- Yuan H, Paskov I, Paskov H, González AJ, Leslie CS. Multitask learning improves prediction of cancer drug sensitivity. Sci Rep. 2016 Aug 23;6:31619. doi: 10.1038/srep31619. [Epub ahead of print]
- van der Veeken J, Gonzalez AJ, Cho H, Arvey A, Hemmers S, Leslie CS, Rudensky AY. Memory of Inflammation in Regulatory T Cells. Cell. 2016 Aug 11;166(4):977-90. doi: 10.1016/j.cell.2016.07.006. [Epub ahead of print]
- Lu Y, Leslie CS. Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data. PLoS Comput Biol. 2016 Jul 20;12(7):e1005026. doi: 10.1371/journal.pcbi.1005026. [Pubmed]
- Taggart J, Ho TC, Amin E, Xu H, Barlowe TS, Perez AR, Durham BH, Tivnan P, Okabe R, Chow A, Vu L, Park SM, Prieto C, Famulare C, Patel M, Lengner CJ, Verma A, Roboz G, Guzman M, Klimek VM, Abdel-Wahab O, Leslie C, Nimer SD, Kharas MG. MSI2 is required for maintaining activated myelodysplastic syndrome stem cells. Nat Commun. 2016 Feb 22;7:10739. doi: 10.1038/ncomms10739. [Pubmed]
- Pelossof R, Chow OS, Fairchild L, Smith JJ, Setty M, Chen CT, Chen Z, Egawa F, Avila K, Leslie CS, Garcia-Aguilar J. Integrated genomic profiling identifies microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer. Genes Chromosomes Cancer. 2016 Apr;55(4):311-21. doi: 10.1002/gcc.22329. [Pubmed]
- Dadi S, Chhangawala S, Whitlock BM, Franklin RA, Luo CT, Oh SA, Toure A, Pritykin Y, Huse M, Leslie CS, Li MO. Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells. Cell. 2016 Jan 28;164(3):365-77. doi: 10.1016/j.cell.2016.01.002. [Pubmed]
- 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. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature. 2015 Nov 25. doi: 10.1038/nature16141. [Pubmed]
- Zhang L, Tran NT, Su H, Wang R, Lu Y, Tang H, Aoyagi S, Guo A, Khodadadi-Jamayran A, Zhou D, Qian K, Hricik T, Côté J, Han X, Zhou W, Laha S, Abdel-Wahab O, Levine RL, Raffel G, Liu Y, Chen D, Li H, Townes T, Wang H, Deng H, Zheng YG, Leslie C, Luo M, Zhao X. Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing. Elife. 2015 Nov 17;4. pii: e07938. doi: 10.7554/eLife.07938. [Pubmed]
- Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Affinity regression predicts the recognition code of nucleic acid-binding proteins. Nat Biotechnol. 2015 Nov 16. doi: 10.1038/nbt.3343. [Pubmed]
- González AJ, Setty M, Leslie CS. Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation. Nat Genet. 2015 Sep 21. doi: 10.1038/ng.3402.[Pubmed]
- 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. A Single miRNA-mRNA Interaction Affects the Immune Response in a Context- and Cell-Type-Specific Manner. Immunity. 2015 Jul 21; 43(1):52-64. doi: 10.1016/j.immuni.2015.04.022. [Pubmed]
- Setty M, Leslie CS. SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps. PLoS Comput Biol. 2015 May 27;11(5):e1004271. doi: 10.1371/journal.pcbi.1004271. [Pubmed]
- Park SM, Gönen M, Vu L, Minuesa G, Tivnan P, Barlowe TS, Taggart J, Lu Y, Deering RP, Hacohen N, Figueroa ME, Paietta E, Fernandez HF, Tallman MS, Melnick A, Levine R, Leslie C, Lengner CJ, Kharas MG. Musashi2 sustains the mixed-lineage leukemia-driven stem cell regulatory program. J Clin Invest. 2015 Feb 9; 78440 doi:10.1172/JCI78440. [Pubmed]
- 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. In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA.Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):767-72. doi: 10.1073/pnas. [Pubmed]
- 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. Characterization of a set of tumor suppressor microRNAs in T cell acute lymphoblastic leukemia. Sci Signal. 2014 Nov 18;7(352):ra111. doi: 10.1126/scisignal.2005500. [Pubmed]
- Osmanbeyoglu HU, Pelossof R, Bromberg JF, Leslie CS. Linking signaling pathways to transcriptional programs in breast cancer. Genome Res. 2014 Nov;24(11):1869-80. doi: 10.1101/gr.173039.114. Epub 2014 Sep 2. [PubMed]
- 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. Analysis of tumour- and stroma-supplied proteolytic networks reveals a brain-metastasis-promoting role for cathepsin S. Nat Cell Biol. 2014 Sep;16(9):876-88. doi: 10.1038/ncb3011. Epub 2014 Aug 3.
