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Papers authored by Pachter L

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Starting early: a life-course perspective on child health disparities--research recommendations.

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DC Baltimore Research Center on Child Health Disparities Writing Group, Horn IB, Cora-Bramble D, Cheng TL, Jenkins R, Pachter L, and Joseph J

Pediatrics 124 Suppl 3:S257-61, 2009 Nov - Who cited this? | PubMed ID: 19861478 | Fulltext

Racism and child health: a review of the literature and future directions.

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Pachter LM and Coll CG

Journal of developmental and behavioral pediatrics : JDBP 30(3):255-63, 2009 Jun - Who cited this? | PubMed ID: 19525720 | Fulltext

TopHat: discovering splice junctions with RNA-Seq.

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Trapnell C, Pachter L, and Salzberg SL

Bioinformatics (Oxford, England) 25(9):1105-11, 2009 May 1 - Who cited this? | PubMed ID: 19289445 | Fulltext

Fast statistical alignment.

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Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, and Pachter L

PLoS computational biology 5(5):e1000392, 2009 May - Who cited this? | PubMed ID: 19478997 | Fulltext

Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing.

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Bradley RK, Pachter L, and Holmes I

Bioinformatics (Oxford, England), 2008 Sep 16 - Who cited this? | PubMed ID: 18796475 | Fulltext

Combinatorics of least-squares trees.

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Mihaescu R and Pachter L

Proceedings of the National Academy of Sciences of the United States of America 105(36):13206, 2008 Sep 9 - Who cited this? | PubMed ID: 18779558 | Fulltext

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

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Satija R, Pachter L, and Hein J

Bioinformatics (Oxford, England) 24(10):1236-42, 2008 May 15 - Who cited this? | PubMed ID: 18353788 | Fulltext

Viral population estimation using pyrosequencing.

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Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, and Beerenwinkel N

PLoS computational biology 4(4), 2008 Apr - Who cited this? | PubMed ID: 18437230 | Fulltext

Comparison of pattern detection methods in microarray time series of the segmentation clock.

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Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, and Pourquié O

PLoS ONE 3(8), 2008 - Who cited this? | PubMed ID: 18682743 | Fulltext

On the optimality of the neighbor-joining algorithm.

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Eickmeyer K, Huggins P, Pachter L, and Yoshida R

Algorithms for molecular biology : AMB 3:5, 2008 - Who cited this? | PubMed ID: 18447942 | 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

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

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Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, , , Hodges E, Hinrichs AS,

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Nature 450(7167):219, 2007 Nov 8 - Who cited this? | PubMed ID: 17994088 | Fulltext

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

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Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, and Langley CH

PLoS biology 5(11), 2007 Nov 6 - Who cited this? | PubMed ID: 17988176 | Fulltext

Toward the human genotope.

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Huggins P, Pachter L, and Sturmfels B

Bulletin of mathematical biology 69(8):2723, 2007 Nov - Who cited this? | PubMed ID: 17874271 | Fulltext

Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor.

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Chatterji S and Pachter L

Genomics 90(1):44-8, 2007 Jul - Who cited this? | PubMed ID: 17499477 | 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

Interpreting the unculturable majority.

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Pachter L

Nature methods 4(6):479-80, 2007 Jun - Who cited this? | PubMed ID: 17538628 | Fulltext

Multiple alignment by sequence annealing.

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Schwartz AS and Pachter L

Bioinformatics (Oxford, England) 23(2):e24-9, 2007 Jan 15 - Who cited this? | PubMed ID: 17237099 | Fulltext

Analysis of epistatic interactions and fitness landscapes using a new geometric approach.

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Beerenwinkel N, Pachter L, Sturmfels B, Elena SF, and Lenski RE

BMC evolutionary biology 7:60, 2007 - Who cited this? | PubMed ID: 17433106 | Fulltext

The cyclohedron test for finding periodic genes in time course expression studies.

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Morton J, Pachter L, Shiu A, and Sturmfels B

Statistical applications in genetics and molecular biology 6:Article 21, 2007 - Who cited this? | PubMed ID: 17764440 | Fulltext

Role of pediatric health care professionals in the provision of parenting advice: a qualitative study with mothers from 4 minority ethnocultural groups.

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Dumont-Mathieu TM, Bernstein BA, Dworkin PH, and Pachter LM

Pediatrics 118(3), 2006 Sep - Who cited this? | PubMed ID: 16950970 | Fulltext

Parametric alignment of Drosophila genomes.

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Dewey CN, Huggins PM, Woods K, Sturmfels B, and Pachter L

PLoS computational biology 2(6):e73, 2006 Jun 23 - Who cited this? | PubMed ID: 16789815 | Fulltext

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

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Dewey CN and Pachter L

Human molecular genetics 15 Spec No 1:R51-6, 2006 Apr 15 - Who cited this? | PubMed ID: 16651369 | Fulltext

Do parenting and the home environment, maternal depression, neighborhood, and chronic poverty affect child behavioral problems differently in different racial-ethnic groups?.

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Pachter LM, Auinger P, Palmer R, and Weitzman M

Pediatrics 117(4):1329-38, 2006 Apr - Who cited this? | PubMed ID: 16585331 | Fulltext

A genome-wide map of conserved microRNA targets in C. elegans.

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Lall S, Grün D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, and Rajewsky N

Current biology : CB 16(5):460, 2006 Mar 7 - Who cited this? | PubMed ID: 16458514 | Fulltext

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.

