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Items: 1 to 50 of 78

1.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J.

Cell. 2019 Mar 7;176(6):1516. doi: 10.1016/j.cell.2019.02.027. No abstract available.

PMID:
30849375
2.

The single-cell transcriptional landscape of mammalian organogenesis.

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J.

Nature. 2019 Feb;566(7745):496-502. doi: 10.1038/s41586-019-0969-x. Epub 2019 Feb 20.

PMID:
30787437
3.

A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets.

Sharon N, Chawla R, Mueller J, Vanderhooft J, Whitehorn LJ, Rosenthal B, Gürtler M, Estanboulieh RR, Shvartsman D, Gifford DK, Trapnell C, Melton D.

Cell. 2019 Feb 7;176(4):790-804.e13. doi: 10.1016/j.cell.2018.12.003. Epub 2019 Jan 17.

PMID:
30661759
4.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J.

Cell. 2019 Jan 10;176(1-2):377-390.e19. doi: 10.1016/j.cell.2018.11.029. Epub 2019 Jan 3. Erratum in: Cell. 2019 Mar 7;176(6):1516.

PMID:
30612741
5.

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome.

Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C.

Cell Syst. 2018 Sep 26;7(3):258-268.e3. doi: 10.1016/j.cels.2018.07.006. Epub 2018 Sep 5.

6.

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J.

Science. 2018 Sep 28;361(6409):1380-1385. doi: 10.1126/science.aau0730. Epub 2018 Aug 30.

PMID:
30166440
7.

Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation.

Wray-Dutra MN, Chawla R, Thomas KR, Seymour BJ, Arkatkar T, Sommer KM, Khim S, Trapnell C, James RG, Rawlings DJ.

J Exp Med. 2018 Sep 3;215(9):2445-2461. doi: 10.1084/jem.20180230. Epub 2018 Aug 20.

8.

iPSC-Derived Macrophages Effectively Treat Pulmonary Alveolar Proteinosis in Csf2rb-Deficient Mice.

Mucci A, Lopez-Rodriguez E, Hetzel M, Liu S, Suzuki T, Happle C, Ackermann M, Kempf H, Hillje R, Kunkiel J, Janosz E, Brennig S, Glage S, Bankstahl JP, Dettmer S, Rodt T, Gohring G, Trapnell B, Hansen G, Trapnell C, Knudsen L, Lachmann N, Moritz T.

Stem Cell Reports. 2018 Sep 11;11(3):696-710. doi: 10.1016/j.stemcr.2018.07.006. Epub 2018 Aug 9.

9.

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C.

Mol Cell. 2018 Sep 6;71(5):858-871.e8. doi: 10.1016/j.molcel.2018.06.044. Epub 2018 Aug 2.

PMID:
30078726
10.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J.

Cell. 2018 Aug 23;174(5):1309-1324.e18. doi: 10.1016/j.cell.2018.06.052. Epub 2018 Aug 2.

PMID:
30078704
11.

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation.

Packer J, Trapnell C.

Trends Genet. 2018 Sep;34(9):653-665. doi: 10.1016/j.tig.2018.06.001. Epub 2018 Jul 11. Review.

PMID:
30007833
12.

Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma.

Mikheev AM, Mikheeva SA, Severs LJ, Funk CC, Huang L, McFaline-Figueroa JL, Schwensen J, Trapnell C, Price ND, Wong S, Rostomily RC.

Mol Oncol. 2018 Jun;12(7):1188-1202. doi: 10.1002/1878-0261.12320. Epub 2018 May 29.

13.

Highly scalable generation of DNA methylation profiles in single cells.

Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC.

Nat Biotechnol. 2018 Jun;36(5):428-431. doi: 10.1038/nbt.4112. Epub 2018 Apr 9.

14.

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ.

Cell Stem Cell. 2018 Apr 5;22(4):575-588.e7. doi: 10.1016/j.stem.2018.03.012.

PMID:
29625070
15.

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

16.

On the design of CRISPR-based single-cell molecular screens.

Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C.

Nat Methods. 2018 Apr;15(4):271-274. doi: 10.1038/nmeth.4604. Epub 2018 Feb 19.

17.

Extreme heterogeneity of influenza virus infection in single cells.

Russell AB, Trapnell C, Bloom JD.

Elife. 2018 Feb 16;7. pii: e32303. doi: 10.7554/eLife.32303.

18.

Reversed graph embedding resolves complex single-cell trajectories.

Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C.

Nat Methods. 2017 Oct;14(10):979-982. doi: 10.1038/nmeth.4402. Epub 2017 Aug 21.

19.

Comprehensive single-cell transcriptional profiling of a multicellular organism.

Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J.

Science. 2017 Aug 18;357(6352):661-667. doi: 10.1126/science.aam8940.

20.

Single-cell mRNA quantification and differential analysis with Census.

Qiu X, Hill A, Packer J, Lin D, Ma YA, Trapnell C.

Nat Methods. 2017 Mar;14(3):309-315. doi: 10.1038/nmeth.4150. Epub 2017 Jan 23.

21.

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency.

Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ.

Cell Stem Cell. 2016 Jul 7;19(1):66-80. doi: 10.1016/j.stem.2016.05.009. Epub 2016 Jun 16.

22.

Single-cell transcriptome sequencing: recent advances and remaining challenges.

Liu S, Trapnell C.

F1000Res. 2016 Feb 17;5. pii: F1000 Faculty Rev-182. doi: 10.12688/f1000research.7223.1. eCollection 2016. Review.

23.

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.

24.

Defining cell types and states with single-cell genomics.

Trapnell C.

Genome Res. 2015 Oct;25(10):1491-8. doi: 10.1101/gr.190595.115. Review.

25.

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS.

Cell. 2015 Jul 16;162(2):412-424. doi: 10.1016/j.cell.2015.06.016.

26.

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J.

Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7.

27.

Pulmonary macrophage transplantation therapy.

Suzuki T, Arumugam P, Sakagami T, Lachmann N, Chalk C, Sallese A, Abe S, Trapnell C, Carey B, Moritz T, Malik P, Lutzko C, Wood RE, Trapnell BC.

Nature. 2014 Oct 23;514(7523):450-4. doi: 10.1038/nature13807. Epub 2014 Oct 1.

28.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.

Nat Biotechnol. 2014 Apr;32(4):381-386. doi: 10.1038/nbt.2859. Epub 2014 Mar 23.

29.

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.

Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL.

Nat Struct Mol Biol. 2014 Feb;21(2):198-206. doi: 10.1038/nsmb.2764. Epub 2014 Jan 26.

30.

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.

Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD.

Genome Biol. 2014 Jan 7;15(1):R3. doi: 10.1186/gb-2014-15-1-r3.

31.

The anatomy of successful computational biology software.

Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C.

Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. No abstract available.

32.

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
33.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A.

Cell. 2013 May 23;153(5):1149-63. doi: 10.1016/j.cell.2013.04.037. Epub 2013 May 9.

34.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL.

Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36.

35.

Long noncoding RNAs regulate adipogenesis.

Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3387-92. doi: 10.1073/pnas.1222643110. Epub 2013 Feb 11.

36.

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.

37.

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.

38.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL.

Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024.

39.

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL.

Genes Dev. 2011 Sep 15;25(18):1915-27. doi: 10.1101/gad.17446611. Epub 2011 Sep 2.

40.

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL.

J Bacteriol. 2011 Oct;193(19):5450-64. doi: 10.1128/JB.05262-11. Epub 2011 Jul 22.

41.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

PMID:
21697122
42.

Modeling and automation of sequencing-based characterization of RNA structure.

Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11069-74. doi: 10.1073/pnas.1106541108. Epub 2011 Jun 3.

43.

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8. doi: 10.1073/pnas.1106501108. Epub 2011 Jun 3.

44.

Computational methods for transcriptome annotation and quantification using RNA-seq.

Garber M, Grabherr MG, Guttman M, Trapnell C.

Nat Methods. 2011 Jun;8(6):469-77. doi: 10.1038/nmeth.1613. Epub 2011 May 27. Review. Erratum in: Nat Methods. 2011 Jun;8(6):following 477.

PMID:
21623353
45.

Improving RNA-Seq expression estimates by correcting for fragment bias.

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L.

Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22. Epub 2011 Mar 16.

46.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

47.

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB.

PLoS Biol. 2010 Mar 23;8(3):e1000343. doi: 10.1371/journal.pbio.1000343.

48.

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment.

Trapnell C, Schatz MC.

Parallel Comput. 2009 Aug 1;35(8):429-440.

49.

How to map billions of short reads onto genomes.

Trapnell C, Salzberg SL.

Nat Biotechnol. 2009 May;27(5):455-7. doi: 10.1038/nbt0509-455.

50.

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.

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