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Items: 1 to 50 of 158

1.

A New EHR Training Curriculum and Assessment for Pediatric Residents.

Stroup K, Sanders B, Bernstein B, Scherzer L, Pachter LM.

Appl Clin Inform. 2017 Oct;8(4):994-1002. doi: 10.4338/ACI-2017-06-RA-0091. Epub 2017 Dec 14.

PMID:
29241239
2.

Discrimination and Mental Health in a Representative Sample of African-American and Afro-Caribbean Youth.

Pachter LM, Caldwell CH, Jackson JS, Bernstein BA.

J Racial Ethn Health Disparities. 2017 Sep 15. doi: 10.1007/s40615-017-0428-z. [Epub ahead of print]

PMID:
28916954
3.

Developing a Community-Wide Initiative to Address Childhood Adversity and Toxic Stress: A Case Study of The Philadelphia ACE Task Force.

Pachter LM, Lieberman L, Bloom SL, Fein JA.

Acad Pediatr. 2017 Sep - Oct;17(7S):S130-S135. doi: 10.1016/j.acap.2017.04.012.

PMID:
28865645
4.

Differential analysis of RNA-seq incorporating quantification uncertainty.

Pimentel H, Bray NL, Puente S, Melsted P, Pachter L.

Nat Methods. 2017 Jul;14(7):687-690. doi: 10.1038/nmeth.4324. Epub 2017 Jun 5.

PMID:
28581496
5.

Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study.

Goin DE, Smed MK, Pachter L, Purdom E, Nelson JL, Kjærgaard H, Olsen J, Hetland ML, Zoffmann V, Ottesen B, Jawaheer D.

Arthritis Res Ther. 2017 May 25;19(1):104. doi: 10.1186/s13075-017-1312-2.

6.

PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.

Li B, Tambe A, Aviran S, Pachter L.

Cell Syst. 2017 May 24;4(5):568-574.e7. doi: 10.1016/j.cels.2017.04.007. Epub 2017 May 10.

PMID:
28501650
7.

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.

Yi L, Pimentel H, Pachter L.

PLoS One. 2017 Apr 27;12(4):e0175744. doi: 10.1371/journal.pone.0175744. eCollection 2017.

8.

Pseudoalignment for metagenomic read assignment.

Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L.

Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106.

PMID:
28334086
9.

Editor-in-Chief's Note.

Pachter LM.

J Dev Behav Pediatr. 2017 Feb/Mar;38 Suppl 1:S1. doi: 10.1097/DBP.0000000000000431. No abstract available.

PMID:
28141704
10.

Hot topics, urgent priorities, and ensuring success for racial/ethnic minority young investigators in academic pediatrics.

Flores G, Mendoza FS, Fuentes-Afflick E, Mendoza JA, Pachter L, Espinoza J, Fernandez CR, Arnold DD, Brown NM, Gonzalez KM, Lopez C, Owen MC, Parks KM, Reynolds KL, Russell CJ.

Int J Equity Health. 2016 Dec 9;15(1):201.

11.

The Lair: a resource for exploratory analysis of published RNA-Seq data.

Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L.

BMC Bioinformatics. 2016 Dec 1;17(1):490.

12.

Estimating intrinsic and extrinsic noise from single-cell gene expression measurements.

Fu AQ, Pachter L.

Stat Appl Genet Mol Biol. 2016 Dec 1;15(6):447-471. doi: 10.1515/sagmb-2016-0002.

13.

Single-cell analysis at the threshold.

Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA.

Nat Biotechnol. 2016 Nov 8;34(11):1111-1118. doi: 10.1038/nbt.3721. No abstract available.

PMID:
27824834
14.

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.

Hateley S, Hosamani R, Bhardwaj SR, Pachter L, Bhattacharya S.

Genomics. 2016 Oct;108(3-4):158-167. doi: 10.1016/j.ygeno.2016.09.002. Epub 2016 Sep 10.

15.

Use of the surgical Apgar score to enhance Veterans Affairs Surgical Quality Improvement Program surgical risk assessment in veterans undergoing major intra-abdominal surgery.

Masi A, Amodeo S, Hatzaras I, Pinna A, Rosman AS, Cohen S, Saunders JK, Berman R, Newman E, Ballantyne GH, Pachter LH, Melis M.

