Publications

For full list of publications, see PubMed.

*Co-first author
#Senior author

Ganesan S, Cortés-López M, Swett AD, Dai X, Hickey S, Chamely P, Hawkins AG, Juul S, Landau DA#, Gaiti F#. GoT-Splice protocol for multi-omics profiling of gene expression, cell-surface proteins, mutational status, and RNA splicing in human cells. STAR Protoc. 2024 Mar 20;5(2):102966. doi: 10.1016/j.xpro.2024.102966. [Epub ahead of print] PubMed PMID: 38512867; PubMed Central PMCID: PMC10966806.

Ashouri A, Zhang C, Gaiti F#. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes. 2023 September; 14(10):1856.

Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F#, Landau DA#. Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. Cell Stem Cell. 2023 Sep 7;30(9):1262-1281.e8. doi: 10.1016/j.stem.2023.07.012. Epub 2023 Aug 14. PubMed PMID: 37582363; PubMed Central PMCID: PMC10528176.

This paper is highlighted in a Cancer Discovery Research Watch.

Nam AS*, Dusaj N*, Izzo F*, Murali R*, Myers RM*, Mouhieddine TH, Sotelo J, Benbarche S, Waarts M, Gaiti F, Tahri S, Levine R, Abdel-Wahab O, Godley LA, Chaligne R, Ghobrial I, Landau DA. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat Genet. 2022 Oct;54(10):1514-1526. doi: 10.1038/s41588-022-01179-9. Epub 2022 Sep 22. PubMed PMID: 36138229.

Chaligne R*, Gaiti F*, Silverbush D*, Schiffman JS*, Weisman HR, Kluegel L, Gritsch S, Deochand S, Gonzalez castro N, Richman AR, Klughammer J, Biancalani T, Muus C, Sheridan C, Alonso A, Izzo F, Park J, Rozenblatt-Rosen O, Regev A, Suva M, Landau DA. Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.​ Nature Genetics, 2021. See news and views piece @ Nature Genetics

Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M. Single cell biology-a Keystone Symposia report. Ann N Y Acad Sci. 2021 Oct 3;. doi: 10.1111/nyas.14692.

Gaiti F*, Chaligne R*, Gu H*, Brand RM, Kothen-Hill S, Schulman RC, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature. 2019 May;569(7757):576-580. doi: 10.1038/s41586-019-1198-z.Epub 2019 May 15. PubMed PMID: 31092926; PubMed Central PMCID: PMC6533116.

This paper is highlighted in a Nature Review Genetics Research Highlight, https://doi.org/10.1038/s41576-019-0143-1

Pastore A*, Gaiti F*, Lu SX, Brand RM, Kulm S, Chaligne R, Gu H, Huang KY, Stamenova EK, Béguelin W, Jiang Y, Schulman RC, Kim KT, Alonso A, Allan JN, Furman RR, Gnirke A, Wu CJ, Melnick AM, Meissner A, Bernstein BE, Abdel-Wahab O, Landau DA. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat Commun. 2019 Apr 23;10(1):1874. doi: 10.1038/s41467-019-09645-5. PubMed PMID: 31015400; PubMed Central PMCID: PMC6478836.

Gu H*, Raman AT*, Wang X, Gaiti F, Chaligne R, Mohammad AW, Arczewska A, Smith ZD, Landau DA, Aryee MJ, Meissner A, Gnirke A. Smart-RRBS for single-cell methylome and transcriptome analysis. Nat Protoc. 2021 Jul 9;. doi: 10.1038/s41596-021-00571-9. [Epub ahead of print] Review. PubMed PMID: 34244697.

Zviran A*, Schulman RC*, Shah M*, Hill STK, Deochand S, Khamnei CC, Maloney D, Patel K, Liao W, Widman AJ, Wong P, Callahan MK, Ha G, Reed S, Rotem D, Frederick D, Sharova T, Miao B, Kim T, Gydush G, Rhoades J, Huang KY, Omans ND, Bolan PO, Lipsky AH, Ang C, Malbari M, Spinelli CF, Kazancioglu S, Runnels AM, Fennessey S, Stolte C, Gaiti F, Inghirami GG, Adalsteinsson V, Houck-Loomis B, Ishii J, Wolchok JD, Boland G, Robine N, Altorki NK, Landau DA. Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat Med. 2020 Jul;26(7):1114-1124. doi: 10.1038/s41591-020-0915-3. Epub 2020 Jun 1. PubMed PMID: 32483360; PubMed Central PMCID: PMC8108131.

Izzo F*, Lee SC*, Poran A, Chaligne R, Gaiti F, Gross B, Murali RR, Deochand SD, Ang C, Jones PW, Nam AS, Kim KT, Kothen-Hill S, Schulman RC, Ki M, Lhoumaud P, Skok JA, Viny AD, Levine RL, Kenigsberg E, Abdel-Wahab O, Landau DA. DNA methylation disruption reshapes the hematopoietic differentiation landscape. Nat Genet. 2020 Apr;52(4):378-387. doi: 10.1038/s41588-020-0595-4. Epub 2020 Mar 23. PubMed PMID: 32203468; PubMed Central PMCID: PMC7216752.

Gaiti F, Jindrich K, Fernandez-Valverde SL, Roper KE, Degnan BM, Tanurdžić M. Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. Elife. 2017 Apr 11;6. doi: 10.7554/eLife.22194. PubMed PMID: 28395144; PubMed Central PMCID: PMC5429095.

Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM. Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Mol Biol Evol. 2015 Sep;32(9):2367-82. doi: 10.1093/molbev/msv117. Epub 2015 May 14. PubMed PMID: 25976353; PubMed Central PMCID: PMC4540969.

Wong ES, Zheng D, Tan SZ, Bower NL, Garside V, Vanwalleghem G, Gaiti F, Scott E, Hogan BM, Kikuchi K, McGlinn E, Francois M, Degnan BM. Deep conservation of the enhancer regulatory code in animals. Science. 2020 Nov 6;370(6517). doi: 10.1126/science.aax8137. PubMed PMID: 33154111.