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Papers authored by Batzoglou S

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Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans.

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Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sánchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S, Myers EW, and Kim SK

Cell 139(3):623-33, 2009 Oct 30 - Who cited this? | PubMed ID: 19879847 | Fulltext

Automatic parameter learning for multiple local network alignment.

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Flannick J, Novak A, Do CB, Srinivasan BS, and Batzoglou S

Journal of computational biology : a journal of computational molecular cell biology 16(8):1001-22, 2009 Aug - Who cited this? | PubMed ID: 19645599 | Fulltext

A Classifier-based approach to identify genetic similarities between diseases.

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Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, and Batzoglou S

Bioinformatics (Oxford, England) 25(12):i21-9, 2009 Jun 15 - Who cited this? | PubMed ID: 19477990 | Fulltext

A serial founder effect model for human settlement out of Africa.

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Deshpande O, Batzoglou S, Feldman MW, and Cavalli-Sforza LL

Proceedings. Biological sciences / The Royal Society 276(1655):291-300, 2009 Jan 22 - Who cited this? | PubMed ID: 18796400 | Fulltext

Genetic and computational identification of a conserved bacterial metabolic module.

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Boutte CC, Srinivasan BS, Flannick JA, Novak AF, Martens AT, Batzoglou S, Viollier PH, and Crosson S

PLoS genetics 4(12):e1000310, 2008 Dec - Who cited this? | PubMed ID: 19096521 | Fulltext

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

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Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, and Sidow A

Nature methods 5(9):829-34, 2008 Sep - Who cited this? | PubMed ID: 19160518 | Fulltext

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

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Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, and Sidow A

Nature methods, 2008 Aug 17 - Who cited this? | PubMed ID: 18711362 | Fulltext

What is the expectation maximization algorithm?.

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Do CB and Batzoglou S

Nature biotechnology 26(8):897-9, 2008 Aug - Who cited this? | PubMed ID: 18688245 | Fulltext

A max-margin model for efficient simultaneous alignment and folding of RNA sequences.

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Do CB, Foo CS, and Batzoglou S

Bioinformatics (Oxford, England) 24(13), 2008 Jul 1 - Who cited this? | PubMed ID: 18586747 | Fulltext

Effect of genetic divergence in identifying ancestral origin using HAPAA.

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Sundquist A, Fratkin E, Do CB, and Batzoglou S

Genome research 18(4):676-82, 2008 Apr - Who cited this? | PubMed ID: 18353807 | Fulltext

Evolution of genes and genomes on the Drosophila phylogeny.

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, 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, Abad JP,

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Nature 450(7167):203, 2007 Nov 8 - Who cited this? | PubMed ID: 17994087 | Fulltext

Current progress in network research: toward reference networks for key model organisms.

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Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, and Batzoglou S

Briefings in bioinformatics 8(5):318-32, 2007 Sep - Who cited this? | PubMed ID: 17728341 | Fulltext

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

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, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S,

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Nature 447(7146):799, 2007 Jun 14 - Who cited this? | PubMed ID: 17571346 | Fulltext

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

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, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S,

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Nature 447(7146):799, 2007 Jun 14 - Who cited this? | PubMed ID: 17611759 | Fulltext

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

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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, Pardi F,

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Genome research 17(6):760, 2007 Jun - Who cited this? | PubMed ID: 17567995 | Fulltext

Bacterial flora-typing with targeted, chip-based Pyrosequencing.

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Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, El-Sayed YY, Taslimi MM, Batzoglou S, and Ronaghi M

BMC microbiology 7:108, 2007 - Who cited this? | PubMed ID: 18047683 | Fulltext

Whole-genome sequencing and assembly with high-throughput, short-read technologies.

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Sundquist A, Ronaghi M, Tang H, Pevzner P, and Batzoglou S

PLoS ONE 2(5):e484, 2007 - Who cited this? | PubMed ID: 17534434 | Fulltext

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

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Gross SS, Do CB, Sirota M, and Batzoglou S

Genome biology 8(12):R269, 2007 - Who cited this? | PubMed ID: 18096039 | Fulltext

Graemlin: general and robust alignment of multiple large interaction networks.

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Flannick J, Novak A, Srinivasan BS, McAdams HH, and Batzoglou S

Genome research 16(9):1169, 2006 Sep - Who cited this? | PubMed ID: 16899655 | Fulltext

MotifCut: regulatory motifs finding with maximum density subgraphs.

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Fratkin E, Naughton BT, Brutlag DL, and Batzoglou S

Bioinformatics (Oxford, England) 22(14), 2006 Jul 15 - Who cited this? | PubMed ID: 16873465 | Fulltext

CONTRAfold: RNA secondary structure prediction without physics-based models.

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Do CB, Woods DA, and Batzoglou S

Bioinformatics (Oxford, England) 22(14), 2006 Jul 15 - Who cited this? | PubMed ID: 16873527 | Fulltext

Multiple sequence alignment.

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Edgar RC and Batzoglou S

Current opinion in structural biology 16(3):368, 2006 Jun - Who cited this? | PubMed ID: 16679011 | Fulltext

Multiple alignment of protein sequences with repeats and rearrangements.

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Phuong TM, Do CB, Edgar RC, and Batzoglou S

Nucleic acids research 34(20):5932, 2006 - Who cited this? | PubMed ID: 17068081 | Fulltext

Evidence for intelligent (algorithm) design.

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Srinivasan BS, Do CB, and Batzoglou S

Genome biology 7(7):322, 2006 - Who cited this? | PubMed ID: 16879725 | Fulltext

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.

