Usage examples for all datasets listed in the Registry of Open Data on AWS.
Tools & Applications
Publications
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"Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data
Commons"
by Galen F. Gao, Joel S. Parker, et al.
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A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples by Han Chen, Chunyan Li, et al.
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An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome
Analytics
by Jianfang Liu, Tara Lichtenberg, et al.
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Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types
of Cancer
by Katherine A. Hoadley, Christina Yau, et al.
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Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas by Yang Liu, Nilay S. Sethi, et al.
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Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients by André Kahles, Kjong-Van Lehmann, et al.
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Comprehensive Characterization of Cancer Driver Genes and Mutations by Matthew H. Bailey, Collin Tokheim, et al.
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Genomic and Functional Approaches to Understanding Cancer Aneuploidy by Alison M. Taylor, Juliann Shih, et al.
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Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome
Atlas
by Theo A. Knijnenburg, Linghua Wang, et al.
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Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas by Joshua D. Campbell, Christina Yau, et al.
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Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types by Zhongqi Ge, Jake S. Leighton, et al.
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Machine Learning Detects Pan-Cancer Ras Pathway Activation in The Cancer Genome Atlas by Gregory P. Way, Francisco Sanchez-Vega, et al.
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Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
by Tathiane M. Malta, Artem Sokolov, et al.
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Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human
Cancers
by Xinxin Peng, Zhongyuan Chen, et al.
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Oncogenic Signaling Pathways in The Cancer Genome Atlas by Francisco Sanchez-Vega, Marco Mina, et al.
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Pan-Cancer Alterations of the MYC Oncogene and its Proximal Network Across The Cancer Genome
Atlas
by Franz X. Schaub, Varsha Dhankani, et al.
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Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each
Tumor Context
by Hua-Sheng Chiu, Sonal Somvanshi, et al.
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Pathogenic Germline Variants in 10,389 Adult Cancers by Kuan-lin Huang, R. Jay Mashl, et al.
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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic
Pipelines
by Kyle Ellrott, Matthew H. Bailey, et al.
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Spatial Organization And Molecular Correlation Of Tumor-Infiltrating Lymphocytes Using Deep
Learning On Pathology Images
by Joel Saltz, Rajarsi Gupta, et al.
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The chromatin accessibility landscape of primary human cancers by M. Ryan Corces, Jeffrey M. Granja, et al.
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The Immune Landscape of Cancer by Vésteinn Thorsson, David L. Gibbs, et al.
Tools & Applications
Publications
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A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms
tumor
by Gadd S, Huff V, Walz AL, et al.
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Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia by Yang JJ, Cheng C, Devidas M, et al.
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Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in osteosarcoma
by Nakka M, Allen-Rhoades W, Li Y, et al.
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CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AM by Maxson JE, Ries RE, Wang YC, et al.
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Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism by Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD,
Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, et al.
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Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and
Dysregulated Developmental Pathways
by Chun HJ, Lim EL, Heravi-Moussavi A, et al.
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Genomic classification and identification of the cell of origin of pediatric mixed phenotype
acute leukemia
by Thomas B. Alexander, Zhaohui Gu, Ilaria Iacobucci, et al.
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Genomics in childhood acute myeloid leukemia comes of age by Brunner AM, Graubert TA.
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Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups
reveal tumors with cytotoxic T cell infiltration
by Hye-Jung E. Chun, Pascal D. Johann, Katy Milne et al.
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MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid
Leukemia
by Lim EL, Trinh DL, Ries RE, et al.
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MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours
by Perlman EJ, Gadd S, Arold ST, et al.
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Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors
by Walz AL, Ooms A, Gadd S, et al.
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Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations by Eleveld TF, Oldridge DA, Bernard V, Koster J, et al.
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Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the
Children's Oncology Group
by Ooms AH, Gadd S, Gerhard DS, et al.
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TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney by Gooskens SL, Gadd S, Guidry Auvil JM, et al.
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The genetic landscape of high-risk neuroblastoma by Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K,
Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, et al.
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The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia
by Yu Liu, John Easton, Ying Shao, et al.
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The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural
alterations and age-specific mutational interactions
by Bolouri H, Farrar JE, Triche T Jr, et al.
Tutorials
Tools & Applications
Publications
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Asynchronous pipeline for processing huge corpora on medium to low resource infrastructures by Pedro Javier Ortiz Suárez, Benoît Sagot, Laurent Romary
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Building a Web-Scale Dependency-Parsed Corpus from CommonCrawl by Alexander Panchenko, Eugen Ruppert, Stefano Faralli, Simone Paolo Ponzetto, Chris Biemann
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C4Corpus: Multilingual Web-Size Corpus with Free License by Ivan Habernal, Omnia Zayed, Iryna Gurevych
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CC-News-En: A large English news corpus by Joel Mackenzie, Rodger Benham, Matthias Petri, Johanne R. Trippas, J. Shane Culpepper, Alistair Moffat
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CCAligned: A Massive collection of cross-lingual web-document pairs by Ahmed El-Kishky, Vishrav Chaudhary, Francisco Guzmán, Philipp Koehn
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Defending against neural fake news by Rowan Zellers, Ari Holtzman, Hannah Rashkin, Yonatan Bisk, Ali Farhadi, Franziska Roesner, et al
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Index fun by Philippe Suter
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Language models are few-shot learners by Tom B. Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared Kaplan, Prafulla Dhariwal, et al
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Large-scale analysis of style injection by relative path overwrite by Sajjad Arshad, Seyed Ali Mirheidari, Tobias Lauinger, Bruno Crispo, Engin Kirda, William Robertson
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Mapping languages: The Corpus of Global Language Use by Jonathan Dunn
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N-gram counts and language models from the Common Crawl by Christian Buck, Kenneth Heafield, Bas van Ooyen
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Of using Common Crawl to play Family Feud by Paul Masurel
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On the impact of publicly available news and information transfer to financial markets by Metod Jazbec, Barna Pásztor, Felix Faltings, Nino Antulov-Fantulin, Petter N. Kolm
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Using open data to predict market movements by DELL EMC
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Web Data Commons - RDFa, microdata, and microformat data sets by Christian Bizer, Robert Meusel, Anna Primpeli
Tutorials
Tools & Applications
Publications
Tools & Applications
Publications
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Clinically Relevant and Minimally Invasive Tumor Surveillance of Pediatric Diffuse Midline Gliomas Using Patient-Derived Liquid Biopsy by Eshini Panditharatna, Lindsay B Kilburn, et al.
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Decreased ACKR3 (CXCR7) function causes oculomotor synkinesis in mice and humans. by Mary C Whitman, Noriko Miyake, et al.
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Deleterious de novo variants of X-linked ZC4H2 in females cause a variable phenotype with neurogenic arthrogryposis multiplex congenita. by Suzanna G M Frints, Friederike Hennig, et al.
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Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers. by Fengqi Chang, Fumin Lin, et al.
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Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. by Allison H Seiden, Felix Richter, et al.
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Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect by Sherin Shaaban, Sarah MacKinnon et al.
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Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. by Madison R Bishop, Kimberly K Diaz Perez, et al.
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Genomic Analyses Implicate Noncoding De Novo Variants in Congenital Heart Disease. by Felix Richter, Sarah U Morton, et al.
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Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. by Laura Egolf, Zalman Vaksman, et al.
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Germline microsatellite genotypes differentiate children with medulloblastoma. by Samuel Rivero-Hinojosa, Nicholas Kinney, et al.
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MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance by William B Dobyns, Kimberly A Aldinger, et al.
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MAGEL2-Related Disorders: A study and case series. by Jameson Patak, James Gilfert, et al.
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Phenotype delineation of ZNF462 related syndrome. by Paul Kruszka, Tommy Hu, et al.
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The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. by Deanne M Taylor, Bruce J Aronow, et al.
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Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. by Nandita Mukhopadhyay, Madison Bishop, et al.
Tutorials
Tools & Applications
Publications
Tutorials
Tools & Applications
Publications
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chiVe 2.0: SudachiとNWJCを用いた実用的な日本語単語ベクトルの実現に向けて by 河村宗一郎, 久本空海, 真鍋陽俊, 髙岡一馬, 内田佳孝, 岡照晃, 浅原正幸
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chiVe: 製品利用可能な日本語単語ベクトル資源の実現へ向けて ~形態素解析器Sudachiと超大規模ウェブコーパスNWJCによる分散表現の獲得と改良~ by 久本空海, 山村崇, 勝田哲弘, 竹林佑斗, 髙岡一馬, 内田佳孝, 岡照晃, 浅原正幸
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Sudachi: a Japanese Tokenizer for Business by Kazuma Takaoka, Sorami Hisamoto, Noriko Kawahara, Miho Sakamoto, Yoshitaka Uchida, Yuji Matsumoto
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形態素解析器『Sudachi』のための大規模辞書開発 by 坂本美保, 川原典子, 久本空海, 髙岡一馬, 内田佳孝
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複数粒度の分割結果に基づく日本語単語分散表現 by 真鍋陽俊, 岡照晃, 海川祥毅, 髙岡一馬, 内田佳孝, 浅原正幸
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詳細化した同義関係をもつ同義語辞書の作成 by 高岡一馬, 岡部裕子, 川原典子, 坂本美保, 内田佳孝
Tutorials
Tools & Applications
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SARS-CoV-2 COVID Moonshot absolute free energy calculations by The Voelz lab at Temple University
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SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) dimer simulations: A 2.9 ms dataset of the SARS-CoV-2 main viral protease (apo, dimer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 2.6 ms equilibrium dataset of the SARS-CoV-2 main viral protease (apo, monomer) by The Chodera lab at MSKCC
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SARS-CoV-2 main viral protease (Mpro, 3CLPro, nsp5) monomer simulations: A 6.4 ms dataset of the SARS-CoV-2 main viral protease (apo, monomer) in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 nsp10 dataset: A 6.1 ms dataset of the SARS-CoV-2 nsp10 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 nsp3 macrodomain dataset: An 11 ms dataset of the SARS-CoV-2 nsp3 macrodomain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 nsp3 pl2pro domain dataset: An 731 µs dataset of the SARS-CoV-2 nsp3 pl2pro domain in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 nsp7 simulations: A 3.7 ms dataset of the SARS-CoV-2 nsp7 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 nsp8 simulations: A 1.8 ms dataset of the SARS-CoV-2 nsp8 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 nsp9 simulations: A 9 ms dataset of the SARS-CoV-2 nsp9 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 RNA polymerase (nsp12, RdRP) dataset: A 3.4 ms dataset of the SARS-CoV-2 nsp12 protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 spike protein dataset: A 1.2 ms dataset of the SARS-CoV-2 spike protein in search of cryptic pockets by The Bowman lab at Washington University in St. Louis
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SARS-CoV-2 spike RBD bound to human ACE2 receptor (173.8 us): Wild-type and mutant simulations by The Chodera lab at the Memorial Sloan Kettering Cancer Center
Publications
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SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome by Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, View ORCID ProfileRafal P. Wiewiora, Matthew F. D. Hurley, Aoife M Harbison, Carl A Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman
Tools & Applications
Publications
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A structural variation reference for medical and population genetics. Nature 581, 444–451 (2020) by Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., Watts, N. A., Solomonson, M., O’Donnell-Luria, A., Baumann, A., Munshi, R., Walker, M., Whelan, C., Huang, Y., Brookings, T., ... Talkowski, M. E.
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Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016) by Lek, M., Karczewski, K., Minikel, E. et al.
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Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals. Nature Communications 11, 2523 (2020) by Whiffin, N., Karczewski, K. J., Zhang, X., Chothani, S., Smith, M. J., Gareth Evans, D., Roberts, A. M., Quaife, N. M., Schafer, S., Rackham, O., Alföldi, J., O’Donnell-Luria, A. H., Francioli, L. C., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, Cook, S. A., Barton, P. J. R., MacArthur, D. G., & Ware, J. S.
