Serafim Batzoglou

63 papers A* 2A 1B 17C 1Misc 1Journal 32Unranked 8

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	ABD: Default Exception Abduction in Finite First Order Worlds. CoRR Serafim Batzoglou
2026	J	`jnl`	INDUCTION: Finite-Structure Concept Synthesis in First-Order Logic. CoRR Serafim Batzoglou
2025	—	`conf`	Stress-Testing the Reasoning Competence of Language Models With Formal Proofs. EMNLP (Findings) Konstantine Arkoudas, Serafim Batzoglou
2022	J	`jnl`	Independence of the Continuum Hypothesis: an Intuitive Introduction. CoRR Serafim Batzoglou
2021	J	`jnl`	Goedel's Incompleteness Theorem. CoRR Serafim Batzoglou
2020	J	`jnl`	Meltos: multi-sample tumor phylogeny reconstruction for structural variants. Bioinform. Camir Ricketts, Daniel Seidman, Victoria Popic, Fereydoun Hormozdiari, Serafim Batzoglou, Iman Hajirasouliha
2018	J	`jnl`	Fast Metagenomic Binning via Hashing and Bayesian Clustering. J. Comput. Biol. Victoria Popic, Volodymyr Kuleshov, Michael P. Snyder, Serafim Batzoglou
2018	J	`jnl`	Network Enhancement: a general method to denoise weighted biological networks. CoRR Bo Wang, Armin Pourshafeie, Marinka Zitnik, Junjie Zhu, Carlos D. Bustamante, Serafim Batzoglou, Jure Leskovec
2017	B	`conf`	GATTACA: Lightweight Metagenomic Binning Using Kmer Counting. RECOMB Victoria Popic, Volodymyr Kuleshov, Michael P. Snyder, Serafim Batzoglou
2017	J	`jnl`	SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning. CoRR Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu, Emma Pierson, Serafim Batzoglou
2017	J	`jnl`	Vicus: Exploiting local structures to improve network-based analysis of biological data. PLoS Comput. Biol. Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg
2016	B	`conf`	Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting. RECOMB Victoria Popic, Serafim Batzoglou
2016	J	`jnl`	Genome assembly from synthetic long read clouds. Bioinform. Volodymyr Kuleshov, Michael P. Snyder, Serafim Batzoglou
2016	J	`jnl`	Reveel: large-scale population genotyping using low-coverage sequencing data. Bioinform. Lin Huang, Bo Wang, Ruitang Chen, Sivan Bercovici, Serafim Batzoglou
2016	—	`conf`	Unsupervised Learning from Noisy Networks with Applications to Hi-C Data. NIPS Bo Wang, Junjie Zhu, Armin Pourshafeie, Oana Ursu, Serafim Batzoglou, Anshul Kundaje
2015	B	`conf`	Read Clouds Uncover Variation in Complex Regions of the Human Genome. RECOMB Alex Bishara, Yuling Liu, Dorna Kashef Haghighi, Ziming Weng, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2014	J	`jnl`	Editorial. Bioinform. Serafim Batzoglou, Russell Schwartz
2014	J	`jnl`	Fast and Scalable Inference of Multi-Sample Cancer Lineages. CoRR Victoria Popic, Raheleh Salari, Iman Hajirasouliha, Dorna Kashef Haghighi, Robert B. West, Serafim Batzoglou
2013	B	`conf`	An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test. RECOMB Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici
2013	J	`jnl`	Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models. J. Comput. Biol. Jesse M. Rodriguez, Sivan Bercovici, Megan Elmore, Serafim Batzoglou
2013	J	`jnl`	Automated cellular annotation for high-resolution images of adult Bioinform. 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
2013	J	`jnl`	Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements. Tiny Trans. Comput. Sci. 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
2013	B	`conf`	Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. RECOMB Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2013	J	`jnl`	Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. J. Comput. Biol. Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2013	J	`jnl`	Short read alignment with populations of genomes. Bioinform. Lin Huang, Victoria Popic, Serafim Batzoglou
2012	B	`conf`	Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models. RECOMB Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou
2012	J	`jnl`	The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. Nucleic Acids Res. Daniel E. Newburger, Georges Natsoulis, Sue Grimes, John M. Bell, Ronald W. Davis, Serafim Batzoglou, Hanlee P. Ji
2011	J	`jnl`	Reconstruction of genealogical relationships with applications to Phase III of HapMap. Bioinform. Sofia Kyriazopoulou-Panagiotopoulou, Dorna Kashef Haghighi, Sarah J. Aerni, Andreas Sundquist, Sivan Bercovici, Serafim Batzoglou
2010	J	`jnl`	Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++. PLoS Comput. Biol. Eugene Davydov, David L. Goode, Marina Sirota, Gregory M. Cooper, Arend Sidow, Serafim Batzoglou
2009	J	`jnl`	A Classifier-based approach to identify genetic similarities between diseases. Bioinform. Marc A. Schaub, Irene M. Kaplow, Marina Sirota, Chuong B. Do, Atul J. Butte, Serafim Batzoglou