[PubMed]
- Furman RR, Cheng S, Lu P, Setty M, Perez AR, Guo A, Racchumi J, Xu G, Wu H, Ma J, Steggerda SM, Coleman M, Leslie C, Wang YL. Ibrutinib resistance in chronic lymphocytic leukemia. N Engl J Med. 2014 Jun 12;370(24):2352-4. doi: 10.1056/NEJMc1402716. Epub 2014 May 28.
[PubMed]
- Schneider C, Setty M, Holmes AB, Maute RL, Leslie CS, Mussolin L, Rosolen A, Dalla-Favera R, Basso K. MicroRNA 28 controls cell proliferation and is down-regulated in B-cell lymphomas. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8185-90. doi: 10.1073/pnas.1322466111. Epub 2014 May 19. [PubMed]
- Park SM, Deering RP, Lu Y, Tivnan P, Lianoglou S, Al-Shahrour F, Ebert BL, Hacohen N, Leslie C, Daley GQ, Lengner CJ, Kharas MG. Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs.
J Exp Med. 2014 Jan 13;211(1):71-87. [PubMed]
- Lianoglou S, Garg V, Yang JL, Leslie CS, Mayr C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression.
Genes Dev. 2013 Nov 1;27(21):2380-96. doi: 10.1101/gad.229328.113. Epub 2013 Oct 21. [PubMed]
- 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. CSF-1R inhibition alters macrophage polarization and blocks glioma progression.
Nat Med. 2013 Oct;19(10):1264-72. doi: 10.1038/nm.3337. Epub 2013 Sep 22. [PubMed]
- Curanovic D, Cohen M, Singh I, Slagle CE, Leslie CS, Jaffrey SR. Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap.
Nat Chem Biol. 2013 Nov;9(11):671-3. doi: 10.1038/nchembio.1334. Epub 2013 Sep 1. [PubMed]
- Kobos R, Nagai M, Tsuda M, Merl MY, Saito T, Laé M, Mo Q, Olshen A, Lianoglou S, Leslie C, Ostrovnaya I, Antczak C, Djaballah H, Ladanyi M. Combining integrated genomics and functional genomics to dissect the biology of a cancer-associated, aberrant transcription factor, the ASPSCR1-TFE3 fusion oncoprotein.
J Pathol. 2013 Apr;229(5):743-54. doi: 10.1002/path.4158. Epub 2013 Mar 5. [PubMed]
- Basso K, Schneider C, Shen Q, Holmes AB, Setty M, Leslie C, Dalla-Favera R. BCL6 positively regulates AID and germinal center gene expression via repression of miR-155.
J Exp Med. 2012 Dec 17;209(13):2455-65. doi: 10.1084/jem.20121387. Epub 2012 Nov 19. [PubMed]
- Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY. Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting.
Mol Cell. 2012 Dec 14;48(5):760-70. doi: 10.1016/j.molcel.2012.10.002. Epub 2012 Nov 8. [PubMed]
- Rudra D, deRoos P, Chaudhry A, Niec RE, Arvey A, Samstein RM, Leslie C, Shaffer SA, Goodlett DR, Rudensky AY. Transcription factor Foxp3 and its protein partners form a complex regulatory network.
Nat Immunol. 2012 Oct;13(10):1010-9. doi: 10.1038/ni.2402. Epub 2012 Aug 26. [PubMed]
- Samstein RM, Arvey A, Josefowicz SZ, Peng X, Reynolds A, Sandstrom R, Neph S, Sabo P, Kim JM, Liao W, Li MO, Leslie C, Stamatoyannopoulos JA, Rudensky AY. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification.