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Levy D, Yoshida R, and Pachter L

Molecular biology and evolution 23(3):491, 2006 Mar - Who cited this? | PubMed ID: 16280538 | Fulltext

Identification of transposable elements using multiple alignments of related genomes.

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Caspi A and Pachter L

Genome research 16(2):260-70, 2006 Feb - Who cited this? | PubMed ID: 16354754 | Fulltext

Reference based annotation with GeneMapper.

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Chatterji S and Pachter L

Genome biology 7(4):R29, 2006 - Who cited this? | PubMed ID: 16600017 | Fulltext

Bioinformatics for whole-genome shotgun sequencing of microbial communities.

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Chen K and Pachter L

PLoS computational biology 1(2):106-12, 2005 Jul - Who cited this? | PubMed ID: 16110337 | Fulltext

Subtree power analysis and species selection for comparative genomics.

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McAuliffe JD, Jordan MI, and Pachter L

Proceedings of the National Academy of Sciences of the United States of America 102(22):7900-5, 2005 May 31 - Who cited this? | PubMed ID: 15911755 | Fulltext

Large multiple organism gene finding by collapsed Gibbs sampling.

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Chatterji S and Pachter L

Journal of computational biology : a journal of computational molecular cell biology 12(6):599-608, 2005 - Who cited this? | PubMed ID: 16108706 | Fulltext

Intraspecies sequence comparisons for annotating genomes.

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Boffelli D, Weer CV, Weng L, Lewis KD, Shoukry MI, Pachter L, Keys DN, and Rubin EM

Genome research 14(12):2406-11, 2004 Dec - Who cited this? | PubMed ID: 15545499 | Fulltext

Parametric inference for biological sequence analysis.

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Pachter L and Sturmfels B

Proceedings of the National Academy of Sciences of the United States of America 101(46):16138-43, 2004 Nov 16 - Who cited this? | PubMed ID: 15534223 | Fulltext

Tropical geometry of statistical models.

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Pachter L and Sturmfels B

Proceedings of the National Academy of Sciences of the United States of America 101(46):16132-7, 2004 Nov 16 - Who cited this? | PubMed ID: 15534224 | Fulltext

Disruptive classroom behavior in an amish school-age child with muscular dystrophy.

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Stein MT, Pachter LM, Schwartz L, and Taras H

Journal of developmental and behavioral pediatrics : JDBP 25(5 Suppl):S102-6, 2004 Oct - Who cited this? | PubMed ID: 15502525 | Fulltext

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.

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McAuliffe JD, Pachter L, and Jordan MI

Bioinformatics (Oxford, England) 20(12):1850, 2004 Aug 12 - Who cited this? | PubMed ID: 14988105 | Fulltext

Disruptive classroom behavior in an Amish school-age child with muscular dystrophy.

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Stein MT, Pachter LM, Schwartz L, and Taras H

Journal of developmental and behavioral pediatrics : JDBP 25(4):280-4, 2004 Aug - Who cited this? | PubMed ID: 15308929 | Fulltext

VISTA: computational tools for comparative genomics.

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Frazer KA, Pachter L, Poliakov A, Rubin EM, and Dubchak I

Nucleic acids research 32(Web Server issue):W273-9, 2004 Jul 1 - Who cited this? | PubMed ID: 15215394 | 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

Identification of evolutionary hotspots in the rodent genomes.

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Yap VB and Pachter L

Genome research 14(4):574-9, 2004 Apr - Who cited this? | PubMed ID: 15059998 | Fulltext

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

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Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, and Pachter L

Genome research 14(4):661-4, 2004 Apr - Who cited this? | PubMed ID: 15060007 | Fulltext

MAVID: constrained ancestral alignment of multiple sequences.

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Bray N and Pachter L

Genome research 14(4):693-9, 2004 Apr - Who cited this? | PubMed ID: 15060012 | Fulltext

Visualization of multiple genome annotations and alignments with the K-BROWSER.

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Chakrabarti K and Pachter L

Genome research 14(4):716-20, 2004 Apr - Who cited this? | PubMed ID: 15060015 | Fulltext

HMM sampling and applications to gene finding and alternative splicing.

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Cawley SL and Pachter L

Bioinformatics (Oxford, England) 19 Suppl 2:ii36-41, 2003 Oct - Who cited this? | PubMed ID: 14534169 | Fulltext

A cross-cultural approach to the study of the folk illness nervios.

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Baer RD, Weller SC, de Alba Garcia JG, Glazer M, Trotter R, Pachter L, and Klein RE

Culture, medicine and psychiatry 27(3):315-37, 2003 Sep - Who cited this? | PubMed ID: 14510097 | Fulltext

SLAM web server for comparative gene finding and alignment.

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Cawley S, Pachter L, and Alexandersson M

Nucleic acids research 31(13):3507-9, 2003 Jul 1 - Who cited this? | PubMed ID: 12824355 | Fulltext

MAVID multiple alignment server.

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Bray N and Pachter L

Nucleic acids research 31(13):3525-6, 2003 Jul 1 - Who cited this? | PubMed ID: 12824358 | Fulltext

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

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Alexandersson M, Cawley S, and Pachter L

Genome research 13(3):496-502, 2003 Mar - Who cited this? | PubMed ID: 12618381 | Fulltext

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