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Naughton BT, Fratkin E, Batzoglou S, and Brutlag DL

Nucleic acids research 34(20):5730-9, 2006 - Who cited this? | PubMed ID: 17041233 | Fulltext

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.

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Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S,

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Nature 438(7071):1105, 2005 Dec 22 - Who cited this? | PubMed ID: 16372000 | Fulltext

Distribution and intensity of constraint in mammalian genomic sequence.

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Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, and Sidow A

Genome research 15(7):901-13, 2005 Jul - Who cited this? | PubMed ID: 15965027 | Fulltext

The many faces of sequence alignment.

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Batzoglou S

Briefings in bioinformatics 6(1):6, 2005 Mar - Who cited this? | PubMed ID: 15826353 | Fulltext

ProbCons: Probabilistic consistency-based multiple sequence alignment.

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Do CB, Mahabhashyam MS, Brudno M, and Batzoglou S

Genome research 15(2):330, 2005 Feb - Who cited this? | PubMed ID: 15687296 | Fulltext

Using multiple alignments to improve seeded local alignment algorithms.

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Flannick J and Batzoglou S

Nucleic acids research 33(14):4563-77, 2005 - Who cited this? | PubMed ID: 16100379 | Fulltext

TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.

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Manohar A and Batzoglou S

Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference:111-9, 2005 - Who cited this? | PubMed ID: 16447969 | Fulltext

A suite of web-based programs to search for transcriptional regulatory motifs.

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Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, and Liu XS

Nucleic acids research 32(Web Server issue):W204-7, 2004 Jul 1 - Who cited this? | PubMed ID: 15215381 | Fulltext

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S,

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Nature 428(6982):493, 2004 Apr 1 - Who cited this? | PubMed ID: 15057822 | Fulltext

Characterization of evolutionary rates and constraints in three Mammalian genomes.

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Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, and Sidow A

Genome research 14(4):539-48, 2004 Apr - Who cited this? | PubMed ID: 15059994 | Fulltext

Automated whole-genome multiple alignment of rat, mouse, and human.

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Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, and Dubchak I

Genome research 14(4):685-92, 2004 Apr - Who cited this? | PubMed ID: 15060011 | Fulltext

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

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Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, and Dubchak I

Bioinformatics (Oxford, England) 20(5):636, 2004 Mar 22 - Who cited this? | PubMed ID: 15033870 | Fulltext

Eukaryotic regulatory element conservation analysis and identification using comparative genomics.

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Liu Y, Liu XS, Wei L, Altman RB, and Batzoglou S

Genome research 14(3):451-8, 2004 Mar - Who cited this? | PubMed ID: 14993210 | Fulltext

Fast and sensitive multiple alignment of large genomic sequences.

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Brudno M, Chapman M, Göttgens B, Batzoglou S, and Morgenstern B

BMC bioinformatics 4:66, 2003 Dec 23 - Who cited this? | PubMed ID: 14693042 | Fulltext

AGenDA: homology-based gene prediction.

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Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, and Morgenstern B

Bioinformatics (Oxford, England) 19(12):1575, 2003 Aug 12 - Who cited this? | PubMed ID: 12912840 | Fulltext

Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay.

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Khambata-Ford S, Liu Y, Gleason C, Dickson M, Altman RB, Batzoglou S, and Myers RM

Genome research 13(7):1765-74, 2003 Jul - Who cited this? | PubMed ID: 12805274 | Fulltext

Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.

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Cooper GM, Brudno M, NISC Comparative Sequencing Program, Green ED, Batzoglou S, and Sidow A

Genome research 13(5):813-20, 2003 May - Who cited this? | PubMed ID: 12727901 | Fulltext

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

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Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, NISC Comparative Sequencing Program, Green ED, Sidow A, and Batzoglou S

Genome research 13(4):721-31, 2003 Apr - Who cited this? | PubMed ID: 12654723 | Fulltext

Glocal alignment: finding rearrangements during alignment.

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Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, and Batzoglou S

Bioinformatics (Oxford, England) 19 Suppl 1:i54-62, 2003 - Who cited this? | PubMed ID: 12855437 | Fulltext

Application of independent component analysis to microarrays.

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Lee SI and Batzoglou S

Genome biology 4(11):R76, 2003 - Who cited this? | PubMed ID: 14611662 | Fulltext

ARACHNE: a whole-genome shotgun assembler.

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Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, and Lander ES

Genome research 12(1):177, 2002 Jan - Who cited this? | PubMed ID: 11779843 | Fulltext

Initial sequencing and analysis of the human genome.

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Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L,

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Nature 409(6822):860, 2001 Feb 15 - Who cited this? | PubMed ID: 11237011 | Fulltext

Human and mouse gene structure: comparative analysis and application to exon prediction.

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Batzoglou S, Pachter L, Mesirov JP, Berger B, and Lander ES

Genome research 10(7):950-8, 2000 Jul - Who cited this? | PubMed ID: 10899144 | Fulltext

A dictionary-based approach for gene annotation.

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Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, and Berger B

Journal of computational biology : a journal of computational molecular cell biology 6(3-4):419 - Who cited this? | PubMed ID: 10582576 | Fulltext

Sequencing a genome by walking with clone-end sequences: a mathematical analysis.

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Batzoglou S, Berger B, Mesirov J, and Lander ES

Genome research 9(12):1163-74, 1999 Dec - Who cited this? | PubMed ID: 10613838 | Fulltext

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model.

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Agarwala R, Batzoglou S, Dancík V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, and Skiena S

Journal of computational biology : a journal of computational molecular cell biology 4(3):275-96, 1997 - Who cited this? | PubMed ID: 9278060 | Fulltext

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