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Luca Pinello, Ph.D.

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Overview

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. UM1HG012010 (PINELLO, LUCA) Sep 1, 2021 - May 31, 2026
    NIH
    Comprehensive characterization of variants underlying heart and blood diseases with CRISPR base editing
    Role: Principal Investigator
  2. R35HG010717 (PINELLO, LUCA) Sep 1, 2019 - Jun 30, 2024
    NIH
    Multiscale exploration of the functional non-coding genome
    Role: Principal Investigator
  3. R00HG008399 (PINELLO, LUCA) Dec 19, 2016 - Nov 30, 2020
    NIH
    Discovering disease-causal variants by linking genetic and epigenetic variation
    Role: Principal Investigator
  4. K99HG008399 (PINELLO, LUCA) Jun 18, 2015 - May 31, 2017
    NIH
    Discovering disease-causal variants by linking genetic and epigenetic variation
    Role: Principal Investigator

Featured Content

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Hu H, Piotrowska Z, Hare PJ, Chen H, Mulvey HE, Mayfield A, Noeen S, Kattermann K, Greenberg M, Williams A, Riley AK, Wilson JJ, Mao YQ, Huang RP, Banwait MK, Ho J, Crowther GS, Hariri LP, Heist RS, Kodack DP, Pinello L, Shaw AT, Mino-Kenudson M, Hata AN, Sequist LV, Benes CH, Niederst MJ, Engelman JA. Three subtypes of lung cancer fibroblasts define distinct therapeutic paradigms. Cancer Cell. 2021 Nov 08; 39(11):1531-1547.e10. PMID: 34624218.
    Citations:    Fields:    
  2. Tognon M, Bonnici V, Garrison E, Giugno R, Pinello L. GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs. PLoS Comput Biol. 2021 Sep; 17(9):e1009444. PMID: 34570769.
    Citations:    Fields:    
  3. Yun JH, Lee C, Liu T, Liu S, Kim EY, Xu S, Curtis JL, Pinello L, Bowler RP, Silverman EK, Hersh CP, Zhou X. Hedgehog interacting protein-expressing lung fibroblasts suppress lymphocytic inflammation in mice. JCI Insight. 2021 Sep 08; 6(17). PMID: 34375314.
    Citations:    Fields:    
  4. Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK. Augmenting and directing long-range CRISPR-mediated activation in human cells. Nat Methods. 2021 09; 18(9):1075-1081. PMID: 34354266.
    Citations: 1     Fields:    Translation:HumansCells
  5. Yamauchi T, Miyawaki K, Semba Y, Takahashi M, Izumi Y, Nogami J, Nakao F, Sugio T, Sasaki K, Pinello L, Bauer DE, Bamba T, Akashi K, Maeda T. Targeting leukemia-specific dependence on the de novo purine synthesis pathway. Leukemia. 2021 Aug 03. PMID: 34344987.
    Citations:    Fields:    
  6. Petri K, Zhang W, Ma J, Schmidts A, Lee H, Horng JE, Kim DY, Kurt IC, Clement K, Hsu JY, Pinello L, Maus MV, Joung JK, Yeh JJ. Author Correction: CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat Biotechnol. 2021 May 13. PMID: 33986547.
    Citations:    Fields:    
  7. Petri K, Zhang W, Ma J, Schmidts A, Lee H, Horng JE, Kim DY, Kurt IC, Clement K, Hsu JY, Pinello L, Maus MV, Joung JK, Yeh JJ. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat Biotechnol. 2021 Apr 29. PMID: 33927418.
    Citations: 5     Fields:    
  8. Vinjamur DS, Yao Q, Cole MA, McGuckin C, Ren C, Zeng J, Hossain M, Luk K, Wolfe SA, Pinello L, Bauer DE. ZNF410 represses fetal globin by singular control of CHD4. Nat Genet. 2021 05; 53(5):719-728. PMID: 33859416.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  9. Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Author Correction: Transcription factor competition at the ?-globin promoters controls hemoglobin switching. Nat Genet. 2021 Apr; 53(4):586. PMID: 33731942.
    Citations:    Fields:    
  10. Wang L, Zhang Q, Qin Q, Trasanidis N, Vinyard M, Chen H, Pinello L. Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate. Curr Opin Syst Biol. 2021 Jun; 26:1-11. PMID: 33997529.
    Citations: 1     
  11. Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Transcription factor competition at the ?-globin promoters controls hemoglobin switching. Nat Genet. 2021 04; 53(4):511-520. PMID: 33649594.
