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Items: 1 to 50 of 64

1.

CRISPResso2 provides accurate and rapid genome editing sequence analysis.

Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L.

Nat Biotechnol. 2019 Mar;37(3):224-226. doi: 10.1038/s41587-019-0032-3. No abstract available.

PMID:
30809026
2.

Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK.

Nat Biotechnol. 2019 Mar;37(3):276-282. doi: 10.1038/s41587-018-0011-0. Epub 2019 Feb 11.

PMID:
30742127
3.

Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia.

Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, Luo HY, Brendel C, Pinello L, Chui DHK, Wolfe SA, Bauer DE.

Blood. 2019 Jan 31. pii: blood-2019-01-895094. doi: 10.1182/blood-2019-01-895094. [Epub ahead of print]

PMID:
30704988
4.

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L.

Nat Methods. 2018 Dec;15(12):992-993. doi: 10.1038/s41592-018-0225-6. No abstract available.

PMID:
30504875
5.

DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways, and protein complexes from CRISPR screens.

Canver MC, Bauer DE, Maeda T, Pinello L.

Bioinformatics. 2018 Nov 5. doi: 10.1093/bioinformatics/bty913. [Epub ahead of print]

PMID:
30395160
6.

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis.

Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L, Bauer DE.

Genome Biol. 2018 Oct 19;19(1):169. doi: 10.1186/s13059-018-1563-5.

7.

In vivo CRISPR editing with no detectable genome-wide off-target mutations.

Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK.

Nature. 2018 Sep;561(7723):416-419. doi: 10.1038/s41586-018-0500-9. Epub 2018 Sep 12.

8.

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk.

Reshef YA, Finucane HK, Kelley DR, Gusev A, Kotliar D, Ulirsch JC, Hormozdiari F, Nasser J, O'Connor L, van de Geijn B, Loh PR, Grossman SR, Bhatia G, Gazal S, Palamara PF, Pinello L, Patterson N, Adams RP, Price AL.

Nat Genet. 2018 Oct;50(10):1483-1493. doi: 10.1038/s41588-018-0196-7. Epub 2018 Sep 3.

9.

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities.

Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK.

Nat Biotechnol. 2018 Nov;36(10):977-982. doi: 10.1038/nbt.4199. Epub 2018 Jul 30.

10.

AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.

Clement K, Farouni R, Bauer DE, Pinello L.

Bioinformatics. 2018 Jul 1;34(13):i202-i210. doi: 10.1093/bioinformatics/bty264.

11.

Author Correction: High-fat diet enhances stemness and tumorigenicity of intestinal progenitors.

Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz ÖH.

Nature. 2018 Aug;560(7717):E26. doi: 10.1038/s41586-018-0187-y.

PMID:
29849139
12.

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L.

Nat Protoc. 2018 May;13(5):946-986. doi: 10.1038/nprot.2018.005. Epub 2018 Apr 12.

13.

Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo".

Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L.

Nat Methods. 2018 Apr;15(4):238-239. doi: 10.1038/nmeth.4541. Epub 2018 Mar 30. No abstract available.

PMID:
29600992
14.

Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS.

Yamauchi T, Masuda T, Canver MC, Seiler M, Semba Y, Shboul M, Al-Raqad M, Maeda M, Schoonenberg VAC, Cole MA, Macias-Trevino C, Ishikawa Y, Yao Q, Nakano M, Arai F, Orkin SH, Reversade B, Buonamici S, Pinello L, Akashi K, Bauer DE, Maeda T.

Cancer Cell. 2018 Mar 12;33(3):386-400.e5. doi: 10.1016/j.ccell.2018.01.012. Epub 2018 Feb 22.

15.

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.

Pinello L, Farouni R, Yuan GC.

Bioinformatics. 2018 Jun 1;34(11):1930-1933. doi: 10.1093/bioinformatics/bty031.

PMID:
29360936
16.

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation.

Huang D, Guo G, Yuan P, Ralston A, Sun L, Huss M, Mistri T, Pinello L, Ng HH, Yuan G, Ji J, Rossant J, Robson P, Han X.

Sci Rep. 2017 Dec 7;7(1):17156. doi: 10.1038/s41598-017-16009-w.

17.

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.

Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM.

