Published Papers That Used O2, Orchestra, or Research Computing

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!

To cite O2 in your paper, please use text similar to the following, modified to reflect the work you used O2 for:

Portions of this research were conducted on the O2 High Performance Compute Cluster, supported by the Research Computing Group, at Harvard Medical School. See https://it.hms.harvard.edu/our-services/research-computing for more information.

If you received support from the Research Computing Consultant Group (RCCG) that contributed to your work, but is not substantial enough to warrant co-authorship, please use text similar to the following. You can optionally mention specific consultants:

We would like to thank the HMS Research Computing Consultant Group for their consulting services, which facilitated the computational analyses detailed in this paper.

Papers Citing Orchestra or O2

• 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

• Romero, J et al. Statistical efficiency of patient data in randomized clinical trials of epilepsy treatments. DOI: 10.1111/epi.16609

• Goldenholz, D et al. Development and Validation of Forecasting Next Reported Seizure Using e-Diaries.  ANN NEUROL 2020;00:1–8

• Oliveira, A et al. Comparing the efficacy, exposure, and cost of clinical trial analysis methods. DOI: 10.1111/epi.16384

• Romero, J et al. Natural variability in seizure frequency: Implications for trials and placebo. Epilepsy Research 162 (2020) 106306

• Letswaart,R et al. GeneWalk identifies relevant gene functions for a biological context using network representation learning. Genome Biology volume 22, Article number: 55 (2021) 

• Schoech, A. P. et al. Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection. Nature Communications 10, 790 (2019).

• AlQuraishi, M. End-to-End Differentiable Learning of Protein Structure. Cell Systems 8, 292-301.e3 (2019).

• Loh, P.-R., Kichaev, G., Gazal, S., Schoech, A. P. & Price, A. L. Mixed-model association for biobank-scale datasets. Nature Genetics 50, 906 (2018).

• 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

• Zhang, C.-H.; Gao, Y.; Jadhav, U.; Hung, H.-H.; Holton, K. M.; Grodzinsky, A. J.; Shivdasani, R. A.; Lassar, A. B. Creb5 Establishes the Competence for Prg4 Expression in Articular Cartilage. Communications Biology 2021, 4 (1), 332. https://doi.org/10.1038/s42003-021-01857-0

• Weber JA, Park SG, Luria V, Jeon S, Kim HM, Jeon Y, Bhak Y, Jun JH, Kim SW, Hong WH, Lee S, Cho YS, Karger A, Cain JW, Manica A, Kim S, Kim JH, Edwards JS, Bhak J, Church GM. Proc Natl Acad Sci U S A. 2020 Aug 4. The whale shark genome reveals how genomic and physiological properties scale with body size.

• Wang, H.; Sheehan, R. P.; Palmer, A. C.; Everley, R. A.; Boswell, S. A.; Ron-Harel, N.; Ringel, A. E.; Holton, K. M.; Jacobson, C. A.; Erickson, A. R.; Maliszewski, L.; Haigis, M. C.; Sorger, P. K. Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming. Cell Systems 2019, 8 (5), 412-426.e7. https://doi.org/10.1016/j.cels.2019.03.009

• 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.