    Citations: 5     Fields:    Translation:HumansCells
  12. Hsu JY, Grünewald J, Szalay R, Shih J, Anzalone AV, Lam KC, Shen MW, Petri K, Liu DR, Joung JK, Pinello L. PrimeDesign software for rapid and simplified design of prime editing guide RNAs. Nat Commun. 2021 02 15; 12(1):1034. PMID: 33589617.
    Citations: 6     Fields:    Translation:HumansCells
  13. Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, Müller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK. A Code of Ethics for Gene Drive Research. CRISPR J. 2021 02; 4(1):19-24. PMID: 33571044.
    Citations: 3     Fields:    
  14. Yao Q, Ferragina P, Reshef Y, Lettre G, Bauer DE, Pinello L. Motif-Raptor: A Cell Type-Specific and Transcription Factor Centric Approach for Post-GWAS Prioritization of Causal Regulators. Bioinformatics. 2021 Feb 03. PMID: 33532840.
    Citations:    Fields:    
  15. Rao S, Yao Y, Soares de Brito J, Yao Q, Shen AH, Watkinson RE, Kennedy AL, Coyne S, Ren C, Zeng J, Serbin AV, Studer S, Ballotti K, Harris CE, Luk K, Stevens CS, Armant M, Pinello L, Wolfe SA, Chiarle R, Shimamura A, Lee B, Newburger PE, Bauer DE. Dissecting ELANE neutropenia pathogenicity by human HSC gene editing. Cell Stem Cell. 2021 05 06; 28(5):833-845.e5. PMID: 33513358.
    Citations: 2     Fields:    Translation:HumansAnimals
  16. Li CM, Shapiro H, Tsiobikas C, Selfors LM, Chen H, Rosenbluth J, Moore K, Gupta KP, Gray GK, Oren Y, Steinbaugh MJ, Guerriero JL, Pinello L, Regev A, Brugge JS. Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing. Cell Rep. 2020 12 29; 33(13):108566. PMID: 33378681.
    Citations: 6     Fields:    Translation:AnimalsCells
  17. Yao Q, Epstein CB, Banskota S, Issner R, Kim Y, Bernstein BE, Pinello L, Asgari MM. Epigenetic Alterations in Keratinocyte Carcinoma. J Invest Dermatol. 2021 05; 141(5):1207-1218. PMID: 33212152.
    Citations: 2     Fields:    
  18. Ten Hacken E, Clement K, Li S, Hernández-Sánchez M, Redd R, Wang S, Ruff D, Gruber M, Baranowski K, Jacob J, Flynn J, Jones KW, Neuberg D, Livak KJ, Pinello L, Wu CJ. High throughput single-cell detection of multiplex CRISPR-edited gene modifications. Genome Biol. 2020 10 20; 21(1):266. PMID: 33081820.
    Citations: 3     Fields:    Translation:HumansAnimals
  19. Kim IS, Wu J, Rahme GJ, Battaglia S, Dixit A, Gaskell E, Chen H, Pinello L, Bernstein BE. Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies. Cell Rep. 2020 10 06; 33(1):108222. PMID: 33027665.
    Citations: 1     Fields:    Translation:HumansCells
  20. Canver MC, Tripathi P, Bullen MJ, Olshansky M, Kumar Y, Wong LH, Turner SJ, Lessard S, Pinello L, Orkin SH, Das PP. A saturating mutagenesis CRISPR-Cas9-mediated functional genomic screen identifies cis- and trans-regulatory elements of Oct4 in murine ESCs. J Biol Chem. 2020 11 20; 295(47):15797-15809. PMID: 32994224.
    Citations:    Fields:    Translation:HumansAnimalsCells
  21. Clement K, Hsu JY, Canver MC, Joung JK, Pinello L. Technologies and Computational Analysis Strategies for CRISPR Applications. Mol Cell. 2020 07 02; 79(1):11-29. PMID: 32619467.
    Citations: 1     Fields:    Translation:Humans
  22. 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. Publisher Correction: Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2020 Jul; 38(7):901. PMID: 32541959.
    Citations: 1     Fields:    
  23. Cancellieri S, Canver MC, Bombieri N, Giugno R, Pinello L. CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing. Bioinformatics. 2020 04 01; 36(7):2001-2008. PMID: 31764961.