2009	J	`jnl`	Automatic Parameter Learning for Multiple Local Network Alignment. J. Comput. Biol. Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou
2009	B	`ed.`	Research in Computational Molecular Biology, 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings RECOMB Serafim Batzoglou
2008	A	`conf`	A max-margin model for efficient simultaneous alignment and folding of RNA sequences. ISMB Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou
2008	B	`conf`	Automatic Parameter Learning for Multiple Network Alignment. RECOMB Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou
2008	B	`conf`	Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. RECOMB Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou
2007	J	`jnl`	Current progress in network research: toward reference networks for key model organisms. Briefings Bioinform. Balaji S. Srinivasan, Nigam H. Shah, Jason Flannick, Eduardo Abeliuk, Antal F. Novak, Serafim Batzoglou
2006	J	`jnl`	A computational model for RNA multiple structural alignment. Theor. Comput. Sci. Eugene Davydov, Serafim Batzoglou
2006	—	`conf`	CONTRAfold: RNA secondary structure prediction without physics-based models. ISMB (Supplement of Bioinformatics) Chuong B. Do, Daniel A. Woods, Serafim Batzoglou
2006	B	`conf`	CONTRAlign: Discriminative Training for Protein Sequence Alignment. RECOMB Chuong B. Do, Samuel S. Gross, Serafim Batzoglou
2006	B	`conf`	Integrated Protein Interaction Networks for 11 Microbes. RECOMB Balaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams
2006	—	`conf`	MotifCut: regulatory motifs finding with maximum density subgraphs. ISMB (Supplement of Bioinformatics) Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou
2006	—	`conf`	Training Conditional Random Fields for Maximum Labelwise Accuracy. NIPS Samuel S. Gross, Olga Russakovsky, Chuong B. Do, Serafim Batzoglou
2005	J	`jnl`	The many faces of sequence alignment. Briefings Bioinform. Serafim Batzoglou
2005	—	`conf`	TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree. CSB Aswath Manohar, Serafim Batzoglou
2004	B	`conf`	A Computational Model for RNA Multiple Structural Alignment.. CPM Eugene Davydov, Serafim Batzoglou
2004	J	`jnl`	A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res. Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, Xiaole Shirley Liu
2004	C	`conf`	Chaining Algorithms for Alignment of Draft Sequence. WABI Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou
2004	A*	`conf`	PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. AAAI Chuong B. Do, Michael Brudno, Serafim Batzoglou
2004	J	`jnl`	Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinform. Nameeta Y. Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak
2003	J	`jnl`	AGenDA: homology-based gene prediction. Bioinform. Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern
2003	J	`jnl`	Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinform. Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern
2003	Misc	`conf`	Gene Regulation - Session Introduction. Pacific Symposium on Biocomputing Serafim Batzoglou, Lior Pachter
2003	—	`conf`	Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou
2003	—	`conf`	ICA-based Clustering of Genes from Microarray Expression Data. NIPS Su-In Lee, Serafim Batzoglou
2000	—	`—`	Computational genomics: mapping, comparison, and annotation of genomes. Serafim Batzoglou
2000	B	`conf`	Human and mouse gene structure: comparative analysis and application to exon prediction. RECOMB Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander
2000	B	`conf`	Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). RECOMB Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander
1999	J	`jnl`	A Dictionary-Based Approach for Gene Annotation. J. Comput. Biol. Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger
1999	B	`conf`	A dictionary based approach for gene annotation. RECOMB Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman
1999	B	`conf`	Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem. CPM Serafim Batzoglou, Sorin Istrail
1997	A*	`conf`	Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. SODA Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena
1997	J	`jnl`	Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. J. Comput. Biol. Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Sridhar Hannenhalli, Martin Farach, S. Muthukrishnan, Steven Skiena
1997	B	`conf`	Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. RECOMB Richa Agarwala, Serafim Batzoglou, Vlado Dancík, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena