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Items: 1 to 50 of 91

1.

Functional interpretation of single cell similarity maps.

DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N.

Nat Commun. 2019 Sep 26;10(1):4376. doi: 10.1038/s41467-019-12235-0.

2.

MPRAnalyze: statistical framework for massively parallel reporter assays.

Ashuach T, Fischer DS, Kreimer A, Ahituv N, Theis FJ, Yosef N.

Genome Biol. 2019 Sep 2;20(1):183. doi: 10.1186/s13059-019-1787-z.

3.

Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS.

Afik S, Raulet G, Yosef N.

Life Sci Alliance. 2019 Aug 26;2(4). pii: e201900371. doi: 10.26508/lsa.201900371. Print 2019 Aug.

4.

Simulating multiple faceted variability in single cell RNA sequencing.

Zhang X, Xu C, Yosef N.

Nat Commun. 2019 Jun 13;10(1):2611. doi: 10.1038/s41467-019-10500-w.

5.

Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.

Kreimer A, Yan Z, Ahituv N, Yosef N.

Hum Mutat. 2019 Sep;40(9):1299-1313. doi: 10.1002/humu.23820. Epub 2019 Jun 18.

6.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.

Shigaki D, Adato O, Adhikari AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DD, Schubach M, Xiong C, Yan Z, Boyle AP, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, Beer MA.

Hum Mutat. 2019 Sep;40(9):1280-1291. doi: 10.1002/humu.23797. Epub 2019 Jun 23.

PMID:
31106481
7.

Molecular recording of mammalian embryogenesis.

Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS.

Nature. 2019 Jun;570(7759):77-82. doi: 10.1038/s41586-019-1184-5. Epub 2019 May 13.

PMID:
31086336
8.

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N.

Cell Syst. 2019 Apr 24;8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010.

PMID:
31022373
9.

Connectivity problems on heterogeneous graphs.

Wu J, Khodaverdian A, Weitz B, Yosef N.

Algorithms Mol Biol. 2019 Mar 8;14:5. doi: 10.1186/s13015-019-0141-z. eCollection 2019.

10.

Deep generative modeling for single-cell transcriptomics.

Lopez R, Regier J, Cole MB, Jordan MI, Yosef N.

Nat Methods. 2018 Dec;15(12):1053-1058. doi: 10.1038/s41592-018-0229-2. Epub 2018 Nov 30.

11.

Impulse model-based differential expression analysis of time course sequencing data.

Fischer DS, Theis FJ, Yosef N.

Nucleic Acids Res. 2018 Nov 16;46(20):e119. doi: 10.1093/nar/gky675.

12.

The phenotypic and functional properties of mouse yolk-sac-derived embryonic macrophages.

Yosef N, Vadakkan TJ, Park JH, Poché RA, Thomas JL, Dickinson ME.

Dev Biol. 2018 Oct 1;442(1):138-154. doi: 10.1016/j.ydbio.2018.07.009. Epub 2018 Jul 30.

13.

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S.

BMC Genomics. 2018 Jun 19;19(1):477. doi: 10.1186/s12864-018-4772-0.

14.

Computation Resources for Molecular Biology: Special Issue 2018.

Sternberg MJE, Yosef N.

J Mol Biol. 2018 Jul 20;430(15):2181-2183. doi: 10.1016/j.jmb.2018.05.041. Epub 2018 May 31. No abstract available.

PMID:
29860026
15.

Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon.

Donnard E, Vangala P, Afik S, McCauley S, Nowosielska A, Kucukural A, Tabak B, Zhu X, Diehl W, McDonel P, Yosef N, Luban J, Garber M.

Cell Syst. 2018 Mar 28;6(3):381-394.e7. doi: 10.1016/j.cels.2018.01.002. Epub 2018 Feb 14.

16.

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers.

Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG.

Genome Biol. 2018 Jan 29;19(1):10. doi: 10.1186/s13059-017-1385-x.

17.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

18.

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB.

Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. doi: 10.1016/j.stem.2017.10.014. Epub 2017 Nov 22.

19.

Regulation of Axon Guidance by the Wnt Receptor Ror/CAM-1 in the PVT Guidepost Cell in Caenorhabditis elegans.

Chien J, Devkota R, Yosef N, Mörck C.

Genetics. 2017 Dec;207(4):1533-1545. doi: 10.1534/genetics.117.300375. Epub 2017 Oct 9.

20.

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.

Afik S, Yates KB, Bi K, Darko S, Godec J, Gerdemann U, Swadling L, Douek DC, Klenerman P, Barnes EJ, Sharpe AH, Haining WN, Yosef N.

Nucleic Acids Res. 2017 Sep 19;45(16):e148. doi: 10.1093/nar/gkx615.

21.

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.

Ryu AH, Eckalbar WL, Kreimer A, Yosef N, Ahituv N.

Sci Rep. 2017 Aug 8;7(1):7533. doi: 10.1038/s41598-017-07757-w.

22.

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.

Mertins P, Przybylski D, Yosef N, Qiao J, Clauser K, Raychowdhury R, Eisenhaure TM, Maritzen T, Haucke V, Satoh T, Akira S, Carr SA, Regev A, Hacohen N, Chevrier N.

Cell Rep. 2017 Jun 27;19(13):2853-2866. doi: 10.1016/j.celrep.2017.06.016.

23.

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J.

Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8. doi: 10.1016/j.stem.2017.04.003. Epub 2017 May 11.

24.

A new way to build cell lineages.

Zhang X, Yosef N.

Elife. 2017 Mar 23;6. pii: e25654. doi: 10.7554/eLife.25654.

25.

Predicting gene expression in massively parallel reporter assays: A comparative study.

Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N.

Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9.

26.

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

Karwacz K, Miraldi ER, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK.

Nat Immunol. 2017 Apr;18(4):412-421. doi: 10.1038/ni.3683. Epub 2017 Feb 6.

27.
28.

Revealing the vectors of cellular identity with single-cell genomics.

Wagner A, Regev A, Yosef N.

Nat Biotechnol. 2016 Nov 8;34(11):1145-1160. doi: 10.1038/nbt.3711. Review.

29.

Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity.

Kishi Y, Kondo T, Xiao S, Yosef N, Gaublomme J, Wu C, Wang C, Chihara N, Regev A, Joller N, Kuchroo VK.

J Exp Med. 2016 Oct 17;213(11):2489-2501. Epub 2016 Sep 26.

30.

ImpulseDE: detection of differentially expressed genes in time series data using impulse models.

Sander J, Schultze JL, Yosef N.

Bioinformatics. 2017 Mar 1;33(5):757-759. doi: 10.1093/bioinformatics/btw665.

31.

The epigenetic landscape of T cell exhaustion.

Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, Tsao HW, Godec J, LaFleur MW, Brown FD, Tonnerre P, Chung RT, Tully DC, Allen TM, Frahm N, Lauer GM, Wherry EJ, Yosef N, Haining WN.

Science. 2016 Dec 2;354(6316):1165-1169. Epub 2016 Oct 27.

32.

Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion.

Ranasinghe S, Lamothe PA, Soghoian DZ, Kazer SW, Cole MB, Shalek AK, Yosef N, Jones RB, Donaghey F, Nwonu C, Jani P, Clayton GM, Crawford F, White J, Montoya A, Power K, Allen TM, Streeck H, Kaufmann DE, Picker LJ, Kappler JW, Walker BD.

Immunity. 2016 Oct 18;45(4):917-930. doi: 10.1016/j.immuni.2016.09.015.

33.

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data.

DeTomaso D, Yosef N.

BMC Bioinformatics. 2016 Aug 23;17(1):315. doi: 10.1186/s12859-016-1176-5.

34.

Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity.

Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK.

ACS Chem Biol. 2016 Aug 19;11(8):2131-9. doi: 10.1021/acschembio.6b00433. Epub 2016 Jul 22.

35.

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, Pandolfi PP, Mak T, Satija R, Shalek AK, Kuchroo VK, Park H, Regev A.

Cell. 2015 Dec 3;163(6):1400-12. doi: 10.1016/j.cell.2015.11.009. Epub 2015 Nov 19.

36.

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity.

Wang C, Yosef N, Gaublomme J, Wu C, Lee Y, Clish CB, Kaminski J, Xiao S, Meyer Zu Horste G, Pawlak M, Kishi Y, Joller N, Karwacz K, Zhu C, Ordovas-Montanes M, Madi A, Wortman I, Miyazaki T, Sobel RA, Park H, Regev A, Kuchroo VK.

Cell. 2015 Dec 3;163(6):1413-27. doi: 10.1016/j.cell.2015.10.068. Epub 2015 Nov 19.

37.

Oct1 and OCA-B are selectively required for CD4 memory T cell function.

Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D.

J Exp Med. 2015 Nov 16;212(12):2115-31. doi: 10.1084/jem.20150363. Epub 2015 Oct 19.

38.