Am J Surg. 2017 Apr;213(4):696-705. doi: 10.1016/j.amjsurg.2016.05.017. Epub 2016 Jul 21.

PMID:
27523923
16.

Erratum: Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L.

Nat Biotechnol. 2016 Aug 9;34(8):888. doi: 10.1038/nbt0816-888d. No abstract available.

PMID:
27504780
17.

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts.

Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN.

Genome Biol. 2016 May 26;17(1):112. doi: 10.1186/s13059-016-0970-8.

18.

Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L.

Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4. Erratum in: Nat Biotechnol. 2016 Aug 9;34(8):888.

PMID:
27043002
19.

Household and community-level Adverse Childhood Experiences and adult health outcomes in a diverse urban population.

Wade R Jr, Cronholm PF, Fein JA, Forke CM, Davis MB, Harkins-Schwarz M, Pachter LM, Bair-Merritt MH.

Child Abuse Negl. 2016 Feb;52:135-45. doi: 10.1016/j.chiabu.2015.11.021. Epub 2015 Dec 23.

PMID:
26726759
20.

Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis.

Mittal A, Pachter L, Nelson JL, Kjærgaard H, Smed MK, Gildengorin VL, Zoffmann V, Hetland ML, Jewell NP, Olsen J, Jawaheer D.

PLoS One. 2015 Dec 18;10(12):e0145204. doi: 10.1371/journal.pone.0145204. eCollection 2015.

21.

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis.

Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, Pachter L, Trapnell C, Buck LB.

Science. 2015 Dec 4;350(6265):1251-5. doi: 10.1126/science.aad2456. Epub 2015 Nov 5.

22.

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG.

Nucleic Acids Res. 2016 Jan 29;44(2):838-51. doi: 10.1093/nar/gkv1168. Epub 2015 Nov 3.

23.

Keeping the Heat on for Children's Health: A Successful Medical-Legal Partnership Initiative to Prevent Utility Shutoffs in Vulnerable Children.

Taylor DR, Bernstein BA, Carroll E, Oquendo E, Peyton L, Pachter LM.

J Health Care Poor Underserved. 2015 Aug;26(3):676-85. doi: 10.1353/hpu.2015.0074.

PMID:
26320904
24.

Adverse Childhood Experiences: Expanding the Concept of Adversity.

Cronholm PF, Forke CM, Wade R, Bair-Merritt MH, Davis M, Harkins-Schwarz M, Pachter LM, Fein JA.

Am J Prev Med. 2015 Sep;49(3):354-61. doi: 10.1016/j.amepre.2015.02.001.

PMID:
26296440
25.

Culture and Dehydration: A Comparative Study of Caída de la Mollera (Fallen Fontanel) in Three Latino Populations.

Pachter LM, Weller SC, Baer RD, de Alba Garcia JE, Glazer M, Trotter R, Klein RE, Gonzalez E.

J Immigr Minor Health. 2016 Oct;18(5):1066-75. doi: 10.1007/s10903-015-0259-0.

PMID:
26239172
26.

The NIH BD2K center for big data in translational genomics.

Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D.

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13.

27.

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J.

N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10.

28.

Controlling for conservation in genome-wide DNA methylation studies.

Singer M, Pachter L.

BMC Genomics. 2015 May 30;16:420. doi: 10.1186/s12864-015-1604-3.

29.

Does lymph node ratio affect prognosis in gastroesophageal cancer?

Melis M, Masi A, Pinna A, Cohen S, Hatzaras I, Berman R, Pachter LH, Newman E.

Am J Surg. 2015 Sep;210(3):443-50. doi: 10.1016/j.amjsurg.2014.12.042. Epub 2015 Apr 24.

PMID:
26003203
30.

A diverse epigenetic landscape at human exons with implication for expression.

Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y.

Nucleic Acids Res. 2015 Apr 20;43(7):3498-508. doi: 10.1093/nar/gkv153. Epub 2015 Mar 12.

31.

New Century Scholars: A Mentorship Program to Increase Workforce Diversity in Academic Pediatrics.

Pachter LM, Kodjo C.

Acad Med. 2015 Jul;90(7):881-7. doi: 10.1097/ACM.0000000000000669.

PMID:
25692562
32.

Prevention of noncommunicable diseases.

Pachter LM, Cheng TL.

JAMA. 2014 Dec 17;312(23):2572-3. doi: 10.1001/jama.2014.15140. No abstract available.

