Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. - Richa Agarwala; Serafim Batzoglou; Vlado Dancík; Scott E. Decatur; Martin Farach; Sridhar Hannenhalli; Steven Skiena (SODA, 1997)

Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. - Richa Agarwala; Serafim Batzoglou; Vlado Dancík; Scott E. Decatur; Sridhar Hannenhalli; Martin Farach; S. Muthukrishnan 001; Steven Skiena (J. Comput. Biol., 1997)

Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. - Serafim Batzoglou; Sorin Istrail (CPM, 1999)

A dictionary based approach for gene annotation. - Lior Pachter; Serafim Batzoglou; Valentin I. Spitkovsky; William S. Beebee; Eric S. Lander; Bonnie Berger; Daniel J. Kleitman (RECOMB, 1999)

A Dictionary-Based Approach for Gene Annotation. - Lior Pachter; Serafim Batzoglou; Valentin I. Spitkovsky; Eric Banks; Eric S. Lander; Daniel J. Kleitman; Bonnie Berger (J. Comput. Biol., 1999)

Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). - Serafim Batzoglou; Bonnie Berger; Jill P. Mesirov; Eric S. Lander (RECOMB, 2000)

Human and mouse gene structure: comparative analysis and application to exon prediction. - Serafim Batzoglou; Lior Pachter; Jill P. Mesirov; Bonnie Berger; Eric S. Lander (RECOMB, 2000)

Computational genomics: mapping, comparison, and annotation of genomes. - Serafim Batzoglou (2000)

Glocal alignment: finding rearrangements during alignment. - Michael Brudno; Sanket Malde; Alexander Poliakov; Chuong B. Do; Olivier Couronne; Inna Dubchak; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2003)

ICA-based Clustering of Genes from Microarray Expression Data. - Su-In Lee; Serafim Batzoglou (NIPS, 2003)

Gene Regulation - Session Introduction. - Serafim Batzoglou; Lior Pachter (Pacific Symposium on Biocomputing, 2003)

AGenDA: homology-based gene prediction. - Leila Taher; Oliver Rinner; Saurabh Garg; Alexander Sczyrba; Michael Brudno; Serafim Batzoglou; Burkhard Morgenstern (Bioinform., 2003)

Fast and sensitive multiple alignment of large genomic sequences. - Michael Brudno; Michael Chapman; Berthold Göttgens; Serafim Batzoglou; Burkhard Morgenstern (BMC Bioinform., 2003)

PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. - Chuong B. Do; Michael Brudno; Serafim Batzoglou (AAAI, 2004)

Chaining Algorithms for Alignment of Draft Sequence. - Mukund Sundararajan; Michael Brudno; Kerrin S. Small; Arend Sidow; Serafim Batzoglou (WABI, 2004)

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. - Nameeta Y. Shah; Olivier Couronne; Len A. Pennacchio; Michael Brudno; Serafim Batzoglou; E. Wes Bethel; Edward M. Rubin; Bernd Hamann; Inna Dubchak (Bioinform., 2004)

A suite of web-based programs to search for transcriptional regulatory motifs. - Yueyi Liu; Liping Wei; Serafim Batzoglou; Douglas L. Brutlag; Jun S. Liu; Xiaole Shirley Liu (Nucleic Acids Res., 2004)

TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree. - Aswath Manohar; Serafim Batzoglou (CSB, 2005)

The many faces of sequence alignment. - Serafim Batzoglou (Briefings Bioinform., 2005)

CONTRAfold: RNA secondary structure prediction without physics-based models. - Chuong B. Do; Daniel A. Woods; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2006)

MotifCut: regulatory motifs finding with maximum density subgraphs. - Eugene Fratkin; Brian T. Naughton; Douglas L. Brutlag; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2006)

Training Conditional Random Fields for Maximum Labelwise Accuracy. - Samuel S. Gross; Olga Russakovsky; Chuong B. Do; Serafim Batzoglou (NIPS, 2006)

CONTRAlign: Discriminative Training for Protein Sequence Alignment. - Chuong B. Do; Samuel S. Gross; Serafim Batzoglou (RECOMB, 2006)

Integrated Protein Interaction Networks for 11 Microbes. - Balaji S. Srinivasan; Antal F. Novak; Jason Flannick; Serafim Batzoglou; Harley H. McAdams (RECOMB, 2006)

A computational model for RNA multiple structural alignment. - Eugene Davydov; Serafim Batzoglou (Theor. Comput. Sci., 2006)

Current progress in network research: toward reference networks for key model organisms. - Balaji S. Srinivasan; Nigam H. Shah; Jason Flannick; Eduardo Abeliuk; Antal F. Novak; Serafim Batzoglou (Briefings Bioinform., 2007)

A max-margin model for efficient simultaneous alignment and folding of RNA sequences. - Chuong B. Do; Chuan-Sheng Foo; Serafim Batzoglou (ISMB, 2008)

Automatic Parameter Learning for Multiple Network Alignment. - Jason Flannick; Antal F. Novak; Chuong B. Do; Balaji S. Srinivasan; Serafim Batzoglou (RECOMB, 2008)

Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. - Andreas Sundquist; Eugene Fratkin; Chuong B. Do; Serafim Batzoglou (RECOMB, 2008)