    Citations: 7     Fields:    Translation:Cells
  24. Zeng J, Wu Y, Ren C, Bonanno J, Shen AH, Shea D, Gehrke JM, Clement K, Luk K, Yao Q, Kim R, Wolfe SA, Manis JP, Pinello L, Joung JK, Bauer DE. Therapeutic base editing of human hematopoietic stem cells. Nat Med. 2020 04; 26(4):535-541. PMID: 32284612.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  25. Albergante L, Mirkes E, Bac J, Chen H, Martin A, Faure L, Barillot E, Pinello L, Gorban A, Zinovyev A. Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. Entropy (Basel). 2020 Mar 04; 22(3). PMID: 33286070.
    Citations: 4     
  26. Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Eleven grand challenges in single-cell data science. Genome Biol. 2020 02 07; 21(1):31. PMID: 32033589.
    Citations: 100     Fields:    Translation:HumansAnimals
  27. Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L. Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biol. 2019 11 18; 20(1):241. PMID: 31739806.
    Citations: 43     Fields:    Translation:HumansAnimals
  28. Rao S, Brito-Frazao J, Serbin AV, Yao Q, Luk K, Wu Y, Zeng J, Ren C, Watkinson R, Armant M, Pinello L, Shimamura A, Lee B, Wolfe SA, Newburger PE, Bauer DE. Gene Editing ELANE in Human Hematopoietic Stem and Progenitor Cells Reveals Disease Mechanisms and Therapeutic Strategies for Severe Congenital Neutropenia. Blood. 2019 Nov 13; 134(Supplement_1):3. PMID: 31723993.
    Citations:    
  29. Hu X, Xiang D, Xie Y, Tao L, Zhang Y, Jin Y, Pinello L, Wan Y, Yuan GC, Li Z. LSD1 suppresses invasion, migration and metastasis of luminal breast cancer cells via activation of GATA3 and repression of TRIM37 expression. Oncogene. 2019 10; 38(44):7017-7034. PMID: 31409898.
    Citations: 9     Fields:    Translation:HumansCells
  30. Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet. 2019 07; 51(7):1149-1159. PMID: 31253978.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  31. Canver MC, Bauer DE, Maeda T, Pinello L. DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens. Bioinformatics. 2019 06 01; 35(11):1981-1984. PMID: 30395160.
    Citations:    Fields:    Translation:HumansCells
  32. Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun. 2019 04 23; 10(1):1903. PMID: 31015418.
    Citations: 42     Fields:    Translation:AnimalsCells
  33. Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. Mol Cell. 2019 06 20; 74(6):1148-1163.e7. PMID: 31005419.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  34. Vinyard ME, Su C, Siegenfeld AP, Waterbury AL, Freedy AM, Gosavi PM, Park Y, Kwan EE, Senzer BD, Doench JG, Bauer DE, Pinello L, Liau BB. CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML. Nat Chem Biol. 2019 05; 15(5):529-539. PMID: 30992567.
    Citations: 17     Fields:    Translation:HumansCells
  35. Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement K, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat Med. 2019 05; 25(5):776-783. PMID: 30911135.
    Citations: 99     Fields:    Translation:HumansCells
  36. Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019 03; 37(3):224-226. PMID: 30809026.
    Citations: 131     Fields:    Translation:HumansCells
  37. 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. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019 03; 37(3):276-282. PMID: 30742127.
    Citations: 94     Fields:    Translation:HumansCells
  38. Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, Luo HY, Brendel C, Pinello L, Chui DHK, Wolfe SA, Bauer DE. Editing aberrant splice sites efficiently restores ß-globin expression in ß-thalassemia. Blood. 2019 05 23; 133(21):2255-2262. PMID: 30704988.
    Citations: 19     Fields:    Translation:HumansCells
  39. 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. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat Methods. 2018 12; 15(12):992-993. PMID: 30504875.
    Citations: 10     Fields:    Translation:HumansCells
  40. Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L, Bauer DE. CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. Genome Biol. 2018 10 19; 19(1):169. PMID: 30340514.
    Citations: 10     Fields:    Translation:HumansCells
  41. 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. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature. 2018 09; 561(7723):416-419. PMID: 30209390.
    Citations: 92     Fields:    Translation:HumansAnimals
  42. 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. Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nat Genet. 2018 10; 50(10):1483-1493. PMID: 30177862.
    Citations: 18     Fields:    Translation:HumansCells
  43. 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. Author Correction: High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature. 2018 08; 560(7717):E26. PMID: 29849139.
    Citations: 2     Fields:    
  44. Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol. 2018 11; 36(10):977-982. PMID: 30059493.
