Selected Publications
Lin J, Luo R#, Pinello L#. EPInformer: a scalable deep learning framework for gene expression prediction by integrating promoter-enhancer sequences with multimodal epigenomic data. bioRxiv [Preprint]. 2024 Aug 1:2024.08.01.606099. doi: 10.1101/2024.08.01.606099. PMID: 39131276; PMCID: PMC11312614.
DaSilva LF*, Senan S*, Patel ZM, Janardhan Reddy A, Gabbita S, Nussbaum Z, Valdez Córdova CM, Wenteler A, Weber N, Tunjic TM, Ahmad Khan T, Li Z, Smith C, Bejan M, Karmel Louis L, Cornejo P, Connell W, Wong ES, Meuleman W, Pinello L. DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements. bioRxiv [Preprint]. 2024 Feb 1:2024.02.01.578352. doi: 10.1101/2024.02.01.578352. PMID: 38352499; PMCID: PMC10862870.
Li Z*, Patel ZM*, Song D, Yan G, Li JJ, Pinello L. Benchmarking computational methods to identify spatially variable genes and peaks. bioRxiv [Preprint]. 2023 Dec 3:2023.12.02.569717. doi: 10.1101/2023.12.02.569717. PMID: 38076922; PMCID: PMC10705556.
Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Bhat V, Lettre G, Ascher DB, Cassa CA, Sherwood RI#, Pinello L.# Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nat Genet. 2024 May;56(5):925-937. doi: 10.1038/s41588-024-01726-6. Epub 2024 Apr 24. PMID: 38658794.
Wang L*, Trasanidis N*, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods. 2023 Sep;20(9):1368-1378. doi: 10.1038/s41592-023-01971-3. Epub 2023 Aug 3. PMID: 37537351.
Chen H, Ryu J, Vinyard ME, Lerer A, Pinello L#. SIMBA: single-cell embedding along with features. Nat Methods. 2023 May 29. doi: 10.1038/s41592-023-01899-8. Epub ahead of print. PMID: 37248389.
Tognon M, Giugno R#, Pinello L#. A survey on algorithms to characterize transcription factor binding sites. Brief Bioinform. 2023 May 19;24(3):bbad156. doi: 10.1093/bib/bbad156. PMID: 37099664; PMCID: PMC10422928.
Cancellieri S*, Zeng J*, Lin LY*, Tognon M, Nguyen MA, Lin J, Bombieri N, Maitland SA, Ciuculescu MF, Katta V, Tsai SQ, Armant M, Wolfe SA, Giugno R#, Bauer DE#, Pinello L#. Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nat Genet. 2023 Jan;55(1):34-43. doi: 10.1038/s41588-022-01257-y. Epub 2022 Dec 15. PMID: 36522432.
Stein DF, Chen H, Vinyard ME, Qin Q, Combs RD, Zhang Q, Pinello L. singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality. Front Genet. 2021 Oct 28;12:764170. doi: 10.3389/fgene.2021.764170. PMID: 34777482; PMCID: PMC8582280.
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 27;17(9):e1009444. doi: 10.1371/journal.pcbi.1009444. PMID: 34570769; PMCID: PMC8519448.
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 Feb 15;12(1):1034. doi: 10.1038/s41467-021-21337-7. PMID: 33589617; PMCID: PMC7884779.
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 Aug 9;37(15):2103-2111. doi: 10.1093/bioinformatics/btab072. PMID: 33532840.
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 Apr 1;36(7):2001-2008. doi: 10.1093/bioinformatics/btz867. PMID: 31764961; PMCID: PMC7141852.
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 Nov 18;20(1):241. doi: 10.1186/s13059-019-1854-5. PMID: 31739806; PMCID: PMC6859644.
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 Apr 23;10(1):1903. doi: 10.1038/s41467-019-09670-4. PubMed PMID: 31015418.
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 Feb 26. doi: 10.1038/s41587-019-0032-3. [Epub ahead of print] PubMed PMID: 30809026.
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 Dec;15(12):992-993. doi:10.1038/s41592-018-0225-6.
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. 2018 Nov 5. doi: 10.1093/bioinformatics/bty913.
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 Oct 19;19(1):169. doi: 10.1186/s13059-018-1563-5.
Clement K, Farouni R, Bauer DE, Pinello L. AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Bioinformatics. 2018 Jul 1;34(13):i202-i210. doi: 10.1093/bioinformatics/bty264.
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 Protocols. 2018 May;13(5):946-986. doi: 10.1038/nprot.2018.005
Canver MC, Joung JK, Pinello L. Impact of Genetic Variation on CRISPR-Cas Targeting. The CRISPR Journal. 2018 Apr 1;1(2):159-170. doi: 10.1089/crispr.2017.0016
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 Apr;15(4):238-239. doi: 10.1038/nmeth.4541.
Pinello L*#, Farouni R*, Yuan GC#. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics. 2018 Jan 17. doi: 10.1093/bioinformatics/bty031.
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 Feb;18(2):184-195. doi: 10.1038/ni.3644.
Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 Jul 12;34(7):695-7. doi: 10.1038/nbt.3583.
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.
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 Nov 12;527(7577):192-72015 Sep 16. doi: 10.1038/nature15521.
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.
Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May;15(3):419-30. doi: 10.1093/bib/bbt078.
Pinello L*, Xu J*, Orkin SH, Yuan GC. Analysis of chromatin state plasticity identifies cell-type specific regulators of H3K27me3 patterns, PNAS. 2014 Jan 21;111(3):E344-53. doi: 10.1073/pnas.1322570111.
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):1303-20. doi: 10.4161/epi.26597.
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. doi: 10.1186/1471-2105-12-408.
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 ISWI. EMBO J. 2011 May 4;30(9):1766-77. doi: 10.1038/emboj.2011.98.
* co-first authors
# co-corresponding authors