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Items: 1 to 50 of 170

1.

Factor analysis for survival time prediction with informative censoring and diverse covariates.

McCurdy S, Molinaro A, Pachter L.

Stat Med. 2019 Sep 10;38(20):3719-3732. doi: 10.1002/sim.8151. Epub 2019 Jun 4.

PMID:
31162708
2.

The Barcode, UMI, Set format and BUStools.

Melsted P, Ntranos V, Pachter L.

Bioinformatics. 2019 May 9. pii: btz279. doi: 10.1093/bioinformatics/btz279. [Epub ahead of print]

PMID:
31073610
3.

Race, Ethnicity, Socioeconomic Factors, and Attention-Deficit Hyperactivity Disorder.

Zuckerman KE, Pachter LM.

J Dev Behav Pediatr. 2019 Feb/Mar;40(2):150-151. doi: 10.1097/DBP.0000000000000645. No abstract available.

PMID:
30741781
4.

Deterministic column subset selection for single-cell RNA-Seq.

McCurdy SR, Ntranos V, Pachter L.

PLoS One. 2019 Jan 25;14(1):e0210571. doi: 10.1371/journal.pone.0210571. eCollection 2019.

5.

A discriminative learning approach to differential expression analysis for single-cell RNA-seq.

Ntranos V, Yi L, Melsted P, Pachter L.

Nat Methods. 2019 Feb;16(2):163-166. doi: 10.1038/s41592-018-0303-9. Epub 2019 Jan 21.

PMID:
30664774
6.

Barcode identification for single cell genomics.

Tambe A, Pachter L.

BMC Bioinformatics. 2019 Jan 17;20(1):32. doi: 10.1186/s12859-019-2612-0.

7.

Expression reflects population structure.

Brown BC, Bray NL, Pachter L.

PLoS Genet. 2018 Dec 19;14(12):e1007841. doi: 10.1371/journal.pgen.1007841. eCollection 2018 Dec.

8.

RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq.

Svensson V, Pachter L.

Mol Cell. 2018 Oct 4;72(1):7-9. doi: 10.1016/j.molcel.2018.09.026.

PMID:
30290149
9.

Accurate design of translational output by a neural network model of ribosome distribution.

Tunney R, McGlincy NJ, Graham ME, Naddaf N, Pachter L, Lareau LF.

Nat Struct Mol Biol. 2018 Jul;25(7):577-582. doi: 10.1038/s41594-018-0080-2. Epub 2018 Jul 2.

10.

Association mapping from sequencing reads using k-mers.

Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L.

Elife. 2018 Jun 13;7. pii: e32920. doi: 10.7554/eLife.32920.

11.

Intergenerational Associations of Parent Adverse Childhood Experiences and Child Health Outcomes.

Lê-Scherban F, Wang X, Boyle-Steed KH, Pachter LM.

Pediatrics. 2018 Jun;141(6). pii: e20174274. doi: 10.1542/peds.2017-4274. Epub 2018 May 21.

12.

Gene-level differential analysis at transcript-level resolution.

Yi L, Pimentel H, Bray NL, Pachter L.

Genome Biol. 2018 Apr 12;19(1):53. doi: 10.1186/s13059-018-1419-z.

13.

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.

14.

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. 2018 Aug;5(4):831-837. doi: 10.1007/s40615-017-0428-z. Epub 2017 Sep 15.

15.

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
16.

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
17.

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.

18.

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.

19.

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.

20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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
26.

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.

27.

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
28.

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
29.

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.

30.

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
31.

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
32.

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.

33.

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.

34.

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.

35.

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
36.

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
37.

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
38.

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.

39.

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.

40.

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.

41.

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
42.

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.

43.

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
44.

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
45.

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.

46.

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
47.

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.

48.

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.

49.

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
50.

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.

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