Serafim Batzoglou - Publications

Affiliations: 
Computer Science Stanford University, Palo Alto, CA 

88 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Ramazzotti D, Lal A, Wang B, Batzoglou S, Sidow A. Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival. Nature Communications. 9: 4453. PMID 30367051 DOI: 10.1038/s41467-018-06921-8  0.32
2018 Bishara A, Moss EL, Kolmogorov M, Parada AE, Weng Z, Sidow A, Dekas AE, Batzoglou S, Bhatt AS. High-quality genome sequences of uncultured microbes by assembly of read clouds. Nature Biotechnology. PMID 30320765 DOI: 10.1038/nbt.4266  0.32
2018 Zhou X, Batzoglou S, Sidow A, Zhang L. HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data. Bmc Genomics. 19: 467. PMID 29914369 DOI: 10.1186/s12864-018-4867-7  0.32
2017 Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A. Genome-wide reconstruction of complex structural variants using read clouds. Nature Methods. PMID 28714986 DOI: 10.1038/nmeth.4366  0.32
2016 Kuleshov V, Snyder MP, Batzoglou S. Genome assembly from synthetic long read clouds. Bioinformatics (Oxford, England). 32: i216-i224. PMID 27307620 DOI: 10.1093/bioinformatics/btw267  0.72
2015 Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nature Biotechnology. PMID 26655498 DOI: 10.1038/nbt.3416  0.72
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: 1570-80. PMID 26286554 DOI: 10.1101/gr.191189.115  0.72
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: 91. PMID 25944252 DOI: 10.1186/s13059-015-0647-8  0.72
2015 Weng Z, Spies N, Zhu SX, Newburger 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: 28. PMID 25918554 DOI: 10.1186/s13073-015-0146-2  0.72
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. PMID 25871848 DOI: 10.7554/eLife.05538  0.72
2015 Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-Dueñas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, et al. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America. 112: E1116-25. PMID 25713363 DOI: 10.1073/pnas.1501199112  0.72
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: 280-9. PMID 25273070 DOI: 10.1101/gr.173641.114  0.72
2015 Bishara A, Liu Y, Kashef-Haghighi D, Weng Z, Newburger DE, West R, Sidow A, Batzoglou S. Read clouds uncover variation in complex regions of the human genome Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 30-31. DOI: 10.1007/978-3-319-16706-0_5  0.72
2014 Batzoglou S, Schwartz R. Computational biology and bioinformatics. Bioinformatics (Oxford, England). 30: i1-2. PMID 24931972 DOI: 10.1093/bioinformatics/btu304  0.72
2014 Huang L, Bercovici S, Rodriguez JM, Batzoglou S. An effective filter for IBD detection in large data sets. Plos One. 9: e92713. PMID 24667521 DOI: 10.1371/journal.pone.0092713  0.72
2013 Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S. Inference of tumor phylogenies with improved somatic mutation discovery. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 933-44. PMID 24195709 DOI: 10.1089/cmb.2013.0106  0.72
2013 Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, ... ... Batzoglou S, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/science.1242510  0.32
2013 Huang L, Popic V, Batzoglou S. Short read alignment with populations of genomes. Bioinformatics (Oxford, England). 29: i361-70. PMID 23813006 DOI: 10.1093/bioinformatics/btt215  0.72
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. Bioinformatics (Oxford, England). 29: i18-26. PMID 23812982 DOI: 10.1093/bioinformatics/btt223  0.72
2013 Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A. Genome evolution during progression to breast cancer. Genome Research. 23: 1097-108. PMID 23568837 DOI: 10.1101/gr.151670.112  0.72
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 : a Journal of Computational Molecular Cell Biology. 20: 199-211. PMID 23421795 DOI: 10.1089/cmb.2012.0088  0.72
2013 Rodriguez JM, Batzoglou S, Bercovici S. An accurate method for inferring relatedness in large datasets of unphased genotypes via an embedded likelihood-ratio test Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 212-229. DOI: 10.1007/978-3-642-37195-0_18  0.72
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/gr.136184.111  0.72
2012 Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Research. 22: 1748-59. PMID 22955986 DOI: 10.1101/gr.136127.111  0.72
2012 Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research. 22: 1735-47. PMID 22955985 DOI: 10.1101/gr.136366.111  0.72
2012 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, ... ... Batzoglou S, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/nature11245  0.72
2012 Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP. The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. Nucleic Acids Research. 40: D1137-43. PMID 22102592 DOI: 10.1093/nar/gkr973  0.72
