Bio

Bio


Batzoglou's research has focused on the development of algorithms and systems for genomics. Some of the topics he is working on include: sequence alignment algorithms, hidden Markov models, whole-genome comparison, annotation of biological features in genomes, microarray analysis, gene regulation, and DNA sequencing.

Academic Appointments


Honors & Awards


  • Best Paper Award, MIT Technology Review Magazine (2003)
  • Top 100 Young Technology Innovators, National Science Foundation
  • Career Award in Computer Science, Alfred P. Sloan Foundation
  • Sloan Research Fellowship, Alfred P. Sloan Foundation

Professional Education


  • PhD, MIT (2000)

Research & Scholarship

Current Research and Scholarly Interests


Computational Genomics

Teaching

2013-14 Courses


Graduate and Fellowship Programs


  • Biomedical Informatics (Phd Program)

Publications

Journal Articles


  • Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Computational Biology Davydov, E. V., Goode, D. L., Sirota, M., Cooper, G. M., Sidow, A., Batzoglou, S. 2010; 6: e1001025
  • RECOMB Conference 2009 Journal of Computational Biology Batzoglou, S., Batzoglou, S. 2010; 3 (17)
  • Genome-wise analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Elisabeth, A., Batzoglou, S. 2008; 9 (5): 829-834
  • Drosophila Comparative Genome Sequencing and Analysis Consortium. Evolution of genes and genomes in the context of the Drosophila phylogeny. Nature Batzoglou, S. 2007; 450: 203-218
  • Bacterial flora typing with deep, targeted, chip-based Pyrosequencing. BMC Microbiology Sundquist, A., Bigdeli, S., Jalili, R., El-Sayed, Y. Y., Taslimi, M. M., Druzin, M. L., Batzoglou, S. 2007; 7: 108
  • CONTAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology Gross, S. S., Do, C. B., Sirota, M., Batzoglou, S. 2007; 8: R269
  • Current progress in network research: towards reference networks for key model organisms. Briefings in Bioinformatics Srinivasan, B. S., Shah, N. H., Flannick, J. A., Abeliuk, E., Novak, A. F., Batzoglou, S. 2007; 5 (8): 318-32
  • Whole-genome sequencing and assembly with high-throughput short-read technologies. PLOS One Sundquist, A., Ronaghi, M., Tang, H., Pevzner, P., Batzoglou, S. 2007; 5 (2): e484
  • Training conditional random fields for maximum parse accuracy. NIPS Gross, S. S., Russakovsky, O., Do, C. B., Batzoglou, S. 2006
  • Sequencing of Aspergillusnidulans and comparative analysis with A. fumigatus and A. oryzae. Nature Galagan, J. E., Calvo, S. E., Cuomo, C., Ma, L. J., Wortman, J., Batzoglou, S. 2005; 438: 1105–1115
  • The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science Batzoglou, S. 2004; 306: 636–640
  • Eukaryotic regulatory element conservation and their identification using comparative genomics. Genome Research Liu, Y., Liu, X. S., Wei, L., Altman, R. B., Batzoglou, S. 2004; 14: 451-458
  • Phylo-VISTA: an interactive visualization tool for multiple DNA sequence alignments. Bioinformatics Shan, N., Couronne, O., Pennacchio, L. A., Brudno, M., Batzoglou, S., Joy, S. 2003; 19: 1575-1577
  • ARACHNE: A whole genome shotgun assembler. Genome Research Batzoglou, S., Jaffe, D., Stanley, K., Butler, J., Gnerre, S., Mauceli, E. 2002; 12: 177-189
  • Prediction of Self-Assembly of Energetic Tiles and Dominos: Experiments Mathematics and Software.Sandia Labs Technical Report Istrail, S., Hurd, A., Lippert, R. A., Walenz, B., Batzoglou, S., Conway, J. H. 2000
  • Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B., Lander, E, S. 2000; 10: 950-958
  • Sequencing a genome by walking with clone-ends: A mathematical analysis. Genome Research Batzoglou, S., Mesirov, J. P., Berger, B., Lander, E, S. 1999; 9: 1163-1174
  • Physical mapping with repeated probes: The hypergraph superstring problem. Lecture Notes in Computer Science Batzoglou, S., Istrail, S. 1999; 1645: 66
  • A dictionary based approach to gene annotation. Journal of Computational Biology Pachter, L., Batzoglou, S., Spitkovsky, V. I., Banks, E., Lander, E. S., Kleitman, D. J. 1999; 6: 419–430
  • Recent developments in computational gene recognition. DocumentaMathematica Extra Volume ICM I Batzoglou, S., Berger, B., Kleitman, D. J., Lander, E. S., Pachter, L. 1998: 649-658
  • Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Journal of Computational Biology Agarwala, R., Batzoglou, S., Dancik, V., Decatur, S. E., Hannenhalli, S., Farach, M. 1997; 4: 275–-296

