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Davide Cacchiarelli, Ph.D., Ph.D.


2007 - 2011
Microsoft Research PhD Scholarship
2012 - 2015
Human Frontier Science Program Fellow

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. Nosi V, Luca A, Milan M, Arigoni M, Benvenuti S, Cacchiarelli D, Cesana M, Riccardo S, Di Filippo L, Cordero F, Beccuti M, Comoglio PM, Calogero RA. MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning. Int J Mol Sci. 2021 Apr 19; 22(8). PMID: 33921709.
    Citations:    Fields:    
  2. Napolitano F, Rapakoulia T, Annunziata P, Hasegawa A, Cardon M, Napolitano S, Vaccaro L, Iuliano A, Wanderlingh LG, Kasukawa T, Medina DL, Cacchiarelli D, Gao X, di Bernardo D, Arner E. Automatic identification of small molecules that promote cell conversion and reprogramming. Stem Cell Reports. 2021 Apr 10. PMID: 33891873.
    Citations:    Fields:    
  3. Barbato A, Iuliano A, Volpe M, D'Alterio R, Brillante S, Massa F, De Cegli R, Carrella S, Salati M, Russo A, Russo G, Riccardo S, Cacchiarelli D, Capone M, Madonna G, Ascierto PA, Franco B, Indrieri A, Carotenuto P. Integrated Genomics Identifies miR-181/TFAM Pathway as a Critical Driver of Drug Resistance in Melanoma. Int J Mol Sci. 2021 Feb 11; 22(4). PMID: 33670365.
    Citations:    Fields:    Translation:HumansCells
  4. Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell. 2021 Jan 07; 28(1):20-32. PMID: 33417869.
    Citations:    Fields:    
  5. Slovin S, Carissimo A, Panariello F, Grimaldi A, Bouché V, Gambardella G, Cacchiarelli D. Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview. Methods Mol Biol. 2021; 2284:343-365. PMID: 33835452.
    Citations:    Fields:    
  6. Passaro F, De Martino I, Zambelli F, Di Benedetto G, Barbato M, D'Erchia AM, Manzari C, Pesole G, Mutarelli M, Cacchiarelli D, Antonini D, Parisi S, Russo T. YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation. J Biol Chem. 2020 Dec 02. PMID: 33268382.
    Citations: 1     Fields:    
  7. Michielin F, Giobbe GG, Luni C, Hu Q, Maroni I, Orford MR, Manfredi A, Di Filippo L, David AL, Cacchiarelli D, De Coppi P, Eaton S, Elvassore N. The Microfluidic Environment Reveals a Hidden Role of Self-Organizing Extracellular Matrix in Hepatic Commitment and Organoid Formation of hiPSCs. Cell Rep. 2020 12 01; 33(9):108453. PMID: 33264615.
    Citations:    Fields:    
  8. Lo Riso P, Villa CE, Gasparoni G, Vingiani A, Luongo R, Manfredi A, Jungmann A, Bertolotti A, Borgo F, Garbi A, Lupia M, Laise P, Das V, Pruneri G, Viale G, Colombo N, Manzo T, Nezi L, Cavallaro U, Cacchiarelli D, Walter J, Testa G. A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer. Genome Med. 2020 10 30; 12(1):94. PMID: 33121525.
    Citations: 1     Fields:    
  9. Modic M, Cacchiarelli D, Ten Berge D. Integrative biology studies in pluripotent stem cells. Stem Cell Res. 2020 01; 42:101686. PMID: 31887610.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  10. Giobbe GG, Crowley C, Luni C, Campinoti S, Khedr M, Kretzschmar K, De Santis MM, Zambaiti E, Michielin F, Meran L, Hu Q, van Son G, Urbani L, Manfredi A, Giomo M, Eaton S, Cacchiarelli D, Li VSW, Clevers H, Bonfanti P, Elvassore N, De Coppi P. Extracellular matrix hydrogel derived from decellularized tissues enables endodermal organoid culture. Nat Commun. 2019 12 11; 10(1):5658. PMID: 31827102.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  11. Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Mol Cell. 2019 06 06; 74(5):951-965.e13. PMID: 31047794.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  12. Giulitti S, Pellegrini M, Zorzan I, Martini P, Gagliano O, Mutarelli M, Ziller MJ, Cacchiarelli D, Romualdi C, Elvassore N, Martello G. Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics. Nat Cell Biol. 2019 02; 21(2):275-286. PMID: 30598530.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  13. Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C. Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Syst. 2018 09 26; 7(3):258-268.e3. PMID: 30195438.
    Citations: 13     Fields:    Translation:HumansCells
  14. Nehme R, Zuccaro E, Ghosh SD, Li C, Sherwood JL, Pietilainen O, Barrett LE, Limone F, Worringer KA, Kommineni S, Zang Y, Cacchiarelli D, Meissner A, Adolfsson R, Haggarty S, Madison J, Muller M, Arlotta P, Fu Z, Feng G, Eggan K. Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. Cell Rep. 2018 05 22; 23(8):2509-2523. PMID: 29791859.
    Citations: 38     Fields:    Translation:HumansCells
  15. Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 2018 04 05; 22(4):575-588.e7. PMID: 29625070.
    Citations: 10     Fields:    Translation:HumansCells
  16. Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K, Gu H, Mohammad AW, Stamenova EK, Cacchiarelli D, Klages S, Timmermann B, Cantz T, Schöler HR, Gnirke A, Ziller MJ, Meissner A. Genome-wide tracking of dCas9-methyltransferase footprints. Nat Commun. 2018 02 09; 9(1):597. PMID: 29426832.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  17. Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet. 2018 02; 50(2):250-258. PMID: 29358654.