2011 Kyriazopoulou-Panagiotopoulou S, Kashef Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S. Reconstruction of genealogical relationships with applications to Phase III of HapMap. Bioinformatics (Oxford, England). 27: i333-41. PMID 21685089 DOI: 10.1093/bioinformatics/btr243  0.72
2010 Davydov EV, 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. PMID 21152010 DOI: 10.1371/journal.pcbi.1001025  0.72
2010 Batzoglou S. RECOMB Main Conference 2009. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 201. PMID 20377440 DOI: 10.1089/cmb.2010.Pr01  0.72
2010 Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Research. 20: 301-10. PMID 20067941 DOI: 10.1101/gr.102210.109  0.72
2009 Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. Plos Genetics. 5: e1000792. PMID 20041220 DOI: 10.1371/journal.pgen.1000792  0.72
2009 Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sánchez-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: 623-33. PMID 19879847 DOI: 10.1016/j.cell.2009.08.044  0.72
2009 Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple local network alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1001-22. PMID 19645599 DOI: 10.1089/cmb.2009.0099  0.72
2009 Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics (Oxford, England). 25: i21-9. PMID 19477990 DOI: 10.1093/bioinformatics/btp226  0.72
2009 Deshpande O, Batzoglou S, Feldman MW, Cavalli-Sforza LL. A serial founder effect model for human settlement out of Africa. Proceedings. Biological Sciences / the Royal Society. 276: 291-300. PMID 18796400 DOI: 10.1098/rspb.2008.0750  0.72
2009 Batzoglou S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: XI.  0.72
2008 Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods. 5: 829-34. PMID 19160518 DOI: 10.1038/nmeth.1246  0.72
2008 Boutte CC, Srinivasan BS, Flannick JA, Novak AF, Martens AT, Batzoglou S, Viollier PH, Crosson S. Genetic and computational identification of a conserved bacterial metabolic module. Plos Genetics. 4: e1000310. PMID 19096521 DOI: 10.1371/journal.pgen.1000310  0.72
2008 Do CB, Batzoglou S. What is the expectation maximization algorithm? Nature Biotechnology. 26: 897-9. PMID 18688245 DOI: 10.1038/nbt1406  0.72
2008 Do CB, Foo CS, Batzoglou S. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics (Oxford, England). 24: i68-76. PMID 18586747 DOI: 10.1093/bioinformatics/btn177  0.72
2008 Sundquist A, Fratkin E, Do CB, Batzoglou S. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Research. 18: 676-82. PMID 18353807 DOI: 10.1101/gr.072850.107  0.72
2008 Sundquist A, Fratkin E, Do CB, Batzoglou S. Effects of genetic divergence in identifying ancestral origin using HAPAA Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 423. DOI: 10.1007/978-3-540-78839-3_36  0.72
2008 Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple network alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 214-231. DOI: 10.1007/978-3-540-78839-3_19  0.72
2007 Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology. 8: R269. PMID 18096039 DOI: 10.1186/gb-2007-8-12-r269  0.72
2007 Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, El-Sayed YY, Taslimi MM, Batzoglou S, Ronaghi M. Bacterial flora-typing with targeted, chip-based Pyrosequencing. Bmc Microbiology. 7: 108. PMID 18047683 DOI: 10.1186/1471-2180-7-108  0.72
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Batzoglou S, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/nature06341  0.72
2007 Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S. Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics. 8: 318-32. PMID 17728341 DOI: 10.1093/bib/bbm038  0.72
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Batzoglou S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/gr.6034307  0.72
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: e484. PMID 17534434 DOI: 10.1371/journal.pone.0000484  0.72
2007 Gross SS, Russakovsky O, Do CB, Batzoglou S. Training conditional random fields for maximum labelwise accuracy Advances in Neural Information Processing Systems. 529-536.  0.72
2006 Phuong TM, Do CB, Edgar RC, Batzoglou S. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Research. 34: 5932-42. PMID 17068081 DOI: 10.1093/nar/gkl511  0.72
2006 Naughton BT, Fratkin E, Batzoglou S, Brutlag DL. A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Research. 34: 5730-9. PMID 17041233 DOI: 10.1093/nar/gkl585  0.72
2006 Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research. 16: 1169-81. PMID 16899655 DOI: 10.1101/gr.5235706  0.72
2006 Srinivasan BS, Do CB, Batzoglou S. Evidence for intelligent (algorithm) design. Genome Biology. 7: 322. PMID 16879725 DOI: 10.1186/gb-2006-7-7-322  0.72
2006 Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics (Oxford, England). 22: e90-8. PMID 16873527 DOI: 10.1093/bioinformatics/btl246  0.72
2006 Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. MotifCut: regulatory motifs finding with maximum density subgraphs. Bioinformatics (Oxford, England). 22: e150-7. PMID 16873465 DOI: 10.1093/bioinformatics/btl243  0.72