J Exp Med. 2017 Oct 2;214(10):2875-2887. doi: 10.1084/jem.20170976. Epub 2017 Sep 6.

18.

A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations.

Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G.

Cell Res. 2017 Jun;27(6):843. doi: 10.1038/cr.2017.78. No abstract available.

19.

A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations.

Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G.

Cell Res. 2017 Jun;27(6):842. doi: 10.1038/cr.2017.77. No abstract available.

20.

Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer.

Min L, Zhang C, Qu L, Huang J, Jiang L, Liu J, Pinello L, Yuan GC, Shou C.

Oncotarget. 2017 Mar 28;8(13):21938-21953. doi: 10.18632/oncotarget.15749.

21.

Multi-scale chromatin state annotation using a hierarchical hidden Markov model.

Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC.

Nat Commun. 2017 Apr 7;8:15011. doi: 10.1038/ncomms15011.

22.

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH.

Nat Genet. 2017 Apr;49(4):625-634. doi: 10.1038/ng.3793. Epub 2017 Feb 20.

23.

A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations.

Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G.

Cell Res. 2017 Mar;27(3):386-401. doi: 10.1038/cr.2017.17. Epub 2017 Jan 27. Erratum in: Cell Res. 2017 Jun;27(6):843. Cell Res. 2017 Jun;27(6):842.

24.

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells.

Beyaz S, Kim JH, Pinello L, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz ÖH, Passegue E, Yuan GC, Orkin SH, Winau F.

Nat Immunol. 2017 Feb;18(2):184-195. doi: 10.1038/ni.3644. Epub 2016 Dec 19.

25.

Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

Blinka S, Reimer MH Jr, Pulakanti K, Pinello L, Yuan GC, Rao S.

Methods Mol Biol. 2017;1468:91-109. doi: 10.1007/978-1-4939-4035-6_8.

26.

Forward genetic screen of human transposase genomic rearrangements.

Henssen AG, Jiang E, Zhuang J, Pinello L, Socci ND, Koche R, Gonen M, Villasante CM, Armstrong SA, Bauer DE, Weng Z, Kentsis A.

BMC Genomics. 2016 Aug 4;17:548. doi: 10.1186/s12864-016-2877-x.

27.

Analyzing CRISPR genome-editing experiments with CRISPResso.

Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC.

Nat Biotechnol. 2016 Jul 12;34(7):695-7. doi: 10.1038/nbt.3583. No abstract available.

28.

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.

Jiang L, Chen H, Pinello L, Yuan GC.

Genome Biol. 2016 Jul 1;17(1):144. doi: 10.1186/s13059-016-1010-4.

29.

Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells.

Jadhav U, Nalapareddy K, Saxena M, O'Neill NK, Pinello L, Yuan GC, Orkin SH, Shivdasani RA.

Cell. 2016 Jun 2;165(6):1389-1400. doi: 10.1016/j.cell.2016.04.031. Epub 2016 May 19.

30.

The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing.

Stelloh C, Reimer MH, Pulakanti K, Blinka S, Peterson J, Pinello L, Jia S, Roumiantsev S, Hessner MJ, Milanovich S, Yuan GC, Rao S.

Epigenetics Chromatin. 2016 Apr 15;9:14. doi: 10.1186/s13072-016-0063-7. eCollection 2016.

31.

High-fat diet enhances stemness and tumorigenicity of intestinal progenitors.

Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz ÖH.

Nature. 2016 Mar 3;531(7592):53-8. doi: 10.1038/nature17173. Erratum in: Nature. 2018 Aug;560(7717):E26.

32.

Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis.

Guo G, Pinello L, Han X, Lai S, Shen L, Lin TW, Zou K, Yuan GC, Orkin SH.

Cell Rep. 2016 Feb 2;14(4):956-965. doi: 10.1016/j.celrep.2015.12.089. Epub 2016 Jan 21.

33.

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia.

Wu JN, Pinello L, Yissachar E, Wischhusen JW, Yuan GC, Roberts CWM.

Epigenetics Chromatin. 2015 Dec 2;8:53. doi: 10.1186/s13072-015-0046-0. eCollection 2015.

34.

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.

Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE.

Nature. 2015 Nov 12;527(7577):192-7. doi: 10.1038/nature15521. Epub 2015 Sep 16.