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Evaluating potential drug targets through human loss-of-function genetic variation. Nature 581, 459–464 (2020) by Minikel, E. V., Karczewski, K. J., Martin, H. C., Cummings, B. B., Whiffin, N., Rhodes, D., Alföldi, J., Trembath, R. C., van Heel, D. A., Daly, M. J., Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Schreiber, S. L., & MacArthur, D. G.
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gnomAD v2.1 by Laurent Francioli, Grace Tiao, Konrad Karczewski, Matthew Solomonson, Nick Watts
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gnomAD v3.0 by Laurent Francioli, Daniel MacArthur
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Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. Nature Communications 11, 2539 (2020) by Wang, Q., Pierce-Hoffman, E., Cummings, B. B., Karczewski, K. J., Alföldi, J., Francioli, L. C., Gauthier, L. D., Hill, A. J., O’Donnell-Luria, A. H., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, & MacArthur, D. G.
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Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-∆32 and other variants in gnomAD. bioRxiv (p. 784157) by Karczewski, K. J., Gauthier, L. D., Daly, M. J.
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The effect of LRRK2 loss-of-function variants in humans. Nature Medicine (2020) by Whiffin, N., Armean, I. M., Kleinman, A., Marshall, J. L., Minikel, E. V., Goodrich, J. K., Quaife, N. M., Cole, J. B., Wang, Q., Karczewski, K. J., Cummings, B. B., Francioli, L., Laricchia, K., Guan, A., Alipanahi, B., Morrison, P., Baptista, M. A. S., Merchant, K. M., Genome Aggregation Database Production Team, ... MacArthur, D. G.
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The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020) by Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., Gauthier, L. D., Brand, H., Solomonson, M., Watts, N. A., Rhodes, D., Singer-Berk, M., England, E. M., Seaby, E. G., Kosmicki, J. A., ... MacArthur, D. G.
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Transcript expression-aware annotation improves rare variant interpretation. Nature 581, 452–458 (2020) by Cummings, B. B., Karczewski, K. J., Kosmicki, J. A., Seaby, E. G., Watts, N. A., Singer-Berk, M., Mudge, J. M., Karjalainen, J., Kyle Satterstrom, F., O’Donnell-Luria, A., Poterba, T., Seed, C., Solomonson, M., Alföldi, J., The Genome Aggregation Database Production Team, The Genome Aggregation Database Consortium, Daly, M. J., & MacArthur, D. G.
Tutorials
Tools & Applications
Publications
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Declines in an abundant aquatic insect, the burrowing mayfly, across major North American waterways by Phillip M. Stepanian, Sally A. Entrekin, Charlotte E. Wainwright, Djordje Mirkovic, Jennifer L. Tank, & Jeffrey F. Kelly
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Extreme Pyroconvective Updrafts During a Megafire by B. Rodriguez, N. P. Lareau, D. E. Kingsmill, & C. B. Clements
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Level 2 Interface Control Document for Message Data Formats: Build 18 by NOAA ROC
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Level 2 Interface Control Document for Transfer: Build 18 by NOAA ROC
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Level 3 Interface Control Document for Message Data Formats: Build 18 by NOAA ROC
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Seasonal abundance and survival of North America’s migratory avifauna determined by weather radar by Adriaan M. Dokter, Andrew Farnsworth, Daniel Fink, Viviana Ruiz-Gutierrez, Wesley M. Hochachka, Frank A. La Sorte, Orin J. Robinson, Kenneth V. Rosenberg & Steve Kelling
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Unlocking the Potential of NEXRAD Data through NOAA’s Big Data Partnership by Steve Ansari and Stephen Del Greco
Tutorials
Tools & Applications
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AICS Volume Viewer by Dan Toloudis
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AICSImageIO by Matthew Bowden, Jackson Brown, Jamie Sherman, Dan Toloudis
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Allen Cell Feature Explorer by Allen Institute for Cell Science
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Allen Cell Structure Segmenter by Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski
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Integrated Mitotic Stem Cell by Allen Institute for Cell Science
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Pytorch 3D Integrated Cell by Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar
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Visual Guide to Human Cells by Allen Institute for Cell Science
Publications
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Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy by Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman & Gregory R. Johnson
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Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable? by Matheus P. Viana, Jianxu Chen*, Theo A. Knijnenburg*, Ritvik Vasan*, Calysta Yan*... Allen Institute for Cell Science... Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski
Tutorials
Tools & Applications
Publications
Tutorials
Tools & Applications
Publications
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Accelerating the Evolution of Nonhuman Primate Neuroimaging by M.P. Milham, C. Petkov
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An Open Resource for Non-human Primate Imaging by M.P. Milham, L. Ai, ..., C.E. Schroeder
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An open resource for transdiagnostic research in pediatric mental health and learning disorders by L.M. Alexander, J. Escalera, ..., M.P. Milham
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Assessment of the impact of shared brain imaging data on the scientific literature by M.P. Milham, R.C. Craddock, ..., A. Klein
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Enhancing studies of the connectome in autism using the autism brain imaging data exchange II. by A. Di Martino, D. O'Connor, M.P. Milham
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Making data sharing work: The FCP/INDI experience by M. Mennes, B.B. Biswal, F.X. Castellanos, M.P. Milham
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The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. by A. Di Martino, C-G Yan, ..., M.P. Milham
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The Healthy Brain Network Serial Scanning Initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions by D. O'Connor, N.V. Potler, ..., M.P. Milham
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The NKI-Rockland sample: a model for accelerating the pace of discovery science in psychiatry by K.B. Nooner, S.J. Colcombe, ..., M.P. Milham
Tools & Applications
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Tutorials
Tools & Applications
Tutorials
Tools & Applications
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Tutorials
Tools & Applications
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Tools & Applications
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Tools & Applications
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Tools & Applications
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Tutorials
Tools & Applications
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Tutorials
Tools & Applications
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Tools & Applications
Publications
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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer by Hui Zhang, Tao Liu, Zhen Zhang, Samuel H. Payne, Bai Zhang, Jason E. McDermott, Jian-Ying
Zhou, Vladislav A. Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing
Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko,
Therese R. Clauss, Caitlin Choi, Matthew E. Monroe, Stefani Thomas, Song Nie, Chaochao Wu,
Ronald J. Moore, Kun-Hsing Yu, David L. Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry
Rodriguez, Emily S. Boja, Tara Hiltke, Robert C. Rivers, Lori Sokoll, Heng Zhu, Ie-Ming
Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P. Snyder, Douglas A. Levine,
Richard D. Smith, Daniel W. Chan, Karin D. Rodland, the CPTAC Investigators
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Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities by Suhas Vasaikar, Chen Huang, Xiaojing Wang. Vladislav A. Petyuk, Sara R. Savage, Bo Wen,
Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman,
Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting
Wang, Matthew C. Chambers, Robbert J.C. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew
Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith,
Karin D. Rodland, Daniel C. Liebler, Tao Liu, Bing Zhang, Clinical Proteomic Tumor Analysis
Consortium
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Proteomic analysis of colon and rectal carcinoma using standard and customized databases
by Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC
Tutorials
Tools & Applications
Publications
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A GAL4-Driver Line Resource for Drosophila Neurobiology by Jenett, A., Rubin, G. M., Ngo, T., Shepherd, D., Murphy, C., Dionne, H., Pfeiffer, B. D., Cavallaro, A., Hall, D., Jeter, J., Iyer, N., Fetter, D., Hausenfluck, J. H., Peng, H., Trautman, E. T., Svirskas, R. R., Myers, E. W., Iwinski, Z. R., Aso, Y., DePasquale, G. M., Enos, A., Hulamm, P., Lam, S. C. B., Li, H., Laverty, T. R., Long, F., Qu, L., Murphy, S. D., Rokicki, K., Safford, T., Shaw, K., Simpson, J. H., Sowell, A., Tae, S., Yu, Y., & Zugates, C. T.
