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Items: 50

1.

The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types.

Hsin JP, Lu Y, Loeb GB, Leslie CS, Rudensky AY.

Nat Immunol. 2018 Sep 17. doi: 10.1038/s41590-018-0208-x. [Epub ahead of print]

PMID:
30224821
2.

Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia.

Lee SH, Singh I, Tisdale S, Abdel-Wahab O, Leslie CS, Mayr C.

Nature. 2018 Sep;561(7721):127-131. doi: 10.1038/s41586-018-0465-8. Epub 2018 Aug 27.

PMID:
30150773
3.

Non-redundant ISGF3 Components Promote NK Cell Survival in an Auto-regulatory Manner during Viral Infection.

Geary CD, Krishna C, Lau CM, Adams NM, Gearty SV, Pritykin Y, Thomsen AR, Leslie CS, Sun JC.

Cell Rep. 2018 Aug 21;24(8):1949-1957.e6. doi: 10.1016/j.celrep.2018.07.060.

4.

Epigenetic control of innate and adaptive immune memory.

Lau CM, Adams NM, Geary CD, Weizman OE, Rapp M, Pritykin Y, Leslie CS, Sun JC.

Nat Immunol. 2018 Sep;19(9):963-972. doi: 10.1038/s41590-018-0176-1. Epub 2018 Aug 6.

PMID:
30082830
5.

Widespread intronic polyadenylation diversifies immune cell transcriptomes.

Singh I, Lee SH, Sperling AS, Samur MK, Tai YT, Fulciniti M, Munshi NC, Mayr C, Leslie CS.

Nat Commun. 2018 Apr 30;9(1):1716. doi: 10.1038/s41467-018-04112-z.

6.

ILC1 Confer Early Host Protection at Initial Sites of Viral Infection.

Weizman OE, Adams NM, Schuster IS, Krishna C, Pritykin Y, Lau C, Degli-Esposti MA, Leslie CS, Sun JC, O'Sullivan TE.

Cell. 2017 Nov 2;171(4):795-808.e12. doi: 10.1016/j.cell.2017.09.052. Epub 2017 Oct 19.

PMID:
29056343
7.

Ets transcription factor GABP controls T cell homeostasis and immunity.

Luo CT, Osmanbeyoglu HU, Do MH, Bivona MR, Toure A, Kang D, Xie Y, Leslie CS, Li MO.

Nat Commun. 2017 Oct 20;8(1):1062. doi: 10.1038/s41467-017-01020-6.

8.

Chromatin states define tumour-specific T cell dysfunction and reprogramming.

Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, Scott AC, Viale A, Lauer P, Merghoub T, Hellmann MD, Wolchok JD, Leslie CS, Schietinger A.

Nature. 2017 May 25;545(7655):452-456. doi: 10.1038/nature22367. Epub 2017 May 17.

9.

An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data.

Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS.

Nat Commun. 2017 May 17;8:15454. doi: 10.1038/ncomms15454.

10.

PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D.

Toska E, Osmanbeyoglu HU, Castel P, Chan C, Hendrickson RC, Elkabets M, Dickler MN, Scaltriti M, Leslie CS, Armstrong SA, Baselga J.

Science. 2017 Mar 24;355(6331):1324-1330. doi: 10.1126/science.aah6893.

11.

The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma.

Nargund AM, Pham CG, Dong Y, Wang PI, Osmangeyoglu HU, Xie Y, Aras O, Han S, Oyama T, Takeda S, Ray CE, Dong Z, Berge M, Hakimi AA, Monette S, Lekaye CL, Koutcher JA, Leslie CS, Creighton CJ, Weinhold N, Lee W, Tickoo SK, Wang Z, Cheng EH, Hsieh JJ.

Cell Rep. 2017 Mar 21;18(12):2893-2906. doi: 10.1016/j.celrep.2017.02.074.

12.

GuideScan software for improved single and paired CRISPR guide RNA design.

Perez AR, Pritykin Y, Vidigal JA, Chhangawala S, Zamparo L, Leslie CS, Ventura A.

Nat Biotechnol. 2017 Apr;35(4):347-349. doi: 10.1038/nbt.3804. Epub 2017 Mar 6.

13.

Prediction of potent shRNAs with a sequential classification algorithm.

Pelossof R, Fairchild L, Huang CH, Widmer C, Sreedharan VT, Sinha N, Lai DY, Guan Y, Premsrirut PK, Tschaharganeh DF, Hoffmann T, Thapar V, Xiang Q, Garippa RJ, Rätsch G, Zuber J, Lowe SW, Leslie CS, Fellmann C.

Nat Biotechnol. 2017 Apr;35(4):350-353. doi: 10.1038/nbt.3807. Epub 2017 Mar 6.

14.

Stage-Specific Human Induced Pluripotent Stem Cells Map the Progression of Myeloid Transformation to Transplantable Leukemia.

Kotini AG, Chang CJ, Chow A, Yuan H, Ho TC, Wang T, Vora S, Solovyov A, Husser C, Olszewska M, Teruya-Feldstein J, Perumal D, Klimek VM, Spyridonidis A, Rampal RK, Silverman L, Reddy EP, Papaemmanuil E, Parekh S, Greenbaum BD, Leslie CS, Kharas MG, Papapetrou EP.

Cell Stem Cell. 2017 Mar 2;20(3):315-328.e7. doi: 10.1016/j.stem.2017.01.009. Epub 2017 Feb 16.

15.

Pancancer modelling predicts the context-specific impact of somatic mutations on transcriptional programs.

Osmanbeyoglu HU, Toska E, Chan C, Baselga J, Leslie CS.

Nat Commun. 2017 Jan 31;8:14249. doi: 10.1038/ncomms14249.

16.

Aerobic glycolysis promotes T helper 1 cell differentiation through an epigenetic mechanism.

Peng M, Yin N, Chhangawala S, Xu K, Leslie CS, Li MO.

Science. 2016 Oct 28;354(6311):481-484. Epub 2016 Sep 29.

17.

Multitask learning improves prediction of cancer drug sensitivity.

Yuan H, Paskov I, Paskov H, González AJ, Leslie CS.

Sci Rep. 2016 Aug 23;6:31619. doi: 10.1038/srep31619.

18.

Memory of Inflammation in Regulatory T Cells.

van der Veeken J, Gonzalez AJ, Cho H, Arvey A, Hemmers S, Leslie CS, Rudensky AY.

Cell. 2016 Aug 11;166(4):977-990. doi: 10.1016/j.cell.2016.07.006. Epub 2016 Aug 4.

19.

Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data.

Lu Y, Leslie CS.

PLoS Comput Biol. 2016 Jul 20;12(7):e1005026. doi: 10.1371/journal.pcbi.1005026. eCollection 2016 Jul.

20.

Integrated genomic profiling identifies microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer.

Pelossof R, Chow OS, Fairchild L, Smith JJ, Setty M, Chen CT, Chen Z, Egawa F, Avila K, Leslie CS, Garcia-Aguilar J.

Genes Chromosomes Cancer. 2016 Apr;55(4):311-321. doi: 10.1002/gcc.22329.

21.

Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells.

Dadi S, Chhangawala S, Whitlock BM, Franklin RA, Luo CT, Oh SA, Toure A, Pritykin Y, Huse M, Leslie CS, Li MO.

Cell. 2016 Jan 28;164(3):365-77. doi: 10.1016/j.cell.2016.01.002. Epub 2016 Jan 21.

22.

A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance.

Feng Y, van der Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, Hoyos BE, Moltedo B, Hemmers S, Treuting P, Leslie CS, Chudakov DM, Rudensky AY.

Nature. 2015 Dec 3;528(7580):132-136. doi: 10.1038/nature16141. Epub 2015 Nov 25.

23.

Affinity regression predicts the recognition code of nucleic acid-binding proteins.

Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS.

Nat Biotechnol. 2015 Dec;33(12):1242-1249. doi: 10.1038/nbt.3343. Epub 2015 Nov 16.

24.

Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation.

González AJ, Setty M, Leslie CS.

Nat Genet. 2015 Nov;47(11):1249-59. doi: 10.1038/ng.3402. Epub 2015 Sep 21.

25.

A Single miRNA-mRNA Interaction Affects the Immune Response in a Context- and Cell-Type-Specific Manner.

Lu LF, Gasteiger G, Yu IS, Chaudhry A, Hsin JP, Lu Y, Bos PD, Lin LL, Zawislak CL, Cho S, Sun JC, Leslie CS, Lin SW, Rudensky AY.

Immunity. 2015 Jul 21;43(1):52-64. doi: 10.1016/j.immuni.2015.04.022. Epub 2015 Jul 7.

26.

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps.

Setty M, Leslie CS.

PLoS Comput Biol. 2015 May 27;11(5):e1004271. doi: 10.1371/journal.pcbi.1004271. eCollection 2015 May.

27.

In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA.

La Rocca G, Olejniczak SH, González AJ, Briskin D, Vidigal JA, Spraggon L, DeMatteo RG, Radler MR, Lindsten T, Ventura A, Tuschl T, Leslie CS, Thompson CB.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):767-72. doi: 10.1073/pnas.1424217112. Epub 2015 Jan 7.

28.

Characterization of a set of tumor suppressor microRNAs in T cell acute lymphoblastic leukemia.

Sanghvi VR, Mavrakis KJ, Van der Meulen J, Boice M, Wolfe AL, Carty M, Mohan P, Rondou P, Socci ND, Benoit Y, Taghon T, Van Vlierberghe P, Leslie CS, Speleman F, Wendel HG.

Sci Signal. 2014 Nov 18;7(352):ra111. doi: 10.1126/scisignal.2005500.

29.

Linking signaling pathways to transcriptional programs in breast cancer.

Osmanbeyoglu HU, Pelossof R, Bromberg JF, Leslie CS.

Genome Res. 2014 Nov;24(11):1869-80. doi: 10.1101/gr.173039.114. Epub 2014 Sep 2.

30.

Analysis of tumour- and stroma-supplied proteolytic networks reveals a brain-metastasis-promoting role for cathepsin S.

Sevenich L, Bowman RL, Mason SD, Quail DF, Rapaport F, Elie BT, Brogi E, Brastianos PK, Hahn WC, Holsinger LJ, Massagué J, Leslie CS, Joyce JA.

Nat Cell Biol. 2014 Sep;16(9):876-88. doi: 10.1038/ncb3011. Epub 2014 Aug 3.

31.

MicroRNA 28 controls cell proliferation and is down-regulated in B-cell lymphomas.

Schneider C, Setty M, Holmes AB, Maute RL, Leslie CS, Mussolin L, Rosolen A, Dalla-Favera R, Basso K.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8185-90. doi: 10.1073/pnas.1322466111. Epub 2014 May 19.

32.

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression.

Lianoglou S, Garg V, Yang JL, Leslie CS, Mayr C.

Genes Dev. 2013 Nov 1;27(21):2380-96. doi: 10.1101/gad.229328.113. Epub 2013 Oct 21.

33.

CSF-1R inhibition alters macrophage polarization and blocks glioma progression.

Pyonteck SM, Akkari L, Schuhmacher AJ, Bowman RL, Sevenich L, Quail DF, Olson OC, Quick ML, Huse JT, Teijeiro V, Setty M, Leslie CS, Oei Y, Pedraza A, Zhang J, Brennan CW, Sutton JC, Holland EC, Daniel D, Joyce JA.

Nat Med. 2013 Oct;19(10):1264-72. doi: 10.1038/nm.3337. Epub 2013 Sep 22.

34.

Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap.

Curanovic D, Cohen M, Singh I, Slagle CE, Leslie CS, Jaffrey SR.

Nat Chem Biol. 2013 Nov;9(11):671-3. doi: 10.1038/nchembio.1334. Epub 2013 Sep 1.