Books and Book Chapters


  • Current progress in static and dynamic modeling of biological networks. Systems Biology for Signaling Networks Daigle, B. J., Srinivasan, B. S., Flannick, J. A., Novak, A. F., Batzoglou, S. edited by Sangdun, C. Springer. 2010: 13-73
  • Proceedings of the 23th Annual International Conference on Research in Computational Molecular Biology. edited by Batzoglou, S. Springer-Verlag. 2009
  • Algorithmic Challenges in Mammalian Genome Sequence Assembly. Special Review, Encyclopedia of Genomics, Proteomics, and Bioinformatics. Encyclopedia of genomics, proteomics and bioinformatics. Batzoglou, S. edited by Dunn, M., Jorde, L., Little, P. Hoboken (New Jersey): John Wiley and Sons. 2005: 1
  • Distributed Algorithms: Instructors Manual. Lynch, N., Batzoglou, S., Boyko, V. Morgan Kauffman. 2001

Conference Proceedings


  • An accurate method for inferring relatedness in large datasets of unphased genotypes via an embedded likelihood-ratio test. Rodriguez, J., Batzoglou, S., Bercovici, S. 2013
  • Automated cellular annotation for high-resolution images of adult Caenorhabditiselegans. Bioinformatics Aerni, S. J., Liu, X., Do, C. B., Gross, S. S., Nguyen, A., Guo, S. D., Batzoglou, S. 2013
  • Ancestry inference in complex admixtures via variable-length Markov chain linkage models. Bercovici, S., Rodriguez, J., Elmore, M., Batzoglou, S. 2012
  • Reconstruction of genealogical relationships with application to Phase III of HapMap. Bioinformatics Kyriazopoulou-Panagiotopoulou, S., KashefHaghighi, D., Aerni, S. J., Sundquist, A., Bercovici, S., Batzoglou, S. 2011
  • A serial founder effect model for human settlements out of Africa. Deshpande, O., Batzoglou, S., Feldman, M., Cavalli-Sforza, L. 2009
  • Automatic parameter learning for multiple network alignment. Flannick, J., Novak, A., Srinivasan, B. S., Batzoglou, S. 2008
  • Effect of genetic divergence in identifying ancestral origin using HAPAA. Sundquist, A., Fratkin, E., Do, C. B., Batzoglou, S. 2008
  • MotifCut: Finding Regulatory Motifs with Maximum Density Subgraphs. Fratkin, E., Naughton, B., Brutlag, D. L., Batzoglou, S. 2006
  • Glocal alignment: finding rearrangements during alignment. Brudno, M., Malde, S., Poliakov, A., Do, C., Couronne, O., Dubchak, I., Batzoglou, S. 2003
  • Gene Regulation, Session Introduction. Batzoglou, S., Pachter, L. 2003
  • Sequencing a genome by walking with clone-ends: A mathematical analysis. Batzoglou, S., Mesirov, J. P., Berger, B., Lander, E, S. 2000
  • Human and mouse gene structure: comparative analysis and application to exon prediction. Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B., Lander, E, S. 2000
  • A dictionary based approach to gene annotation. Pachter, L., Batzoglou, S., Spitkovsky, V. I., Beebee, W., Lander, E. S., Berger, B. 1999
  • Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Agarwala, R., Batzoglou, S., Dancik, V., Decatur, S. E., Hannenhalli, S., Farach, M. 1997
  • Protein folding in the hydrophobic-polar model on the 3D triangular lattice. Decatur, S., Batzoglou, S. 1997
  • Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. Agarwala, R., Batzoglou, S., Dancik, V., Decatur, S. E., Hannenhalli, S., Farach, M. 1997

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