Improved Angiogenesis in Response to Localized Delivery of Macrophage-Recruiting Molecules.

Hsu CW, Poché RA, Saik JE, Ali S, Wang S, Yosef N, Calderon GA, Scott L Jr, Vadakkan TJ, Larina IV, West JL, Dickinson ME.

PLoS One. 2015 Jul 1;10(7):e0131643. doi: 10.1371/journal.pone.0131643. eCollection 2015.

39.

Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor.

Tian R, Wang H, Gish GD, Petsalaki E, Pasculescu A, Shi Y, Mollenauer M, Bagshaw RD, Yosef N, Hunter T, Gingras AC, Weiss A, Pawson T.

Proc Natl Acad Sci U S A. 2015 Mar 31;112(13):E1594-603. doi: 10.1073/pnas.1503286112. Epub 2015 Mar 17.

40.

MicroRNA-21 promotes Th17 differentiation and mediates experimental autoimmune encephalomyelitis.

Murugaiyan G, da Cunha AP, Ajay AK, Joller N, Garo LP, Kumaradevan S, Yosef N, Vaidya VS, Weiner HL.

J Clin Invest. 2015 Mar 2;125(3):1069-80. doi: 10.1172/JCI74347. Epub 2015 Feb 2.

41.

Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion.

Shakya A, Callister C, Goren A, Yosef N, Garg N, Khoddami V, Nix D, Regev A, Tantin D.

Mol Cell Biol. 2015 Mar;35(6):1014-25. doi: 10.1128/MCB.01105-14. Epub 2015 Jan 12.

42.

The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis.

Uziel O, Yosef N, Sharan R, Ruppin E, Kupiec M, Kushnir M, Beery E, Cohen-Diker T, Nordenberg J, Lahav M.

Genomics. 2015 Jan;105(1):5-16. doi: 10.1016/j.ygeno.2014.10.013. Epub 2014 Nov 13.

43.

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A.

Nature. 2014 Jun 19;510(7505):363-9. doi: 10.1038/nature13437. Epub 2014 Jun 11.

44.

Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms.

Xiao S, Yosef N, Yang J, Wang Y, Zhou L, Zhu C, Wu C, Baloglu E, Schmidt D, Ramesh R, Lobera M, Sundrud MS, Tsai PY, Xiang Z, Wang J, Xu Y, Lin X, Kretschmer K, Rahl PB, Young RA, Zhong Z, Hafler DA, Regev A, Ghosh S, Marson A, Kuchroo VK.

Immunity. 2014 Apr 17;40(4):477-89. doi: 10.1016/j.immuni.2014.04.004.

45.

CCR2 gene deletion and pharmacologic blockade ameliorate a severe murine experimental autoimmune neuritis model of Guillain-Barré syndrome.

Yuan F, Yosef N, Lakshmana Reddy C, Huang A, Chiang SC, Tithi HR, Ubogu EE.

PLoS One. 2014 Mar 14;9(3):e90463. doi: 10.1371/journal.pone.0090463. eCollection 2014.

46.

Understanding Th17 cells through systematic genomic analyses.

Peters A, Yosef N.

Curr Opin Immunol. 2014 Jun;28:42-8. doi: 10.1016/j.coi.2014.01.017. Epub 2014 Mar 6. Review.

PMID:
24594517
47.

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells.

Kurachi M, Barnitz RA, Yosef N, Odorizzi PM, DiIorio MA, Lemieux ME, Yates K, Godec J, Klatt MG, Regev A, Wherry EJ, Haining WN.

Nat Immunol. 2014 Apr;15(4):373-83. doi: 10.1038/ni.2834. Epub 2014 Mar 2.

48.

VEGF-A165 potently induces human blood-nerve barrier endothelial cell proliferation, angiogenesis, and wound healing in vitro.

Reddy CL, Yosef N, Ubogu EE.

Cell Mol Neurobiol. 2013 Aug;33(6):789-801. doi: 10.1007/s10571-013-9946-3. Epub 2013 May 26.

49.

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A.

Nature. 2013 Jun 13;498(7453):236-40. doi: 10.1038/nature12172. Epub 2013 May 19.

50.

Metallothioneins negatively regulate IL-27-induced type 1 regulatory T-cell differentiation.

Wu C, Pot C, Apetoh L, Thalhamer T, Zhu B, Murugaiyan G, Xiao S, Lee Y, Rangachari M, Yosef N, Kuchroo VK.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7802-7. doi: 10.1073/pnas.1211776110. Epub 2013 Apr 29.

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