35.

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting.

Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY.

Mol Cell. 2012 Dec 14;48(5):760-70. doi: 10.1016/j.molcel.2012.10.002. Epub 2012 Nov 8.

36.

Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma.

Setty M, Helmy K, Khan AA, Silber J, Arvey A, Neezen F, Agius P, Huse JT, Holland EC, Leslie CS.

Mol Syst Biol. 2012;8:605. doi: 10.1038/msb.2012.37.

37.

Cooperative control of tumor suppressor genes by a network of oncogenic microRNAs.

Mavrakis KJ, Leslie CS, Wendel HG.

Cell Cycle. 2011 Sep 1;10(17):2845-9. Epub 2011 Sep 1.

38.

A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL).

Mavrakis KJ, Van Der Meulen J, Wolfe AL, Liu X, Mets E, Taghon T, Khan AA, Setty M, Rondou P, Vandenberghe P, Delabesse E, Benoit Y, Socci NB, Leslie CS, Van Vlierberghe P, Speleman F, Wendel HG.

Nat Genet. 2011 Jun 5;43(7):673-8. doi: 10.1038/ng.858. Erratum in: Nat Genet. 2011 Aug;43(8):815. Setti, Manu [corrected to Setty, Manu].

39.

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans.

Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC.

Genome Res. 2011 Feb;21(2):286-300. doi: 10.1101/gr.113050.110. Epub 2010 Dec 22.

40.

Target mRNA abundance dilutes microRNA and siRNA activity.

Arvey A, Larsson E, Sander C, Leslie CS, Marks DS.

Mol Syst Biol. 2010 Apr 20;6:363. doi: 10.1038/msb.2010.24.

41.

Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia.

Mavrakis KJ, Wolfe AL, Oricchio E, Palomero T, de Keersmaecker K, McJunkin K, Zuber J, James T, Khan AA, Leslie CS, Parker JS, Paddison PJ, Tam W, Ferrando A, Wendel HG.

Nat Cell Biol. 2010 Apr;12(4):372-9. doi: 10.1038/ncb2037. Epub 2010 Feb 28.

42.

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.

Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS.

Nat Biotechnol. 2009 Jun;27(6):549-55. doi: 10.1038/nbt.1543. Erratum in: Nat Biotechnol. 2009 Jul;27(7):671.

43.

Combining classifiers for improved classification of proteins from sequence or structure.

Melvin I, Weston J, Leslie CS, Noble WS.

BMC Bioinformatics. 2008 Sep 22;9:389. doi: 10.1186/1471-2105-9-389.

44.

Computational searches for splicing signals.

Zhang XH, Leslie CS, Chasin LA.

Methods. 2005 Dec;37(4):292-305.

PMID:
16314258
45.

Dichotomous splicing signals in exon flanks.

Zhang XH, Leslie CS, Chasin LA.

Genome Res. 2005 Jun;15(6):768-79.

46.

Protein ranking: from local to global structure in the protein similarity network.

Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS.

Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63. Epub 2004 Apr 15.

47.

Mismatch string kernels for discriminative protein classification.

Leslie CS, Eskin E, Cohen A, Weston J, Noble WS.

Bioinformatics. 2004 Mar 1;20(4):467-76. Epub 2004 Jan 22.

PMID:
14990442
48.

Protein backbone angle prediction with machine learning approaches.

Kuang R, Leslie CS, Yang AS.

Bioinformatics. 2004 Jul 10;20(10):1612-21. Epub 2004 Feb 26.

PMID:
14988121
49.

Sequence information for the splicing of human pre-mRNA identified by support vector machine classification.

Zhang XH, Heller KA, Hefter I, Leslie CS, Chasin LA.

Genome Res. 2003 Dec;13(12):2637-50.

50.

Intracellular Staphylococcus aureus induces apoptosis in mouse osteoblasts.

Tucker KA, Reilly SS, Leslie CS, Hudson MC.

FEMS Microbiol Lett. 2000 May 15;186(2):151-6.

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