A Classifier-based approach to identify genetic similarities between diseases. - Marc A. Schaub; Irene M. Kaplow; Marina Sirota; Chuong B. Do; Atul J. Butte; Serafim Batzoglou (Bioinform., 2009)

Automatic Parameter Learning for Multiple Local Network Alignment. - Jason Flannick; Antal F. Novak; Chuong B. Do; Balaji S. Srinivasan; Serafim Batzoglou (J. Comput. Biol., 2009)

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++. - Eugene Davydov; David L. Goode; Marina Sirota; Gregory M. Cooper; Arend Sidow; Serafim Batzoglou (PLoS Comput. Biol., 2010)

Reconstruction of genealogical relationships with applications to Phase III of HapMap. - Sofia Kyriazopoulou-Panagiotopoulou; Dorna Kashef Haghighi; Sarah J. Aerni; Andreas Sundquist; Sivan Bercovici; Serafim Batzoglou (Bioinform., 2011)

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. - Daniel E. Newburger; Georges Natsoulis; Sue Grimes; John M. Bell; Ronald W. Davis; Serafim Batzoglou; Hanlee P. Ji (Nucleic Acids Res., 2012)

An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test. - Jesse M. Rodriguez; Serafim Batzoglou; Sivan Bercovici (RECOMB, 2013)

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. - Sarah J. Aerni; Xiao Liu; Chuong B. Do; Samuel S. Gross; Andy Nguyen; Stephen D. Guo; Fuhui Long; Hanchuan Peng; Stuart S. Kim; Serafim Batzoglou (Bioinform., 2013)

Short read alignment with populations of genomes. - Lin Huang; Victoria Popic; Serafim Batzoglou (Bioinform., 2013)

Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models. - Jesse M. Rodriguez; Sivan Bercovici; Megan Elmore; Serafim Batzoglou (J. Comput. Biol., 2013)

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. - Raheleh Salari; Syed Shayon Saleh; Dorna Kashef Haghighi; David Khavari; Daniel E. Newburger; Robert B. West; Arend Sidow; Serafim Batzoglou (J. Comput. Biol., 2013)

Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements. - Anshul Kundaje; Sofia Kyriazopoulou-Panagiotopoulou; Max W. Libbrecht; Cheryl L. Smith; Debasish Raha; Elliott E. Winters; Steven M. Johnson; Michael P. Snyder; Serafim Batzoglou; Arend Sidow (Adv. Math. Commun., 2013)

Editorial. - Serafim Batzoglou; Russell Schwartz (Bioinform., 2014)

Fast and Scalable Inference of Multi-Sample Cancer Lineages. - Victoria Popic; Raheleh Salari; Iman Hajirasouliha; Dorna Kashef Haghighi; Robert B. West; Serafim Batzoglou (CoRR, 2014)

Read Clouds Uncover Variation in Complex Regions of the Human Genome. - Alex Bishara; Yuling Liu; Dorna Kashef Haghighi; Ziming Weng; Daniel E. Newburger; Robert B. West; Arend Sidow; Serafim Batzoglou (RECOMB, 2015)

Unsupervised Learning from Noisy Networks with Applications to Hi-C Data. - Bo Wang 044; Junjie Zhu; Armin Pourshafeie; Oana Ursu; Serafim Batzoglou; Anshul Kundaje (NIPS, 2016)

Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting. - Victoria Popic; Serafim Batzoglou (RECOMB, 2016)

Reveel: large-scale population genotyping using low-coverage sequencing data. - Lin Huang; Bo Wang 044; Ruitang Chen; Sivan Bercovici; Serafim Batzoglou (Bioinform., 2016)

Genome assembly from synthetic long read clouds. - Volodymyr Kuleshov; Michael P. Snyder; Serafim Batzoglou (Bioinform., 2016)

GATTACA: Lightweight Metagenomic Binning Using Kmer Counting. - Victoria Popic; Volodymyr Kuleshov; Michael P. Snyder; Serafim Batzoglou (RECOMB, 2017)

SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning. - Bo Wang 044; Daniele Ramazzotti; Luca De Sano; Junjie Zhu; Emma Pierson; Serafim Batzoglou (CoRR, 2017)

Vicus: Exploiting local structures to improve network-based analysis of biological data. - Bo Wang 044; Lin Huang; Yuke Zhu; Anshul Kundaje; Serafim Batzoglou; Anna Goldenberg (PLoS Comput. Biol., 2017)

Network Enhancement: a general method to denoise weighted biological networks. - Bo Wang 044; Armin Pourshafeie; Marinka Zitnik; Junjie Zhu; Carlos D. Bustamante; Serafim Batzoglou; Jure Leskovec (CoRR, 2018)

Fast Metagenomic Binning via Hashing and Bayesian Clustering. - Victoria Popic; Volodymyr Kuleshov; Michael P. Snyder; Serafim Batzoglou (J. Comput. Biol., 2018)

Meltos: multi-sample tumor phylogeny reconstruction for structural variants. - Camir Ricketts; Daniel Seidman; Victoria Popic; Fereydoun Hormozdiari; Serafim Batzoglou; Iman Hajirasouliha (Bioinform., 2020)

Goedel's Incompleteness Theorem. - Serafim Batzoglou (CoRR, 2021)

Independence of the Continuum Hypothesis: an Intuitive Introduction. - Serafim Batzoglou (CoRR, 2022)