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An unbiased template of the Drosophila brain and ventral nerve cord by Bogovic, J.A., Otsuna, H., Heinrich, L., Ito, M., Jeter, J., Meissner, G., Nern, A., Colonell, J., Malkesman, O., Ito, K., & Saalfeld, S.
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Color depth MIP mask search: a new tool to expedite Split-GAL4 creation by Otsuna, H., Ito, M., & Kawase, T.
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The neuronal architecture of the mushroom body provides a logic for associative learning by Aso, Y., Hattori, D., Yu, Y., Johnston, R. M., Iyer, N. A., Ngo, T., Dionne, H., Abbott, L., Axel, R., Tanimoto, H., & Rubin, G. M.
Tutorials
Tools & Applications
Publications
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Overview and Meteorological Validation of the Wind Integration National Dataset Toolkit by Caroline Draxl, Bri-Mathias Hodge, Andrew Clifton, Jim McCaa
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Power from wind: Open data on AWS by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer
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The Wind Integration National Dataset (WIND) Toolkit by Caroline Draxl, Andrew Clifton, Bri-Mathias Hodge, Jim McCaa
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Validation of Power Output for the WIND Toolkit by J. King, Andrew Clifton, Bri-Mathias Hodge
Tools & Applications
Publications
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Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics by Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H
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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B,
Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L1, Krek A, Li Y, Rykunov D, Li QK, Chen
LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong
A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W,
Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li
K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh
JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR,
Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B,
Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang
P, Zhang H; Clinical Proteomic Tumor Analysis Consortium
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Tutorials
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Publications
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A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data by J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns
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From cosmos to connectomes: The evolution of data-intensive science by R. Burns, J. T. Vogelstein, and A. S. Szalay
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The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience by R. Burns, W. G. Roncal, D. Kleissas, K. Lillaney, P. Manavalan, E. Perlman, D. R. Berger, D. D. Bock, K. Chung, L. Grosenick, N. Kasthuri, N. C. Weiler, K. Deisseroth, M. Kazhdan, J. Lichtman, R. C. Reid, S. J. Smith, A. S. Szalay, J. T. Vogelstein, and R. J. Vogelstein.
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To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery by J. T. Vogelstein, B. Mensh, M. Häusser, N. Spruston, A. C. Evans, K. Kording, K. Amunts, C. Ebell, J. Muller, M. Telefont, S. Hill, S. P. Koushika, C. Calì, P. A. Valdés-Sosa, P. B. Littlewood, C. Koch, S. Saalfeld, A. Kepecs, H. Peng, Y. O. Halchenko, G. Kiar, M. M. Poo, J. B. Poline, M. P. Milham, A. P. Schaffer, R. Gidron, H. Okano, V. D. Calhoun, M. Chun, D. M. Kleissas, R. J. Vogelstein, E. Perlman, R. Burns, R. Huganir, and M. I. Miller
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"Identification of Initiating Trunk Mutations and Distinct Molecular Subtypes: An Interim
Analysis of the Mmrf Commpass Study"
by Jonathan J Keats, PhD, Gil Speyer, Legendre Christophe, Christofferson Austin, Kristi
Stephenson, BS, Ahmet Kurdoglu, Megan Russell, Aldrich Jessica, Cuyugan Lori, Jonathan
Adkins, Jackie McDonald, Adrienne Helland, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar
Jagannath, MD, David Siegel, MD PhD, Ravi Vij, MD MBA, Gregory Orloff, MD, Todd Zimmerman,
MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD PhD, Robert M.
Rifkin, Norma C Gutierrez, The MMRF CoMMpass Network, Jen Toups, Mary Derome, MS, Winnie
Liang, PhD, Seunchan Kim, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John
David Carpten, PhD, Sagar Lonial, MD
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"Interim Analysis Of The MMRF CoMMpass Trial: a Longitudinal Study In Multiple Myeloma
Relating Clinical Outcomes To Genomic and Immunophenotypic Profiles"
by Keats JJ, Craig DW, Liang W, Venkata Y, Kurdoglu A, Aldrich J, Auclair D, Allen K, Harrison
B, Jewell S, Kidd PG, Correll M, Jagannath S, Siegel DS, Vij R, Orloff G, Zimmerman TM, MMRF
CoMMpass Network, Capone W, Carpten J, Lonial S.