2006 Edgar RC, Batzoglou S. Multiple sequence alignment. Current Opinion in Structural Biology. 16: 368-73. PMID 16679011 DOI: 10.1016/j.sbi.2006.04.004  0.72
2006 Davydov E, Batzoglou S. A computational model for RNA multiple structural alignment Theoretical Computer Science. 368: 205-216. DOI: 10.1016/j.tcs.2006.09.013  0.72
2006 Do CB, Gross SS, Batzoglou S. CONTRAlign: Discriminative training for protein sequence alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 160-174. DOI: 10.1007/11732990_15  0.72
2006 Srinivasan BS, Novak AF, Flannick JA, Batzoglou S, McAdams HH. Integrated protein interaction networks for 11 microbes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 1-14.  0.72
2005 Manohar A, Batzoglou S. TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 111-9. PMID 16447969 DOI: 10.1109/CSB.2005.53  0.72
2005 Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, BaÅŸtürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 438: 1105-15. PMID 16372000 DOI: 10.1038/nature04341  0.72
2005 Flannick J, Batzoglou S. Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Research. 33: 4563-77. PMID 16100379 DOI: 10.1093/nar/gki767  0.72
2005 Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Research. 15: 901-13. PMID 15965027 DOI: 10.1101/gr.3577405  0.72
2005 Batzoglou S. The many faces of sequence alignment. Briefings in Bioinformatics. 6: 6-22. PMID 15826353 DOI: 10.1093/bib/6.1.6  0.72
2005 Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research. 15: 330-40. PMID 15687296 DOI: 10.1101/gr.2821705  0.72
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Batzoglou S, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/science.1105136  0.72
2004 Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research. 32: W204-7. PMID 15215381 DOI: 10.1093/nar/gkh461  0.72
2004 Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Research. 14: 685-92. PMID 15060011 DOI: 10.1101/gr.2067704  0.72
2004 Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Research. 14: 539-48. PMID 15059994 DOI: 10.1101/gr.2034704  0.48
2004 Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics (Oxford, England). 20: 636-43. PMID 15033870 DOI: 10.1093/bioinformatics/btg459  0.72
2004 Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Research. 14: 451-8. PMID 14993210 DOI: 10.1101/gr.1327604  0.72
2004 Do CB, Brudno M, Batzoglou S. PROBCONS: Probabilistic consistency-based multiple alignment of amino acid sequences Proceedings of the National Conference On Artificial Intelligence. 703-708.  0.72
2004 Sundararajan M, Brudno M, Small K, Sidow A, Batzoglou S. Chaining algorithms for alignment of draft sequence Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3240: 326-337.  0.72
2004 Lee SI, Batzoglou S. ICA-based clustering of genes from microarray expression data Advances in Neural Information Processing Systems 0.72
2003 Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. Bmc Bioinformatics. 4: 66. PMID 14693042 DOI: 10.1186/1471-2105-4-66  0.72
2003 Lee SI, Batzoglou S. Application of independent component analysis to microarrays. Genome Biology. 4: R76. PMID 14611662 DOI: 10.1186/gb-2003-4-11-r76  0.72
2003 Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AGenDA: homology-based gene prediction. Bioinformatics (Oxford, England). 19: 1575-7. PMID 12912840 DOI: 10.1093/bioinformatics/btg181  0.72
2003 Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Bioinformatics (Oxford, England). 19: i54-62. PMID 12855437 DOI: 10.1093/bioinformatics/btg1005  0.72
2003 Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Research. 13: 813-20. PMID 12727901 DOI: 10.1101/gr.1064503  0.72
2003 Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research. 13: 721-31. PMID 12654723 DOI: 10.1101/gr.926603  0.72
2002 Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Research. 12: 177-89. PMID 11779843 DOI: 10.1101/gr.208902  0.72
2000 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: 950-8. PMID 10899144 DOI: 10.1101/gr.10.7.950  0.72
1999 Batzoglou S, Berger B, Mesirov J, Lander ES. Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Genome Research. 9: 1163-74. PMID 10613838 DOI: 10.1101/gr.9.12.1163  0.72
1999 Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary-based approach for gene annotation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 419-30. PMID 10582576 DOI: 10.1089/106652799318364  0.72
1999 Pachter L, Batzoglou S, Spitkovsky VI, Beebee WS, Lander ES, Berger B, Kleitman DJ. Dictionary based approach for gene annotation Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 285-294.  0.72
1997 Agarwala R, Batzoglou S, Dancik V, Decatur SE, Farach M, Hannenhalli S, Muthukrishnan S, Skiena S. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model Proceedings of Thr Annual International Conference On Computational Molecular Biology, Recomb. 1-2.  0.72
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