    Citations: 41     Fields:    Translation:HumansCells
  18. Maddalena A, Tornabene P, Tiberi P, Minopoli R, Manfredi A, Mutarelli M, Rossi S, Simonelli F, Naggert JK, Cacchiarelli D, Auricchio A. Triple Vectors Expand AAV Transfer Capacity in the Retina. Mol Ther. 2018 02 07; 26(2):524-541. PMID: 29292161.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  19. Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature. 2017 09 28; 549(7673):543-547. PMID: 28959968.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  20. Aguilar CA, Pop R, Shcherbina A, Watts A, Matheny RW, Cacchiarelli D, Han WM, Shin E, Nakhai SA, Jang YC, Carrigan CT, Gifford CA, Kottke MA, Cesana M, Lee J, Urso ML, Meissner A. Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma. Stem Cell Reports. 2016 11 08; 7(5):983-997. PMID: 27773702.
    Citations: 12     Fields:    Translation:AnimalsCells
  21. Brenan L, Andreev A, Cohen O, Pantel S, Kamburov A, Cacchiarelli D, Persky NS, Zhu C, Bagul M, Goetz EM, Burgin AB, Garraway LA, Getz G, Mikkelsen TS, Piccioni F, Root DE, Johannessen CM. Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants. Cell Rep. 2016 10 18; 17(4):1171-1183. PMID: 27760319.
    Citations: 28     Fields:    Translation:HumansCells
  22. Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. 2016 07 07; 19(1):66-80. PMID: 27320042.
    Citations: 82     Fields:    Translation:HumansAnimalsCells
  23. Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell. 2015 Jul 16; 162(2):412-424. PMID: 26186193.
    Citations: 74     Fields:    Translation:HumansCells
  24. Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19; 518(7539):355-359. PMID: 25533951.
    Citations: 73     Fields:    Translation:HumansCells
  25. Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. Cell Rep. 2014 Jul 10; 8(1):284-96. PMID: 24981863.
    Citations: 343     Fields:    Translation:HumansAnimalsCells
  26. Herlofsen SR, Høiby T, Cacchiarelli D, Zhang X, Mikkelsen TS, Brinchmann JE. Brief report: importance of SOX8 for in vitro chondrogenic differentiation of human mesenchymal stromal cells. Stem Cells. 2014 Jun; 32(6):1629-35. PMID: 24449344.
    Citations: 7     Fields:    Translation:HumansCells
  27. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014 Apr; 32(4):381-386. PMID: 24658644.
    Citations: 894     Fields:    Translation:HumansCells
  28. Twayana S, Legnini I, Cesana M, Cacchiarelli D, Morlando M, Bozzoni I. Biogenesis and function of non-coding RNAs in muscle differentiation and in Duchenne muscular dystrophy. Biochem Soc Trans. 2013 Aug; 41(4):844-9. PMID: 23863142.
    Citations: 14     Fields:    Translation:Humans
  29. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011 Oct 14; 147(2):358-69. PMID: 22000014.
    Citations: 1038     Fields:    Translation:HumansAnimalsCells
  30. Cacchiarelli D, Legnini I, Martone J, Cazzella V, D'Amico A, Bertini E, Bozzoni I. miRNAs as serum biomarkers for Duchenne muscular dystrophy. EMBO Mol Med. 2011 May; 3(5):258-65. PMID: 21425469.
    Citations: 101     Fields:    Translation:HumansAnimals
  31. Cacchiarelli D, Incitti T, Martone J, Cesana M, Cazzella V, Santini T, Sthandier O, Bozzoni I. miR-31 modulates dystrophin expression: new implications for Duchenne muscular dystrophy therapy. . 2011 Feb; 12(2):136-41. PMID: 21212803.
    Citations: 66     Translation:HumansAnimalsCells
  32. Cacchiarelli D, Martone J, Girardi E, Cesana M, Incitti T, Morlando M, Nicoletti C, Santini T, Sthandier O, Barberi L, Auricchio A, Musarò A, Bozzoni I. MicroRNAs involved in molecular circuitries relevant for the Duchenne muscular dystrophy pathogenesis are controlled by the dystrophin/nNOS pathway. Cell Metab. 2010 Oct 06; 12(4):341-351. PMID: 20727829.
    Citations: 111     Fields:    Translation:AnimalsCells
  33. Ballarino M, Pagano F, Girardi E, Morlando M, Cacchiarelli D, Marchioni M, Proudfoot NJ, Bozzoni I. Coupled RNA processing and transcription of intergenic primary microRNAs. Mol Cell Biol. 2009 Oct; 29(20):5632-8. PMID: 19667074.
    Citations: 50     Fields:    Translation:HumansCells
  34. Cacchiarelli D, Santoni D, Bozzoni I. MicroRNAs as prime players in a combinatorial view of evolution. RNA Biol. 2008 Jul-Sep; 5(3):120-122. PMID: 18698151.
    Citations: 5     Fields:    Translation:HumansAnimals
  35. Pavoni E, Cacchiarelli D, Tittarelli R, Orsini M, Galtieri A, Giardina B, Brancaccio A. Duplication of the dystroglycan gene in most branches of teleost fish. BMC Mol Biol. 2007 May 17; 8:34. PMID: 17509131.
    Citations: 4     Fields:    Translation:AnimalsCells
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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.