Serafim Batzoglou

CoRR, 2022

2021

Goedel's Incompleteness Theorem.

[BibT_eX]

[DOI]

CoRR, 2021

2020

Meltos: multi-sample tumor phylogeny reconstruction for structural variants.

[BibT_eX]

[DOI]

Camir Ricketts

Daniel Seidman

Fereydoun Hormozdiari

Iman Hajirasouliha

Bioinform., 2020

2018

Fast Metagenomic Binning via Hashing and Bayesian Clustering.

[BibT_eX]

[DOI]

J. Comput. Biol., 2018

Network Enhancement: a general method to denoise weighted biological networks.

[BibT_eX]

[DOI]

CoRR, 2018

2017

Vicus: Exploiting local structures to improve network-based analysis of biological data.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2017

SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning.

[BibT_eX]

[DOI]

CoRR, 2017

GATTACA: Lightweight Metagenomic Binning Using Kmer Counting.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2017

2016

Genome assembly from synthetic long read clouds.

[BibT_eX]

[DOI]

Volodymyr Kuleshov

Michael P. Snyder

Bioinform., 2016

Reveel: large-scale population genotyping using low-coverage sequencing data.

[BibT_eX]

[DOI]

Bioinform., 2016

Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Unsupervised Learning from Noisy Networks with Applications to Hi-C Data.

[BibT_eX]

[DOI]

Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016

2015

Read Clouds Uncover Variation in Complex Regions of the Human Genome.

[BibT_eX]

[DOI]

Alex Bishara

Yuling Liu

Proceedings of the Research in Computational Molecular Biology, 2015

2014

Fast and Scalable Inference of Multi-Sample Cancer Lineages.

[BibT_eX]

[DOI]

Raheleh Salari

Iman Hajirasouliha

Robert B. West

CoRR, 2014

Editorial.

[BibT_eX]

[DOI]

Sofia Kyriazopoulou-Panagiotopoulou

Russell Schwartz

Bioinform., 2014

2013

Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements.

[BibT_eX]

[DOI]

Anshul Kundaje

Tiny Trans. Comput. Sci., 2013

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery.

[BibT_eX]

[DOI]

Raheleh Salari

Syed Shayon Saleh

J. Comput. Biol., 2013

Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models.

[BibT_eX]

[DOI]

J. Comput. Biol., 2013

Short read alignment with populations of genomes.

[BibT_eX]

[DOI]

Lin Huang

Bioinform., 2013

Automated cellular annotation for high-resolution images of adult <i>Caenorhabditis elegans</i>.

[BibT_eX]

[DOI]

Bioinform., 2013

An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test.

[BibT_eX]

[DOI]

Jesse M. Rodriguez

Sofia Kyriazopoulou-Panagiotopoulou

Sivan Bercovici

Proceedings of the Research in Computational Molecular Biology, 2013

2012

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2012

2011

Reconstruction of genealogical relationships with applications to Phase III of HapMap.

[BibT_eX]

[DOI]

Bioinform., 2011

2010

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2010

2009

Automatic Parameter Learning for Multiple Local Network Alignment.

[BibT_eX]

[DOI]

J. Comput. Biol., 2009

A Classifier-based approach to identify genetic similarities between diseases.

[BibT_eX]

[DOI]

Bioinform., 2009

2008

Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2008

Automatic Parameter Learning for Multiple Network Alignment.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2008

A max-margin model for efficient simultaneous alignment and folding of RNA sequences.

[BibT_eX]

[DOI]

Chuan-Sheng Foo

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007

Current progress in network research: toward reference networks for key model organisms.

[BibT_eX]

[DOI]

Briefings Bioinform., 2007

2006

A computational model for RNA multiple structural alignment.

[BibT_eX]

[DOI]

Eugene Davydov

Theor. Comput. Sci., 2006

Integrated Protein Interaction Networks for 11 Microbes.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2006

CONTRAlign: Discriminative Training for Protein Sequence Alignment.

[BibT_eX]

[DOI]

Samuel S. Gross

Proceedings of the Research in Computational Molecular Biology, 2006

Training Conditional Random Fields for Maximum Labelwise Accuracy.

[BibT_eX]

[DOI]

Proceedings of the Advances in Neural Information Processing Systems 19, 2006

MotifCut: regulatory motifs finding with maximum density subgraphs.

[BibT_eX]

[DOI]

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

CONTRAfold: RNA secondary structure prediction without physics-based models.

[BibT_eX]

[DOI]

Daniel A. Woods

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

2005

The many faces of sequence alignment.

[BibT_eX]

[DOI]

Briefings Bioinform., 2005

TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree.

[BibT_eX]

[DOI]

Aswath Manohar

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

2004

A suite of web-based programs to search for transcriptional regulatory motifs.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

[BibT_eX]

[DOI]

Bioinform., 2004

Chaining Algorithms for Alignment of Draft Sequence.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences.

[BibT_eX]

[DOI]

Michael Brudno

Proceedings of the Nineteenth National Conference on Artificial Intelligence, 2004

2003

Fast and sensitive multiple alignment of large genomic sequences.

[BibT_eX]

[DOI]

BMC Bioinform., 2003

AGenDA: homology-based gene prediction.

[BibT_eX]

[DOI]

Bioinform., 2003

Gene Regulation - Session Introduction.

[BibT_eX]

[DOI]

Lior Pachter

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

ICA-based Clustering of Genes from Microarray Expression Data.

[BibT_eX]

[DOI]

Su-In Lee

Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003

Glocal alignment: finding rearrangements during alignment.

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2000

Computational genomics: mapping, comparison, and annotation of genomes.

[BibT_eX]

[DOI]

PhD thesis, 2000

Human and mouse gene structure: comparative analysis and application to exon prediction.

[BibT_eX]

[DOI]

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract).

[BibT_eX]

[DOI]

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999

A Dictionary-Based Approach for Gene Annotation.

[BibT_eX]

[DOI]

Lior Pachter

Valentin I. Spitkovsky

J. Comput. Biol., 1999

A dictionary based approach for gene annotation.

[BibT_eX]

[DOI]

Lior Pachter

Valentin I. Spitkovsky

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem.

[BibT_eX]

[DOI]