    Citations: 99     Fields:    Translation:HumansCells
  45. Clement K, Farouni R, Bauer DE, Pinello L. AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Bioinformatics. 2018 07 01; 34(13):i202-i210. PMID: 29949956.
    Citations: 4     Fields:    
  46. Pinello L, Farouni R, Yuan GC. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics. 2018 06 01; 34(11):1930-1933. PMID: 29360936.
    Citations: 6     Fields:    Translation:HumansCells
  47. Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protoc. 2018 05; 13(5):946-986. PMID: 29651054.
    Citations: 19     Fields:    Translation:Cells
  48. Canver MC, Joung JK, Pinello L. Impact of Genetic Variation on CRISPR-Cas Targeting. CRISPR J. 2018 04; 1(2):159-170. PMID: 31021199.
    Citations: 5     Fields:    
  49. Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L. Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods. 2018 04; 15(4):238-239. PMID: 29600992.
    Citations: 10     Fields:    Translation:Cells
  50. 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. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. Cancer Cell. 2018 03 12; 33(3):386-400.e5. PMID: 29478914.
    Citations: 29     Fields:    Translation:HumansAnimalsCells
  51. 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. The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation. Sci Rep. 2017 12 07; 7(1):17156. PMID: 29214996.
    Citations: 8     Fields:    Translation:AnimalsCells
  52. 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. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med. 2017 Oct 02; 214(10):2875-2887. PMID: 28878000.
    Citations: 40     Fields:    Translation:AnimalsCells
  53. 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. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res. 2017 06; 27(6):843. PMID: 28572571.
    Citations:    Fields:    
  54. 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. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res. 2017 06; 27(6):842. PMID: 28572570.
    Citations: 3     Fields:    
  55. Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. Nat Commun. 2017 04 07; 8:15011. PMID: 28387224.
    Citations: 15     Fields:    Translation:HumansCells
  56. Min L, Zhang C, Qu L, Huang J, Jiang L, Liu J, Pinello L, Yuan GC, Shou C. Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer. Oncotarget. 2017 Mar 28; 8(13):21938-21953. PMID: 28423538.
    Citations: 7     Fields:    Translation:Humans
  57. 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. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017 Apr; 49(4):625-634. PMID: 28218758.
    Citations: 38     Fields:    Translation:HumansCells
  58. 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. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res. 2017 03; 27(3):386-401. PMID: 28128194.
    Citations: 8     Fields:    Translation:AnimalsCells
  59. Blinka S, Reimer MH, Pulakanti K, Pinello L, Yuan GC, Rao S. Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. Methods Mol Biol. 2017; 1468:91-109. PMID: 27662872.
    Citations: 3     Fields:    Translation:AnimalsCells
  60. 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. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol. 2017 02; 18(2):184-195. PMID: 27992400.
    Citations: 20     Fields:    Translation:AnimalsCells
  61. Henssen AG, Jiang E, Zhuang J, Pinello L, Socci ND, Koche R, Gonen M, Villasante CM, Armstrong SA, Bauer DE, Weng Z, Kentsis A. Forward genetic screen of human transposase genomic rearrangements. BMC Genomics. 2016 Aug 04; 17:548. PMID: 27491780.
    Citations: 3     Fields:    Translation:HumansCells
  62. Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 07 12; 34(7):695-7. PMID: 27404874.
    Citations: 156     Fields:    Translation:HumansAnimalsCells
  63. Jiang L, Chen H, Pinello L, Yuan GC. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. Genome Biol. 2016 07 01; 17(1):144. PMID: 27368803.
    Citations: 68     Fields:    Translation:AnimalsCells
  64. Jadhav U, Nalapareddy K, Saxena M, O'Neill NK, Pinello L, Yuan GC, Orkin SH, Shivdasani RA. Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells. Cell. 2016 Jun 02; 165(6):1389-1400. PMID: 27212235.
    Citations: 39     Fields:    Translation:AnimalsCells
  65. Stelloh C, Reimer MH, Pulakanti K, Blinka S, Peterson J, Pinello L, Jia S, Roumiantsev S, Hessner MJ, Milanovich S, Yuan GC, Rao S. The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing. Epigenetics Chromatin. 2016; 9:14. PMID: 27087855.
    Citations: 5     Fields:    
  66. 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. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature. 2016 Mar 03; 531(7592):53-8. PMID: 26935695.
    Citations: 180     Fields:    Translation:HumansAnimalsCells
  67. Guo G, Pinello L, Han X, Lai S, Shen L, Lin TW, Zou K, Yuan GC, Orkin SH. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. Cell Rep. 2016 Feb 02; 14(4):956-965. PMID: 26804902.
