Serafim Batzoglou

Affiliations:
  • Stanford University, USA


According to our database1, Serafim Batzoglou authored at least 55 papers between 1997 and 2022.

Collaborative distances:
  • Dijkstra number2 of three.
  • Erdős number3 of two.

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
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Links

Online presence:

On csauthors.net:

Bibliography

2022
Independence of the Continuum Hypothesis: an Intuitive Introduction.
CoRR, 2022

2021
Goedel's Incompleteness Theorem.
CoRR, 2021

2020
Meltos: multi-sample tumor phylogeny reconstruction for structural variants.
Bioinform., 2020

2018
Fast Metagenomic Binning via Hashing and Bayesian Clustering.
J. Comput. Biol., 2018

Network Enhancement: a general method to denoise weighted biological networks.
CoRR, 2018

2017
Vicus: Exploiting local structures to improve network-based analysis of biological data.
PLoS Comput. Biol., 2017

SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning.
CoRR, 2017

GATTACA: Lightweight Metagenomic Binning Using Kmer Counting.
Proceedings of the Research in Computational Molecular Biology, 2017

2016
Genome assembly from synthetic long read clouds.
Bioinform., 2016

Reveel: large-scale population genotyping using low-coverage sequencing data.
Bioinform., 2016

Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Unsupervised Learning from Noisy Networks with Applications to Hi-C Data.
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.
Proceedings of the Research in Computational Molecular Biology, 2015

2014
Fast and Scalable Inference of Multi-Sample Cancer Lineages.
CoRR, 2014

Editorial.
Bioinform., 2014

2013
Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements.
Adv. Math. Commun., 2013

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery.
J. Comput. Biol., 2013

Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models.
J. Comput. Biol., 2013

Short read alignment with populations of genomes.
Bioinform., 2013

Automated cellular annotation for high-resolution images of adult <i>Caenorhabditis elegans</i>.
Bioinform., 2013

An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test.
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.
Nucleic Acids Res., 2012

2011
Reconstruction of genealogical relationships with applications to Phase III of HapMap.
Bioinform., 2011

2010
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++.
PLoS Comput. Biol., 2010

2009
Automatic Parameter Learning for Multiple Local Network Alignment.
J. Comput. Biol., 2009

A Classifier-based approach to identify genetic similarities between diseases.
Bioinform., 2009

2008
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA.
Proceedings of the Research in Computational Molecular Biology, 2008

Automatic Parameter Learning for Multiple Network Alignment.
Proceedings of the Research in Computational Molecular Biology, 2008

A max-margin model for efficient simultaneous alignment and folding of RNA sequences.
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.
Briefings Bioinform., 2007

2006
A computational model for RNA multiple structural alignment.
Theor. Comput. Sci., 2006

Integrated Protein Interaction Networks for 11 Microbes.
Proceedings of the Research in Computational Molecular Biology, 2006

CONTRAlign: Discriminative Training for Protein Sequence Alignment.
Proceedings of the Research in Computational Molecular Biology, 2006

Training Conditional Random Fields for Maximum Labelwise Accuracy.
Proceedings of the Advances in Neural Information Processing Systems 19, 2006

MotifCut: regulatory motifs finding with maximum density subgraphs.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

CONTRAfold: RNA secondary structure prediction without physics-based models.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
The many faces of sequence alignment.
Briefings Bioinform., 2005

TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree.
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.
Nucleic Acids Res., 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.
Bioinform., 2004

Chaining Algorithms for Alignment of Draft Sequence.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences.
Proceedings of the Nineteenth National Conference on Artificial Intelligence, 2004

2003
Fast and sensitive multiple alignment of large genomic sequences.
BMC Bioinform., 2003

AGenDA: homology-based gene prediction.
Bioinform., 2003

Gene Regulation - Session Introduction.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

ICA-based Clustering of Genes from Microarray Expression Data.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003

Glocal alignment: finding rearrangements during alignment.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2000
Computational genomics: mapping, comparison, and annotation of genomes.
PhD thesis, 2000

Human and mouse gene structure: comparative analysis and application to exon prediction.
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).
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999
A Dictionary-Based Approach for Gene Annotation.
J. Comput. Biol., 1999

A dictionary based approach for gene annotation.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem.
Proceedings of the Combinatorial Pattern Matching, 10th Annual Symposium, 1999

1997
Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model.
J. Comput. Biol., 1997

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model.
Proceedings of the Eighth Annual ACM-SIAM Symposium on Discrete Algorithms, 1997


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