PMID:
25514311
33.

Rational experiment design for sequencing-based RNA structure mapping.

Aviran S, Pachter L.

RNA. 2014 Dec;20(12):1864-77. doi: 10.1261/rna.043844.113. Epub 2014 Oct 20.

34.

Adverse events in children: predictors of adult physical and mental conditions.

Van Niel C, Pachter LM, Wade R Jr, Felitti VJ, Stein MT.

J Dev Behav Pediatr. 2014 Oct;35(8):549-51. doi: 10.1097/DBP.0000000000000102. Erratum in: J Dev Behav Pediatr. 2014 Nov-Dec;35(9):581.

PMID:
25225793
35.

Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells.

Forster R, Chiba K, Schaeffer L, Regalado SG, Lai CS, Gao Q, Kiani S, Farin HF, Clevers H, Cost GJ, Chan A, Rebar EJ, Urnov FD, Gregory PD, Pachter L, Jaenisch R, Hockemeyer D.

Stem Cell Reports. 2014 Jun 3;2(6):838-52. doi: 10.1016/j.stemcr.2014.05.001. eCollection 2014 Jun 3. Erratum in: Stem Cell Reports. 2014 Jul 8;3(1):215.

36.

Structural variation among wild and industrial strains of Penicillium chrysogenum.

Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB.

PLoS One. 2014 May 13;9(5):e96784. doi: 10.1371/journal.pone.0096784. eCollection 2014.

37.

Efforts to diversify the academic pediatric workforce.

Thompson DA, Pachter LM, Keller D.

JAMA Pediatr. 2014 Apr;168(4):390-1. doi: 10.1001/jamapediatrics.2013.4867. No abstract available.

PMID:
24710589
38.

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity.

Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DI, Boffelli D.

Genome Res. 2014 May;24(5):821-30. doi: 10.1101/gr.162412.113. Epub 2014 Feb 20.

39.

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG.

Nucleic Acids Res. 2014 Apr;42(6):4031-42. doi: 10.1093/nar/gkt1388. Epub 2014 Jan 17.

40.

Fragment assignment in the cloud with eXpress-D.

Roberts A, Feng H, Pachter L.

BMC Bioinformatics. 2013 Dec 7;14:358. doi: 10.1186/1471-2105-14-358.

41.

SHAPE-Seq: High-Throughput RNA Structure Analysis.

Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB.

Curr Protoc Chem Biol. 2012 Dec 1;4(4):275-97. doi: 10.1002/9780470559277.ch120019.

PMID:
23788555
42.

Updating RNA-Seq analyses after re-annotation.

Roberts A, Schaeffer L, Pachter L.

Bioinformatics. 2013 Jul 1;29(13):1631-7. doi: 10.1093/bioinformatics/btt197. Epub 2013 May 14.

43.

CGAL: computing genome assembly likelihoods.

Rahman A, Pachter L.

Genome Biol. 2013 Jan 29;14(1):R8. doi: 10.1186/gb-2013-14-1-r8.

44.

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L.

Nat Biotechnol. 2013 Jan;31(1):46-53. doi: 10.1038/nbt.2450. Epub 2012 Dec 9.

45.

Streaming fragment assignment for real-time analysis of sequencing experiments.

Roberts A, Pachter L.

Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251. Epub 2012 Nov 18.

46.

Quantifying uniformity of mapped reads.

Hower V, Starfield R, Roberts A, Pachter L.

Bioinformatics. 2012 Oct 15;28(20):2680-2. doi: 10.1093/bioinformatics/bts451. Epub 2012 Jul 18.

47.

Complementary and alternative medicine use and adherence with pediatric asthma treatment.

Philp JC, Maselli J, Pachter LM, Cabana MD.

Pediatrics. 2012 May;129(5):e1148-54. doi: 10.1542/peds.2011-2467. Epub 2012 Apr 9.

48.

A closer look at RNA editing.

Pachter L.

Nat Biotechnol. 2012 Mar 7;30(3):246-7. doi: 10.1038/nbt.2156. No abstract available.

PMID:
22398619
49.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Erratum in: Nat Protoc. 2014 Oct;9(10):2513.

50.

RNA-Seq and find: entering the RNA deep field.

Roberts A, Pachter L.

Genome Med. 2011 Nov 22;3(11):74. doi: 10.1186/gm290.

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