Computational Genomics
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Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long read sequencing reveals interspecies diversity in the human microbiome. Nature Biotechnology doi:10.1038/nbt.3416, 2016.
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S. Reveel: large-scale population genotyping using low-coverage sequencing data. Bioinformatics 10: 1093/bioinformatics/btv530, 2015.
Bishara A*, Liu Y*, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S. Read clouds uncover variation in complex regions of the human genome. Genome Research 25:1570-1580, 2015.
Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S. Fast and scalable inference of multi-sample cancer lineages. Genome Biology 16(1):91, 2015.
Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A. Constraint and divergence of global gene expression in the mammalian embryo. eLife 4:e05538, 2015.
Weng Z, Spies N, Xhu SX, Neuburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB. Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia. Genome Medicine 7(1): 28, 2015.
Green MR, Kihira S, Liu CL et al. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences 112(10): E1116-1125, 2015.
Rodriguez JM*, Bercovici S*, Huang L, Frostig R, Batzoglou S. Parente2: a fast and accurate method for detecting identity by descent. Genome Research 25(2):280-289, 2015.
Huang L*, Popic V*, Batzoglou S. Short read alignment with populations of genomes. Proceedings of ISMB, Bioinformatics 29(13): i361-i370, 2013.
Aerni SJ, Liu X, Do CB, Gross SS, Nguyen A, Guo SD, Long F, Peng H, Kim SS, Batzoglou S. Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. Proceedings of ISMB, Bioinformatics 29(13): i18-i26, 2013.
Newburger DE*, Kashef-Haghighi D*, Weng Z, Salari R, Sweeney R, Brunner AL, Zhu SX, Guo X, Varna S, Troxell ML, West RB, Batzoglou S, Sidow A. Genome evolution during progression to breast cancer. Genome Research 23(7): 1097-1108, 2013.
Rodriguez JM*, Bercovici S*, Elmore M, Batzoglou S. Ancestry inference in complex admixtures via variable-length Markov chain linkage models. Journal of Computational Biology 20(3):199-211, 2013.
Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F et al. Extensive variation in chromatin states across humans. Science 342(6159):750-752, 2013.
* Joint first authors
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S. Reveel: large-scale population genotyping using low-coverage sequencing data. Bioinformatics 10: 1093/bioinformatics/btv530, 2015.
Bishara A*, Liu Y*, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S. Read clouds uncover variation in complex regions of the human genome. Genome Research 25:1570-1580, 2015.
Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S. Fast and scalable inference of multi-sample cancer lineages. Genome Biology 16(1):91, 2015.
Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A. Constraint and divergence of global gene expression in the mammalian embryo. eLife 4:e05538, 2015.
Weng Z, Spies N, Xhu SX, Neuburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB. Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia. Genome Medicine 7(1): 28, 2015.
Green MR, Kihira S, Liu CL et al. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences 112(10): E1116-1125, 2015.
Rodriguez JM*, Bercovici S*, Huang L, Frostig R, Batzoglou S. Parente2: a fast and accurate method for detecting identity by descent. Genome Research 25(2):280-289, 2015.
Huang L*, Popic V*, Batzoglou S. Short read alignment with populations of genomes. Proceedings of ISMB, Bioinformatics 29(13): i361-i370, 2013.
Aerni SJ, Liu X, Do CB, Gross SS, Nguyen A, Guo SD, Long F, Peng H, Kim SS, Batzoglou S. Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. Proceedings of ISMB, Bioinformatics 29(13): i18-i26, 2013.
Newburger DE*, Kashef-Haghighi D*, Weng Z, Salari R, Sweeney R, Brunner AL, Zhu SX, Guo X, Varna S, Troxell ML, West RB, Batzoglou S, Sidow A. Genome evolution during progression to breast cancer. Genome Research 23(7): 1097-1108, 2013.
Rodriguez JM*, Bercovici S*, Elmore M, Batzoglou S. Ancestry inference in complex admixtures via variable-length Markov chain linkage models. Journal of Computational Biology 20(3):199-211, 2013.
Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F et al. Extensive variation in chromatin states across humans. Science 342(6159):750-752, 2013.
* Joint first authors
Select Older Publications
Schaub MA, Boyle A, Kundaje A, Batzoglou S, Snyder MP. Linking disease associations with regulatory information in the human genome. Genome Research 22(9):1748-59. PMID: 22955986, 2012.
Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder MP, Batzoglou S, Sidow S. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research 22(9):1735-47. PMID: 22955985, 2012.
Kyriazopoulou-Panagiotopoulou S, Kashef-Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S. Reconstruction of genealogical relationships with application to Phase III of HapMap. Bioinformatics, Special issue on the Proceedings of the ISMB 2011, Jul 1;27(13):i333-41, 2011.
Davydov E, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Computational Biology 6: e1001025, 2010.
Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sanchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S, Myers EW, Kim SK. Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell 139(3):623-633, 2009.
Flannick JA, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple local network alignment. Journal of Computational Biology 16(8): 1001-1022, 2009.
Deshpande O, Batzoglou S, Feldman M, Cavalli-Sforza L. A serial founder effect model for human settlements out of Africa. Proceedings of the Royal Society 276(1655): 291-300, 2009.
Valouev A, Johnson DS, Sundquist A, Medina C, Elisabeth A, Batzoglou S, Myers RM, Sidow A. Genome-wise analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods 5(9): 829-834, 2008.
Do CB, Foo CS, Batzoglou S. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Special issue on the Proceedings of the ISMB 2008, Bioinformatics 24(13):i68-76, 2008.
Sundquist A, Fratkin E, Do CB, Batzoglou S. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Research 18:676-682, 2008.
