The Human Sleep Project

Tools & Applications

• The Human Sleep Project by Westover MB, Moura Junior V, Thomas R, Cash S, Nasiri S, Sun H, et al.
  

Publications

• A cost-effectiveness analysis of nasal surgery to increase CPAP compliance in sleep apnea patients with nasal obstruction. The Laryngoscope. 2017 Apr;127(4):977-983. PMCID: PMC5483184. by Kempfle J, Westover MB, Bianchi MT.
  
• A Systematic Review and Meta-Analysis Examining the Impact of Sleep Disturbance on Postoperative Delirium. Critical Care Medicine. 2018 Dec;46(12):e1204-e1212. PMCID: PMC6274586. by Fadayomi AB, Ibala R, Bilotta F, Westover MB, Akeju O.
  
• Age estimation from sleep studies using deep learning predicts life expectancy. NPJ Digit Med. 2022 Jul 22;5(1):103. doi: 10.1038/s41746-022-00630-9. PMCID: PMC9307657. by Brink-Kjaer A, Leary EB, Sun H, Westover MB, Stone KL, Peppard PE, et al.
  
• Algorithm for automatic detection of self-similarity and prediction of residual central respiratory events during continuous positive airway pressure. Sleep. 2021 Apr 9;44(4):zsaa215. doi: 10.1093/sleep/zsaa215. PMCID: PMC8631077. by Oppersma E, Ganglberger W, Sun H, Thomas RJ*, Westover MB*
  
• Alternative remedies for insomnia: a proposed method for personalized therapeutic trials. Nature and Science of Sleep. 2017;9:97-108. PMCID: PMC5364017. by Romero K, Goparaju B, Russo K, Westover MB, Bianchi MT.
  
• Applications of a Capacitor-Based Respiratory Position Sensing Device: Implications for Radiation Therapy. Austin Journal of Medical Oncology 2014;1(2). PMCID: PMC6956860. by Weng Y, Westover MB, Speier C, Sharp G, Bianchi MT, Westover KD.
  
• Artificial Intelligence in Sleep Medicine: An American Academy of Sleep Medicine Position Statement. Journal of Clinical Sleep Medicine. 2020 Feb 5. doi: 10.5664/jcsm.8288. PMCID: PMC7161449. by Goldstein CA, Berry RB, Kent DT, Kristo DA, Seixas AA, Redline S, et al.
  
• Artificial intelligence in sleep medicine: Background and implications for clinicians. Journal of Clinical Sleep Medicine. 2020 Feb 17. doi: 10.5664/jcsm.8388. PMCID: PMC7161463. by Goldstein CA, Berry RB, Kent DT, Kristo DA, Seixas AA, Redline S, et al.
  
• Automated Scoring of Respiratory Events in Sleep with a Single Effort Belt and Deep Neural Networks. IEEE Transactions on Biomedical Engineering. 2021 Dec 20;PP. doi: 10.1109/TBME.2021.3136753. Epub ahead of print. PMCID: PMC9119908. by Nassi TE, Ganglberger W, Sun H, Bucklin AA, Biswal S, van Putten MJAM, et al.
  
• Automated Sleep Apnea Quantification Based on Respiratory Movement. International Journal of Medical Sciences 2014; 11(8):796-802. PMCID: PMC4057486. by Bianchi MT, Lipoma T, Darling C, Alameddine Y, Westover MB.
  
• Brain Age from the Electroencephalogram of Sleep. Neurobiol Aging. 2019 Feb;74:112-120. PMCID: PMC6478501. by Sun H, Paixao L, Oliva JT, Goparaju B, Carvalho DZ, van Leeuwen KG, et al.
  
• Classification algorithms for predicting sleepiness and sleep apnea severity. Journal of Sleep Research. 2012 Feb;21(1):101-12. PMCID: PMC3698244. by Eiseman NA, Westover MB, Mietus JE, Thomas RJ, Bianchi MT
  
• Computational Evidence for a Competitive Thalamocortical Model of Spikes and Spindle Activity in Rolandic Epilepsy. Front Comput Neurosci. 2021 Jun 18;15:680549. doi: 10.3389/fncom.2021.680549. PMCID: PMC8249809. by Li Q, Westover MB, Zhang R, Chu CJ.
  