35.

Predicting chromatin organization using histone marks.

Huang J, Marco E, Pinello L, Yuan GC.

Genome Biol. 2015 Aug 14;16:162. doi: 10.1186/s13059-015-0740-z.

36.

Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity.

Hu T, Yeh JE, Pinello L, Jacob J, Chakravarthy S, Yuan GC, Chopra R, Frank DA.

Mol Cell Biol. 2015 Oct;35(19):3284-300. doi: 10.1128/MCB.00060-15. Epub 2015 Jul 13.

37.

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.

Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM.

Mol Cell. 2015 Feb 19;57(4):636-647. doi: 10.1016/j.molcel.2015.01.011.

38.

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH.

Mol Cell. 2015 Jan 22;57(2):304-316. doi: 10.1016/j.molcel.2014.12.009. Epub 2015 Jan 8.

39.

LincRNA-p21 regulates neointima formation, vascular smooth muscle cell proliferation, apoptosis, and atherosclerosis by enhancing p53 activity.

Wu G, Cai J, Han Y, Chen J, Huang ZP, Chen C, Cai Y, Huang H, Yang Y, Liu Y, Xu Z, He D, Zhang X, Hu X, Pinello L, Zhong D, He F, Yuan GC, Wang DZ, Zeng C.

Circulation. 2014 Oct 21;130(17):1452-1465. doi: 10.1161/CIRCULATIONAHA.114.011675. Epub 2014 Aug 25.

40.

Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns.

Pinello L, Xu J, Orkin SH, Yuan GC.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):E344-53. doi: 10.1073/pnas.1322570111. Epub 2014 Jan 6.

41.

Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity.

Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, Daley G, Hochedlinger K, Kim J, Orkin SH.

Mol Cell. 2014 Jan 9;53(1):32-48. doi: 10.1016/j.molcel.2013.11.011. Epub 2013 Dec 19.

42.

Applications of alignment-free methods in epigenomics.

Pinello L, Lo Bosco G, Yuan GC.

Brief Bioinform. 2014 May;15(3):419-30. doi: 10.1093/bib/bbt078. Epub 2013 Nov 6. Review.

43.

Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions.

Pulakanti K, Pinello L, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblawi S, Peterson J, Wang A, Yuan GC, Rao S.

Epigenetics. 2013 Dec;8(12):1303-20. doi: 10.4161/epi.26597. Epub 2013 Oct 17.

44.

An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level.

Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH.

Science. 2013 Oct 11;342(6155):253-7. doi: 10.1126/science.1242088.

45.

Visual, motor, and psychomotor development in small-for-gestational-age preterm infants.

Pinello L, Manea S, Visonà Dalla Pozza L, Mazzarolo M, Facchin P.

J AAPOS. 2013 Aug;17(4):352-6. doi: 10.1016/j.jaapos.2013.03.026.

PMID:
23993714
46.

STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6.

Walker SR, Nelson EA, Yeh JE, Pinello L, Yuan GC, Frank DA.

Mol Cell Biol. 2013 Aug;33(15):2879-90. doi: 10.1128/MCB.01620-12. Epub 2013 May 28.

47.

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis.

Giancarlo R, Lo Bosco G, Pinello L, Utro F.

BMC Bioinformatics. 2013;14 Suppl 1:S6. doi: 10.1186/1471-2105-14-S1-S6. Epub 2013 Jan 14.

48.

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis.

Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HK, Yuan GC, Orkin SH.

Dev Cell. 2012 Oct 16;23(4):796-811. doi: 10.1016/j.devcel.2012.09.003. Epub 2012 Oct 4.

49.

The role of visual electrophysiology in mucopolysaccharidoses.

Suppiej A, Rampazzo A, Cappellari A, Traverso A, Tormene AP, Pinello L, Scarpa M.

J Child Neurol. 2013 Oct;28(10):1203-9. doi: 10.1177/0883073812453322. Epub 2012 Aug 21.

PMID:
22914380
50.

Illusory contours over pathological retinal scotomas.

De Stefani E, Pinello L, Campana G, Mazzarolo M, Lo Giudice G, Casco C.

PLoS One. 2011;6(10):e26154. doi: 10.1371/journal.pone.0026154. Epub 2011 Oct 12.

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