Cell. 2012 Sep 28;151(1):153-66. doi: 10.1016/j.cell.2012.06.053. [PubMed]
- Arvey A, Agius P, Noble WS, Leslie C. Sequence and chromatin determinants of cell-type-specific transcription factor binding.
Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111. [PubMed]
- Pastar I, Khan AA, Stojadinovic O, Lebrun EA, Medina MC, Brem H, Kirsner RS, Jimenez JJ, Leslie C, Tomic-Canic M. Induction of specific microRNAs inhibits cutaneous wound healing.
J Biol Chem. 2012 Aug 24;287(35):29324-35. doi: 10.1074/jbc.M112.382135. Epub 2012 Jul 6. [PubMed]
- Arvey A, Tempera I, Tsai K, Chen HS, Tikhmyanova N, Klichinsky M, Leslie C, Lieberman PM. An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions.
Cell Host Microbe. 2012 Aug 16;12(2):233-45. doi: 10.1016/j.chom.2012.06.008. [PubMed]
- Setty M, Helmy K, Khan AA, Silber J, Arvey A, Neezen F, Agius P, Huse JT, Holland EC, Leslie CS. Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma.
Mol Syst Biol. 2012;8:605. doi: 10.1038/msb.2012.37. [PubMed]
- Mavrakis KJ, Leslie CS, Wendel HG. Cooperative control of tumor suppressor genes by a network of oncogenic microRNAs.
Cell Cycle. 2011 Sep 1;10(17):2845-9. Epub 2011 Sep 1. [PubMed]
- 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. A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL).
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]. [PubMed]
- Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC. Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans.
Genome Res. 2011 Feb;21(2):286-300. doi: 10.1101/gr.113050.110. Epub 2010 Dec 22. [PubMed]
- Melvin I, Weston J, Noble WS, Leslie C. Detecting remote evolutionary relationships among proteins by large-scale semantic embedding.
PLoS Comput Biol. 2011 Jan 27;7(1):e1001047. doi: 10.1371/journal.pcbi.1001047. [PubMed]
- Papapetrou EP, Lee G, Malani N, Setty M, Riviere I, Tirunagari LM, Kadota K, Roth SL, Giardina P, Viale A, Leslie C, Bushman FD, Studer L, Sadelain M. Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells.
Nat Biotechnol. 2011 Jan;29(1):73-8. doi: 10.1038/nbt.1717. Epub 2010 Dec 12. [PubMed]
- Yao X, Balamurugan P, Arvey A, Leslie C, Zhang L. Heme controls the regulation of protein tyrosine kinases Jak2 and Src.
Biochem Biophys Res Commun. 2010 Dec 3;403(1):30-5. doi: 10.1016/j.bbrc.2010.10.101. Epub 2010 Oct 29. [PubMed]
- Agius P, Arvey A, Chang W, Noble WS, Leslie C. High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
PLoS Comput Biol. 2010 Sep 9;6(9). doi:pii: e1000916. 10.1371/journal.pcbi.1000916. [PubMed]
- Rapaport F, Leslie C. Determining frequent patterns of copy number alterations in cancer.
PLoS One. 2010 Aug 12;5(8):e12028. doi: 10.1371/journal.pone.0012028. [PubMed]
- Li X, Panea C, Wiggins CH, Reinke V, Leslie C. Learning "graph-mer" motifs that predict gene expression trajectories in development.
PLoS Comput Biol. 2010 Apr 29;6(4):e1000761. doi: 10.1371/journal.pcbi.1000761. [PubMed]
- Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity.
Mol Syst Biol. 2010 Apr 20;6:363. doi: 10.1038/msb.2010.24. [PubMed]
- 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. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia.
Nat Cell Biol. 2010 Apr;12(4):372-9. doi: 10.1038/ncb2037. Epub 2010 Feb 28. [PubMed]
- Nimrod G, Schushan M, Szilágyi A, Leslie C, Ben-Tal N. iDBPs: a web server for the identification of DNA binding proteins.
