Harvard Catalyst Profiles

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Simone Rubinacci, Ph.D.

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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. Neuenschwander S, Cruz Dávalos DI, Anchieri L, Sousa da Mota B, Bozzi D, Rubinacci S, Delaneau O, Rasmussen S, Malaspinas AS. Mapache: a flexible pipeline to map ancient DNA. Bioinformatics. 2023 Feb 03; 39(2). PMID: 36637197; PMCID: PMC9901408.
    Citations:    Fields:    
  2. Hofmeister RJ, Rubinacci S, Ribeiro DM, Buil A, Kutalik Z, Delaneau O. Parent-of-Origin inference for biobanks. Nat Commun. 2022 11 05; 13(1):6668. PMID: 36335127; PMCID: PMC9637181.
    Citations: 2     Fields:    Translation:Humans
  3. Parikh VN, Ioannidis AG, Jimenez-Morales D, Gorzynski JE, De Jong HN, Liu X, Roque J, Cepeda-Espinoza VP, Osoegawa K, Hughes C, Sutton SC, Youlton N, Joshi R, Amar D, Tanigawa Y, Russo D, Wong J, Lauzon JT, Edelson J, Mas Montserrat D, Kwon Y, Rubinacci S, Delaneau O, Cappello L, Kim J, Shoura MJ, Raja AN, Watson N, Hammond N, Spiteri E, Mallempati KC, Montero-Martín G, Christle J, Kim J, Kirillova A, Seo K, Huang Y, Zhao C, Moreno-Grau S, Hershman SG, Dalton KP, Zhen J, Kamm J, Bhatt KD, Isakova A, Morri M, Ranganath T, Blish CA, Rogers AJ, Nadeau K, Yang S, Blomkalns A, O'Hara R, Neff NF, DeBoever C, Szalma S, Wheeler MT, Gates CM, Farh K, Schroth GP, Febbo P, deSouza F, Cornejo OE, Fernandez-Vina M, Kistler A, Palacios JA, Pinsky BA, Bustamante CD, Rivas MA, Ashley EA. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Nat Commun. 2022 08 30; 13(1):5107. PMID: 36042219; PMCID: PMC9426371.
    Citations:    Fields:    Translation:HumansCellsPHPublic Health
  4. Wertenbroek R, Rubinacci S, Xenarios I, Thoma Y, Delaneau O. XSI-a genotype compression tool for compressive genomics in large biobanks. Bioinformatics. 2022 08 02; 38(15):3778-3784. PMID: 35748697; PMCID: PMC9344850.
    Citations:    Fields:    
  5. Ribeiro DM, Rubinacci S, Ramisch A, Hofmeister RJ, Dermitzakis ET, Delaneau O. The molecular basis, genetic control and pleiotropic effects of local gene co-expression. Nat Commun. 2021 08 10; 12(1):4842. PMID: 34376650; PMCID: PMC8355184.
    Citations: 3     Fields:    Translation:HumansCells
  6. Rubinacci S, Ribeiro DM, Hofmeister RJ, Delaneau O. Publisher Correction: Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat Genet. 2021 Mar; 53(3):412. PMID: 33473199.
    Citations: 3     Fields:    
  7. Rubinacci S, Ribeiro DM, Hofmeister RJ, Delaneau O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat Genet. 2021 01; 53(1):120-126. PMID: 33414550.
    Citations: 44     Fields:    Translation:Humans
  8. Rubinacci S, Delaneau O, Marchini J. Genotype imputation using the Positional Burrows Wheeler Transform. PLoS Genet. 2020 11; 16(11):e1009049. PMID: 33196638; PMCID: PMC7704051.
    Citations: 28     Fields:    Translation:Humans
  9. Gorzynski JE, De Jong HN, Amar D, Hughes CR, Ioannidis A, Bierman R, Liu D, Tanigawa Y, Kistler A, Kamm J, Kim J, Cappello L, Neff NF, Rubinacci S, Delaneau O, Shoura MJ, Seo K, Kirillova A, Raja A, Sutton S, Huang C, Sahoo MK, Mallempati KC, Montero-Martin G, Osoegawa K, Jimenez-Morales D, Watson N, Hammond N, Joshi R, Fernandez-Vina M, Christle JW, Wheeler MT, Febbo P, Farh K, Schroth G, Desouza F, Palacios J, Salzman J, Pinsky BA, Rivas MA, Bustamante CD, Ashley EA, Parikh VN. High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs. medRxiv. 2020 Sep 01. PMID: 32766602; PMCID: PMC7402057.
    Citations:    
  10. Rubinacci S, Graudenzi A, Caravagna G, Mauri G, Osborne J, Pitt-Francis J, Antoniotti M. CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer. Cancer Inform. 2015; 14(Suppl 4):53-65. PMID: 26380549; PMCID: PMC4559197.
    Citations: 6     
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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.