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots.
Journal of Computational Biology, 2006

Structural Alignment of Pseudoknotted RNA.
Proceedings of the Research in Computational Molecular Biology, 2006

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.
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.
Theor. Comput. Sci., 2005

Searching Genomes for Noncoding RNA Using FastR.
IEEE/ACM Trans. Comput. Biology Bioinform., 2005

Consensus Folding of Unaligned RNA Sequences Revisited.
Proceedings of the Research in Computational Molecular Biology, 2005

Improved Recombination Lower Bounds for Haplotype Data.
Proceedings of the Research in Computational Molecular Biology, 2005

Identification of Post-Translational Modifications via Blind Search of Mass-Spectra.
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.
IEEE/ACM Trans. Comput. Biology Bioinform., 2004

A Note on Efficient Computation of Haplotypes via Perfect Phylogeny.
Journal of Computational Biology, 2004

FastR: Fast Database Search Tool for Non-Coding RNA.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003
Robustness of Inference of Haplotype Block Structure.
Journal of Computational Biology, 2003

Haplotyping as Perfect Phylogeny: A Direct Approach.
Journal of Computational Biology, 2003

Haplotypes and informative SNP selection algorithms: don't block out information.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

On de novo interpretation of tandem mass spectra for peptide identification.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

Combinatorial Problems Arising in SNP and Haplotype Analysis.
Proceedings of the Discrete Mathematics and Theoretical Computer Science, 2003

2002
Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

A Survey of Computational Methods for Determining Haplotypes.
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.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

SNPs Problems, Complexity, and Algorithms.
Proceedings of the Algorithms, 2001

2000
Ligand-Receptor Pairing Via Tree Comparison.
Journal of Computational Biology, 2000

The Conserved Exon Method for Gene Finding.
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.
SIAM J. Discrete Math., 1999

A Polynomial-Time Approximation Scheme for Minimum Routing Cost Spanning Trees.
SIAM J. Comput., 1999

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics).
SIAM J. Comput., 1999

1998
Sorting by Transpositions.
SIAM J. Discrete Math., 1998

A Polynomial Time Approximation Scheme for Minimum Routing Cost Spanning Trees.
Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, 1998

Detecting non-adjoining correlations with signals in DNA.
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.
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.
Theor. Comput. Sci., 1997

1996
Genome Rearrangements and Sorting by Reversals.
SIAM J. Comput., 1996

Nonoverlapping Local Alignments (weighted Independent Sets of Axis-parallel Rectangles).
Discrete Applied Mathematics, 1996

On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics).
Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, 1996

1995
Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles).
Proceedings of the Algorithms and Data Structures, 4th International Workshop, 1995

Sorting Permutations by Transpositions.
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.
Proceedings of the Algorithms and Computation, 6th International Symposium, 1995

Computing Similarity between RNA Strings.
CPM, 1995

1994
Not All Insertion Methods Yield Constant Approximate Tours in the Euclidean Plane.
Theor. Comput. Sci., 1994

Approximation Algorithms for Multiple Sequence Alignment.
Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

1993
Genome Rearrangements and Sorting by Reversals
Proceedings of the 34th Annual Symposium on Foundations of Computer Science, 1993

1990
Parallel Implementation of Logic Languages.
Proceedings of the CONPAR 90, 1990


  Loading...