Bioinformatics. 2010 Mar 1;26(5):692-3. doi: 10.1093/bioinformatics/btq019. Epub 2010 Jan 19. [PubMed]
- Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.
Genome Biol. 2010;11(8):R90. doi: 10.1186/gb-2010-11-8-r90. Epub 2010 Aug 27. [PubMed]
- Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.
Nat Biotechnol. 2009 Jun;27(6):549-55. doi: 10.1038/nbt.1543. Erratum in: Nat Biotechnol. 2009 Jul;27(7):671. [PubMed]
- Nimrod G, Szilágyi A, Leslie C, Ben-Tal N. Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.
J Mol Biol. 2009 Apr 10;387(4):1040-53. doi: 10.1016/j.jmb.2009.02.023. Epub 2009 Feb 20. [PubMed]
- Melvin I, Weston J, Leslie C, Noble WS. RANKPROP: a web server for protein remote homology detection.
Bioinformatics. 2009 Jan 1;25(1):121-2. doi: 10.1093/bioinformatics/btn567. Epub 2008 Nov 6. [PubMed]
- Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C. A predictive model of the oxygen and heme regulatory network in yeast.
PLoS Comput Biol. 2008 Nov;4(11):e1000224. doi: 10.1371/journal.pcbi.1000224. Epub 2008 Nov 14. [PubMed]
- Melvin I, Weston J, Leslie CS, Noble WS. Combining classifiers for improved classification of proteins from sequence or structure.
BMC Bioinformatics. 2008 Sep 22;9:389. doi: 10.1186/1471-2105-9-389. [PubMed]
- Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA.
Ann N Y Acad Sci. 2007 Dec;1115:178-202. Epub 2007 Oct 12. [PubMed]
- Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.
BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2. [PubMed]
- Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C. A classification-based framework for predicting and analyzing gene regulatory response.
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S5. [PubMed]
- Weston J, Kuang R, Leslie C, Noble WS. Protein ranking by semi-supervised network propagation.
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S10. [PubMed]
- Zhang XH, Leslie CS, Chasin LA. Computational searches for splicing signals.
Methods. 2005 Dec;37(4):292-305. [PubMed]
- Noble WS, Kuang R, Leslie C, Weston J. Identifying remote protein homologs by network propagation.
FEBS J. 2005 Oct;272(20):5119-28. Review. [PubMed]
- Kuang R, Weston J, Noble WS, Leslie C. Motif-based protein ranking by network propagation.
Bioinformatics. 2005 Oct 1;21(19):3711-8. Epub 2005 Aug 2. [PubMed]
- Weston J, Leslie C, Ie E, Zhou D, Elisseeff A, Noble WS. Semi-supervised protein classification using cluster kernels.
Bioinformatics. 2005 Aug 1;21(15):3241-7. Epub 2005 May 19. [PubMed]
- Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C. Combining sequence and time series expression data to learn transcriptional modules.
IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202. [PubMed]
- Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction.
J Bioinform Comput Biol. 2005 Jun;3(3):527-50. [PubMed]
- Zhang XH, Leslie CS, Chasin LA. Dichotomous splicing signals in exon flanks.
Genome Res. 2005 Jun;15(6):768-79. [PubMed]
- Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification.
Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40. [PubMed]
- Kuang R, Leslie CS, Yang AS. Protein backbone angle prediction with machine learning approaches.
Bioinformatics. 2004 Jul 10;20(10):1612-21. Epub 2004 Feb 26. [PubMed]
- Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS. Protein ranking: from local to global structure in the protein similarity network.
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63. Epub 2004 Apr 15. [PubMed]
- Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification.
Bioinformatics. 2004 Mar 1;20(4):467-76. Epub 2004 Jan 22. [PubMed]
- Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction.
Proc IEEE Comput Syst Bioinform Conf. 2004:152-60. [PubMed]
- Zhang XH, Heller KA, Hefter I, Leslie CS, Chasin LA. Sequence information for the splicing of human pre-mRNA identified by support vector machine classification.
Genome Res. 2003 Dec;13(12):2637-50. [PubMed]
- Leslie C, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification.
Pac Symp Biocomput. 2002:564-75. [PubMed]