    Citations: 33     Fields:    Translation:AnimalsCells
  68. Wu JN, Pinello L, Yissachar E, Wischhusen JW, Yuan GC, Roberts CWM. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics Chromatin. 2015; 8:53. PMID: 26633995.
    Citations: 6     Fields:    
  69. 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. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Nov 12; 527(7577):192-7. PMID: 26375006.
    Citations: 271     Fields:    Translation:HumansAnimalsCells
  70. Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biol. 2015 Aug 14; 16:162. PMID: 26272203.
    Citations: 42     Fields:    Translation:HumansCells
  71. Hu T, Yeh JE, Pinello L, Jacob J, Chakravarthy S, Yuan GC, Chopra R, Frank DA. Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity. Mol Cell Biol. 2015 Oct; 35(19):3284-300. PMID: 26169829.
    Citations: 16     Fields:    Translation:AnimalsCells
  72. 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. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell. 2015 Feb 19; 57(4):636-647. PMID: 25699710.
    Citations: 153     Fields:    Translation:HumansCells
  73. Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH. Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell. 2015 Jan 22; 57(2):304-316. PMID: 25578878.
    Citations: 51     Fields:    Translation:HumansCells
  74. 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. LincRNA-p21 regulates neointima formation, vascular smooth muscle cell proliferation, apoptosis, and atherosclerosis by enhancing p53 activity. Circulation. 2014 Oct 21; 130(17):1452-1465. PMID: 25156994.
    Citations: 166     Fields:    Translation:HumansAnimalsCells
  75. Pinello L, Xu J, Orkin SH, Yuan GC. Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns. Proc Natl Acad Sci U S A. 2014 Jan 21; 111(3):E344-53. PMID: 24395799.
    Citations: 36     Fields:    Translation:HumansCells
  76. 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. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell. 2014 01 09; 53(1):32-48. PMID: 24361252.
    Citations: 57     Fields:    Translation:AnimalsCells
  77. Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May; 15(3):419-30. PMID: 24197932.
    Citations: 6     Fields:    Translation:Humans
  78. Pulakanti K, Pinello L, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblawi S, Peterson J, Wang A, Yuan GC, Rao S. Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions. Epigenetics. 2013 Dec; 8(12):1303-20. PMID: 24135681.
    Citations: 33     Fields:    Translation:AnimalsCells
  79. 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. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science. 2013 Oct 11; 342(6155):253-7. PMID: 24115442.
    Citations: 235     Fields:    Translation:HumansAnimalsCells
  80. Walker SR, Nelson EA, Yeh JE, Pinello L, Yuan GC, Frank DA. STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6. Mol Cell Biol. 2013 Aug; 33(15):2879-90. PMID: 23716595.
    Citations: 39     Fields:    Translation:HumansCells
  81. Giancarlo R, Lo Bosco G, Pinello L, Utro F. A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis. BMC Bioinformatics. 2013; 14 Suppl 1:S6. PMID: 23369037.
    Citations:    Fields:    Translation:Cells
  82. Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HK, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell. 2012 Oct 16; 23(4):796-811. PMID: 23041383.
    Citations: 100     Fields:    Translation:HumansCells
  83. Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21; 12:408. PMID: 22017798.
    Citations: 5     Fields:    Translation:HumansCells
  84. Sala A, Toto M, Pinello L, Gabriele A, Di Benedetto V, Ingrassia AM, Lo Bosco G, Di Gesù V, Giancarlo R, Corona DF. Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI. EMBO J. 2011 May 04; 30(9):1766-77. PMID: 21448136.
    Citations: 37     Fields:    Translation:AnimalsCells
  85. Pinello L. [Ophthalmology problems in pediatric patients: what to do and what not to do]. Minerva Pediatr. 2009 Dec; 61(6):831-4. PMID: 19935566.
    Citations:    Fields:    Translation:Humans
  86. Di Gesù V, Lo Bosco G, Pinello L, Yuan GC, Corona DF. A multi-layer method to study genome-scale positions of nucleosomes. Genomics. 2009 Feb; 93(2):140-5. PMID: 18951969.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  87. Battistella PA, Pisan P, Carollo C, Pinello L, Mira MA, Pellone M. [Intraorbital tumors in children. Two cases and review of the literature]. Minerva Pediatr. 1998 Dec; 50(12):519-28. PMID: 10210943.
    Citations:    Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.