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"Interim Analysis of the Mmrf Commpass Trial: Identification of Novel Rearrangements
Potentially Associated with Disease Initiation and Progression"
by Sagar Lonial, MD, Venkata D Yellapantula, Winnie Liang, PhD, Ahmet Kurdoglu, BS, Jessica
Aldrich, MSc, Christophe M. Legendre, MD, Kristi Stephenson, Jonathan Adkins, Jackie
McDonald, Adrienne Helland, Megan Russell, Austin Christofferson, Lori Cuyugan, Dan Rohrer,
Alex Blanski, Meghan Hodges, Mmrf CoMMpass Network, Mary Derome, Daniel Auclair, PhD, Pamela
G. Kidd, MD, Scott Jewell, PhD, David Craig, PhD, John Carpten, PhD, Jonathan J. Keats, PhD
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"Molecular Predictors of Outcome and Drug Response in Multiple Myeloma: An Interim Analysis
of the Mmrf CoMMpass Study"
by Jonathan J Keats, PhD, Gil Speyer, Austin Christofferson, Christophe Legendre, PhD, Jessica
Aldrich, Megan Russell, Lori Cuyugan, Jonathan Adkins, Alex Blanski, Meghan Hodges, Dan
Rohrer, Sundar Jagannath, MD, Ravi Vij, MD, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben
Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD, Robert M Rifkin, Norma C
Gutierrez, MD PhD, Mmrf CoMMpass Network, Jennifer Yesil, MS, Mary Derome, MS, Seungchan
Kim, PhD, Winnie Liang, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD,
Daniel Auclair, PhD, Sagar Lonial, MD FACP
Tools & Applications
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Tutorials
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Tools & Applications
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HSDS Examples by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer, Michael Rossol
Publications
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Publications
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On the Use of Coupled Wind, Wave, and Current Fields in the Simulation of Loads on BottomSupported Offshore Wind Turbines during Hurricanes by E. Kim, L. Manuel, M. Curcic, S. S. Chen, C. Phillips, P. Veers
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The Distributed Generation Market Demand Model (dGen):Documentation by B. Sigrin, M. Gleason, R. Preus, I. Baring-Gould, R. Margolis
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Tracking the Sun Pricing and Design Trends for Distributed Photovoltaic Systems in the United States: 2019 Edition by G. Barbose, N. Darghouth
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Tools & Applications
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BLAST+: Architecture and Applications by Christiam Camacho 1 , George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden
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Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs by S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman
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A multiprotein supercomplex controlling oncogenic signalling in lymphoma by Phelan JD, Young RM, Webster DE, Roulland S, Wright GW, Kasbekar M, Shaffer AL 3rd,
Ceribelli M, Wang JQ, Schmitz R, Nakagawa M, Bachy E, Huang DW, Ji Y, Chen L, Yang Y, Zhao
H, Yu X, Xu W, Palisoc MM, Valadez RR, Davies-Hill T, Wilson WH, Chan WC, Jaffe ES, Gascoyne
RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Rodriguez FJ, Estephan F, Holdhoff M,
Kruhlak MJ, Hewitt SM, Thomas CJ, Pittaluga S, Oellerich T, Staudt LM
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Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., Calvin A. Johnson,
Ph.D., James D. Phelan, Ph.D., James Q. Wang, Ph.D., Sandrine Roulland, Ph.D., Monica
Kasbekar, Ph.D., Ryan M. Young, Ph.D., Arthur L. Shaffer, Ph.D., Daniel J. Hodson, M.D.,
Ph.D., Wenming Xiao, Ph.D., et al.
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High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer
Pathogenesis
by Ryan J. Hartmaier, Lee A. Albacker, Juliann Chmielecki, Mark Bailey, Jie He, Michael E.