Sundquist A, Bigdeli S, Jalili R, El-Sayed YY, Taslimi MM, Druzin ML, Waller S, Pullen KM, Batzoglou S, Ronaghi M. Bacterial flora typing with deep, targeted, chip-based Pyrosequencing. BMC Microbiology, 7:108, 2007.
Gross SS, Do CB, Sirota M, Batzoglou S. CONTAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology 8:R269, 2007.
Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput short-read technologies. PLOS One 2(5): e484, 2007.
Flannick JA, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research, 16:1169-1181, 2006.
Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Special Issue on the Proceedings of the ISMB, Bioinformatics 22:e90-98, 2006. Best Paper Award, ISMB 2006.
Do CB, Gross SS, Batzoglou S. CONTRAlign: Discriminative training for protein sequence alignment. Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB), pp. 160–164, 2006.
Srinivasan BS, Novak A, Flannick JA, Batzoglou S, McAdams H. Integrated protein interaction networks for 11 microbes. Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB), pp. 1–14, 2006.
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Research 15:330–340, 2005.
Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Special Issue on the Proceedings of the ISMB 2003, Bioinformatics 19: 54i-62i, 2003.
Lee S-I, Batzoglou S. Application of independent component analysis to microarrays. Genome Biology 4:R76, 2003.
Cooper GM, Brudno M, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Research 13:813-820, 2003.
Brudno M, Do C, Cooper GM, Kim MF, Davydov E, NISC Comparative Sequencing Program, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Research 13: 721-731, 2003.
Batzoglou S, Jaffe D, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: A whole genome shotgun assembler. Genome Research 12:177-189, 2002.
Lander ES et al. Initial sequencing and analysis of the human genome. Nature 409:860-921, 2001.
Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research 10:950-958, 2000.
Batzoglou S, Mesirov JP, Berger B, Lander ES. Sequencing a genome by walking with clone-ends: A mathematical analysis. Genome Research 9:1163-1174, 1999.
Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary based approach to gene annotation. Journal of Computational Biology 6:419–430, 1999.
Agarwala R, Batzoglou S, Dancik V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan M, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Journal of Computational Biology 4: 275–296, 1997.
Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder MP, Batzoglou S, Sidow S. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research 22(9):1735-47. PMID: 22955985, 2012.
Kyriazopoulou-Panagiotopoulou S, Kashef-Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S. Reconstruction of genealogical relationships with application to Phase III of HapMap. Bioinformatics, Special issue on the Proceedings of the ISMB 2011, Jul 1;27(13):i333-41, 2011.
Davydov E, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Computational Biology 6: e1001025, 2010.
Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sanchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S, Myers EW, Kim SK. Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell 139(3):623-633, 2009.
Flannick JA, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple local network alignment. Journal of Computational Biology 16(8): 1001-1022, 2009.
Deshpande O, Batzoglou S, Feldman M, Cavalli-Sforza L. A serial founder effect model for human settlements out of Africa. Proceedings of the Royal Society 276(1655): 291-300, 2009.
Valouev A, Johnson DS, Sundquist A, Medina C, Elisabeth A, Batzoglou S, Myers RM, Sidow A. Genome-wise analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods 5(9): 829-834, 2008.
Do CB, Foo CS, Batzoglou S. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Special issue on the Proceedings of the ISMB 2008, Bioinformatics 24(13):i68-76, 2008.
Sundquist A, Fratkin E, Do CB, Batzoglou S. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Research 18:676-682, 2008.
Sundquist A, Bigdeli S, Jalili R, El-Sayed YY, Taslimi MM, Druzin ML, Waller S, Pullen KM, Batzoglou S, Ronaghi M. Bacterial flora typing with deep, targeted, chip-based Pyrosequencing. BMC Microbiology, 7:108, 2007.
Gross SS, Do CB, Sirota M, Batzoglou S. CONTAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology 8:R269, 2007.
Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput short-read technologies. PLOS One 2(5): e484, 2007.
Flannick JA, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research, 16:1169-1181, 2006.
Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Special Issue on the Proceedings of the ISMB, Bioinformatics 22:e90-98, 2006. Best Paper Award, ISMB 2006.
Do CB, Gross SS, Batzoglou S. CONTRAlign: Discriminative training for protein sequence alignment. Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB), pp. 160–164, 2006.
Srinivasan BS, Novak A, Flannick JA, Batzoglou S, McAdams H. Integrated protein interaction networks for 11 microbes. Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB), pp. 1–14, 2006.
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Research 15:330–340, 2005.
Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Special Issue on the Proceedings of the ISMB 2003, Bioinformatics 19: 54i-62i, 2003.
Lee S-I, Batzoglou S. Application of independent component analysis to microarrays. Genome Biology 4:R76, 2003.
Cooper GM, Brudno M, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Research 13:813-820, 2003.
Brudno M, Do C, Cooper GM, Kim MF, Davydov E, NISC Comparative Sequencing Program, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Research 13: 721-731, 2003.
Batzoglou S, Jaffe D, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: A whole genome shotgun assembler. Genome Research 12:177-189, 2002.
Lander ES et al. Initial sequencing and analysis of the human genome. Nature 409:860-921, 2001.
Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research 10:950-958, 2000.
Batzoglou S, Mesirov JP, Berger B, Lander ES. Sequencing a genome by walking with clone-ends: A mathematical analysis. Genome Research 9:1163-1174, 1999.
Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary based approach to gene annotation. Journal of Computational Biology 6:419–430, 1999.
Agarwala R, Batzoglou S, Dancik V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan M, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Journal of Computational Biology 4: 275–296, 1997.
Copyright © 2015 Serafim Batzoglou