This page is an incomplete list of published papers which harnessed the O2 cluster, the now-retired Orchestra cluster, and/or acknowledge members of the HMS RC group. We always encourage researchers to mention HMS RC staff and O2 in their acknowledgements as appropriate, or as co-authors for substantial contributions. We appreciate it if you could contact us about such papers, so we can list them below. For computational labs doing work on O2 (or previously on Orchestra), we're happy to link your publications page!
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- Bahdila, D et al. (2021) Emergency department visits for infectious oral conditions in Massachusetts, 2014 through 2018. DOI: 10.1016/j.adaj.2021.03.014
- Loh PR, Danecek P, Palamara PF, Fuchsberger C, Reshef YA, Finucane HK, Schoenherr S, Forer L, McCarthy S, Abecasis GR, Durbin R, Price AL. (2016) "Reference-based phasing using the Haplotype Reference Consortium panel", Nature Genetics 48, 1443.
- Virginia Savova, Jon Patsenker, Sébastien Vigneau and Alexander A. Gimelbrant. (2015) "dbMAE: the database of autosomal monoallelic expression", Nucleic Acids Research, 10.1093/nar/gkv1106
- Li Li and Jack W. Szostak, (2014) "The Free Energy Landscape of Pseudorotation in 3′–5′ and 2′–5′ Linked Nucleic Acids", JACS, 2014 Feb 5; 136 (7), pp 2858–2865
- Gilad D. Evrony, Xuyu Cai, Eunjung Lee, L. Benjamin Hills, Princess C. Elhosary, Hillel S. Lehmann, J.J. Parker, Kutay D. Atabay, Edward C. Gilmore, Annapurna Poduri, Peter J. Park, Christopher A. Walsh. (2012) "Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain", Cell, 151 (3): 483–496
- Deluca TF, Cui J, Jung JY, St Gabriel KC, Wall DP. (2012) "Roundup 2.0: Enabling comparative genomics for over 1800 genomes", Bioinformatics, 28 (5): 715-716
- M. Ernebjerg and R. Kishony, (2011) "Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking", American Society for Microbiology, 10.1128/AEM.06585-11
- Barstow, B., C. M. Agapakis, et al. (2011). "A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism." J Biol Eng 5: 7.
- M. Ernebjerg and R. Kishony, (2011) "Dynamic phenotypic clustering in noisy ecosystems", PLoS Computational Biology, 7(3) e1002017
- J.M. Higgins and L. Mahadevan, (2010) "Physiological and pathological population dynamics of circulating human red blood cells.", PNAS, 2010 Nov 23;107(47):20587-92
- Alan Le Goallec, Samuel Diai, Sasha Collin, Jean-Baptiste Prost, Théo Vincent & Chirag J. Patel, "Using deep learning to predict abdominal age from liver and pancreas magnetic resonance images", Nature Communications volume 13, Article number: 1979 (2022)
HMS RC staff as authors
Kim HM, Weber JA, Lee N, Park SG, Cho YS, Bhak Y, Lee N, Jeon Y, Jeon S, Luria V, Karger A, Kirschner MW, Jo YJ, Woo S, Shin K, Chung O, Ryu JC, Yim HS, Lee JH, Edwards JS, Manica A, Bhak J, Yum S. BMC Biol. 2019 Mar 29;17(1):28. The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.
- Hanschen ER, Marriage TN, Ferris PJ, Hamaji T, Toyoda A, Fujiyama A, Neme R, Noguchi H, Minakuchi Y, Suzuki M, Kawai-Toyooka H, Smith DR, Sparks H, Anderson J, Bakarić R, Luria V, Karger A, Kirschner MW, Durand PM, Michod RE, Nozaki H, Olson BJ. (2016). The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nature Communications 7, 11370
Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. (2015). Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350, 94–98.