Dana-Farber Cancer Institute

Harvard School of Public Health

Ciao, I am Luca – PhD in Computer Science and Mathematics

I am currently an Instructor in Yuan's lab at Dana-Farber Cancer Institute - Harvard School of Public Health

(epi)Genomics

I develop new computational approaches to investigate different epigenetic factors that regulate the chromatin structure and the gene expression integrating NGS for instance: ChIP-seq, RNA-seq, Bisulfite-seq.

Single Cell Analysis

I have experience analizing data from recent single cell assays for gene expression, such as single cell RNA-seq and multiplexed qPCR.

Genome Editing

I am embracing the new revolution in functional genomics made possible by the novel genome editing approaches such as CRISPR/Cas9 and TALEN developing new tools to undestand and visualize the outcome of these wet lab experiments.

I am a computational biologist with background in computer science and extensive experience in machine learning and data mining.

I have had the good fortune to be part of the "omics" revolution and the opportunity to work on many computationally-challenging problems on the role of chromatin structure in gene regulation.

Over the course of my academic career, my major focus has been to unravel the role of epigenetic mechanisms that influence gene expression, including nucleosome positioning, DNA methylation and histone modifications. My research has emphasized the critical interplay between epigenetic mechanisms and linear DNA sequences: in fact I showed that epigenetic patterns can be characterized and predicted from DNA sequences.

I aim to become an independent investigator with a research program that uses computational approaches to systematically analyze the sources of variation that affect gene regulation: epigenetic variation, genetic variation and (single-cell) gene expression variability.


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Publications

Selected publication

  1. 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 3;531(7592):53-8. doi: 10.1038/nature17173. PubMed PMID: 26935695.
  2. 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 2;14(4):956-65. doi: 10.1016/j.celrep.2015.12.089. Epub 2016 Jan 21. PubMed PMID: 26804902; PubMed Central PMCID: PMC4740311.
  3. Wu JN*, Pinello L*, Yissachar E, Wischhusen JW, Yuan GC, Roberts CW. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics Chromatin. 2015 Dec 2;8:53. doi: 10.1186/s13072-015-0046-0. eCollection 2015. PubMed PMID:26633995; PubMed Central PMCID: PMC4667523.
  4. 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 G-C, Zhang F, Orkin SH & Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Sep 16. doi: 10.1038/nature15521. [Epub ahead of print]
  5. Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biol. 2015 Aug 14;16(1):162.
  6. 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):636-47.
  7. 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 Jul 13. pii: MCB.00060-15.
  8. 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):304-16.
  9. 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 Aug 25. pii: CIRCULATIONAHA.114.011675.
  10. Pinello L*, Xu J*, Orkin SH, Yuan GC. Analysis of chromatin state plasticity identifies cell-type specific regulators of H3K27me3 patterns, PNAS 2014 Jan 6; 10.1073/pnas.1322570111.
  11. 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 Jan 9;53(1):32-48. doi: 10.1016/j.molcel.2013.11.011.
  12. Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods inepigenomics. Brief Bioinform. 2014 May;15(3):419-30. doi: 10.1093/bib/bbt078.
  13. 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 Oct 17; 8(12).
  14. 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.
  15. Meyer P, Siwo G, Zeevi D, Sharon E, Norel R; DREAM6 Promoter Prediction Consortium, Segal E, Stolovitzky G. Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Research. 2013 Oct 4; 23: 1928-1937.
  16. 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.
  17. 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 Jan 14; (Suppl 1), S6, BioMed Central Ltd.
  18. 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. Developmental Cell, 2012 Oct 16; 23(4):796-811.
  19. Sala A*, Toto M*, Pinello L*, Gabriele A, Di Benedetto V, Ingrassia AM, Lo Bosco G, Di Gesù V, Giancarlo R, Corona DFV. Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISW. EMBO Journal, 2011 May 4; 30(9): 1766–1777.
  20. Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21; 12(1):408+.
  21. Di Gesù V, Lo Bosco G, Pinello L, Yuan GC, Corona DFV. A multi-layer method to study genome-scale positions of nucleosomes. Genomics 2009; 93(2):140-5.
  22. Di Gesù V, Lo Bosco G, Pinello L. A one class KNN for Signal identification: a biological case study. International Journal of Knowledge Engineering and Soft Data Paradigms (IJKESDP) 2009; 1(4): N.4.

Software

Tools and software for Computational Biology

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CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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Haystack

Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
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Motif Independent Metric (MIM)

Calculates a general and unbiased measure of DNA sequence specificity
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Python Bioutilities

Python library to streamline the analysis of genomics data
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N-score

Nuclesome/Histone modification prediction based on DNA-sequences
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Multi Layer Analysis

Nucleosome Prediction based on tiling-microarray data

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Get in touch with me

Luca Pinello