Goldberg, Shakti Ramkissoon, James Suh, Julia A. Elvin, Samuel Chiacchia, Garrett M.
Frampton, Jeffrey S. Ross, Vincent Miller, Philip J. Stephens and Doron Lipson
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Targeted next-generation sequencing of advanced prostate cancer identifies potential
therapeutic targets and disease heterogeneity.
by Beltran H, Yelensky R, Frampton GM, Park K, Downing SR, MacDonald TY, Jarosz M, Lipson D,
Tagawa ST, Nanus DM, Stephens PJ, Mosquera JM, Cronin MT, Rubin MA
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Tutorials
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Tutorials
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HSDS Examples by Caleb Phillips, Caroline Draxl, John Readey, Jordan Perr-Sauer, Michael Rossol
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NSRDB Viewer by Manajit Sengupta, Yu Xe, Anthony Lopez, Aron Habte, Galen Maclaurin, James Shelby, Paul Edwards
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New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract by Ranjit Kumar, Jayleen Grams, Daniel I. Chu, David K.Crossman, Richard Stahl, Peter Eipers, et al
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Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, et al.
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The Human Microbiome Project by Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon
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The World Ocean Database Introduction by Tim P. Boyer, Olga K. Baranova, Carla Coleman, Hernan E. Garcia, Alexandra Grodsky, Ricardo A. Locarnini, Alexey V. Mishonov, Christopher R. Paver, James R. Reagan, Dan Seidov, Igor V. Smolyar, Katharine W. Weathers, Melissa M. Zweng
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The World Ocean Database User's Manual by Hernan E. Garcia, Tim P. Boyer, Ricardo A. Locarnini, Olga K. Baranova, Melissa M. Zweng
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Benchmarking in Manipulation Research: Using the Yale-CMU-Berkeley Object and Model Set by Berk Calli, Aaron Walsman, Arjun Singh, Siddhartha Srinivasa, Pieter Abbeel, Aaron M Dollar
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Label Fusion: A Pipeline for Generating Ground Truth Labels for Real RGBD Data of Cluttered Scenes by Pat Marion, Peter R. Florence, Lucas Manuelli, Russ Tedrake
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Pre-touch sensing for sequential manipulation by Boling Yang, Patrick Lancaster, Joshua R. Smith
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The Closure Signature: A Functional Approach to Model Underactuated Compliant Robotic Hands by Maria Pozzi, Gionata Salvietti, João Bimbo, Monica Malvezzi, Domenico Prattichizzo
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DAS and DTS at Brady Hot Springs: Observations about Coupling and Coupled Interpretations by Douglas E. Miller, Thomas Coleman, Xiangfang Zeng, Jeremy R. Patterson , Elena C. Reinnisch, Michael A. Cardiff, Herbert F. Wang, Dante Fratta, Whitney Trainor-Guitton, Clifford H. Thurber, Michelle ROBERTSON, Kurt FEIGL, and The PoroTomo Team
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Ground motion response to an ML 4.3 earthquake using co-located distributed acoustic sensing and seismometer arrays by Herbert F Wang, Xiangfang Zeng, Douglas E Miller, Dante Fratta, Kurt L Feigl, Clifford H Thurber, Robert J Mellors
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Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. by David P. Hoffman1, Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, H. Amalia Pasolli, Nirmala Iyer, John A. Bogovic, Daniel R. Stabley, Abbas Shirinifard, Song Pang, David Peale, Kathy Schaefer, Wim Pomp, Chi-Lun Chang, Jennifer Lippincott-Schwartz, Tom Kirchhausen1, David J. Solecki, Eric Betzig, Harald F. Hess.
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Enhanced FIB-SEM systems for large-volume 3D imaging by C. Shan Xu, Kenneth J. Hayworth, Zhiyuan Lu, Patricia Grob, Ahmed M. Hassan, José G. García-Cerdán, Krishna K. Niyogi, Eva Nogales, Richard J. Weinberg, Harald F. Hess.
Tutorials
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If you want to add a dataset or usage example to this registry, please follow the instructions on the Registry of Open Data on AWS GitHub repository.
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