• Data-Driven Modeling of Sleep States from EEG. Proceedings of the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'12). 2012;2012:5090-3. PMCID: PMC6788787. by Van Esbroeck A, Westover MB
  
• Decision modeling in sleep apnea: the critical roles of pre-test probability, cost of untreated OSA, and time horizon. Journal of Clinical Sleep Medicine. 2016 Mar;12(3):409-418. PMCID: PMC4773629. by Moro M, Westover MB, Kelly J, Bianchi MT.
  
• Dementia Detection from Brain Activity During Sleep. Sleep. Nov 30:zsac286. doi: 10.1093/sleep/zsac286. Epub ahead of print. PMID: 36448766.* by Ye E*, Sun H*, Krishnamurthy PV, Adra N, Ganglberger W, Thomas RJ, et al.
  
• Effects of cholinergic neuromodulation on thalamocortical rhythms during NREM sleep: a model study. Frontiers in Computational Neuroscience. 2020 Jan 23;13:100. doi: 10.3389/fncom.2019.00100. eCollection 2019. PMCID: PMC6990259. by Li Q, Song JL, Li SH, Westover MB, Zhang R.
  
• Emergence of stable functional networks in long-term human EEG. The Journal of Neuroscience, Feb 2012; 32(8): 2703-2713. PMCID: PMC3361717. by Chu-Shore C, Kramer MA, Pathmanathan J, Bianchi MT, Westover MB, Wizon L, et al.
  
• Excess Brain Age Reflected in the Electroencephalogram of Sleep Predicts Reduced Life Expectancy. Neurobiology of Aging. 2019 Dec 23. pii: S0197-4580(19)30443-9. doi: 10.1016/j.neurobiolaging.2019.12.015. PMCID: PMC7085452. by Paixao L, Sikka P, Sun H, Jain A, Hogan J, Thomas RJ, et al.
  
• Expert-level automated sleep staging of long-term scalp EEG recordings using deep learning. SLEEP. June 2020;zsaa112. doi:10.1093/sleep/zsaa112. PMCID: PMC7686563. by Jaoude MA, Sun H, Pellerin KR, Pavlova M, Sarkis RA, Cash SS, et al.
  
• Expert-level Sleep Scoring with Deep Neural Networks. Journal of the American Medical Informatics Association (JAMIA). 2018 Dec 1;25(12):1643-1650. PMCID: PMC6289549. by Biswal S, Kulas J, Sun H, Goparaju B, Westover MB*, Bianchi MT*, et al.
  
• Focal sleep spindle deficits reveal focal thalamocortical dysfunction and predict cognitive deficits in childhood epilepsy with centrotemporal spikes. Journal of Neuroscience. 2021 Jan 14:JN-RM-2009-20. doi: 10.1523/JNEUROSCI.2009-20.2020. Epub ahead of print. PMCID: PMC8115887. by Kramer M, Stoyell S, Chinappen D, Ostrowski L, Spencer E, Morgan A, et al.
  
• High prevalence of sleep-disordered breathing in the intensive care unit - a cross-sectional study. Sleep Breath. 2022 Aug 16. doi: 10.1007/s11325-022-02698-9. Epub ahead of print. PMID: 35971023. by Bucklin AA, Ganglberger W, Quadri SA, Tesh RA, Adra N, Da Silva Cardoso M, et al.
  
• HIV Increases Sleep-based Brain Age Despite Antiretroviral Therapy. SLEEP. 2021 Mar 30:zsab058. doi: 10.1093/sleep/zsab058. Epub ahead of print. PMCID: PMC8361332. by Leone MJ*, Sun H*, Boutros CL, Liu L, Ye E, Sullivan L, et al.
  
• How Machine Learning is Powering Neuroimaging to Improve Brain Health. Neuroinformatics. 2022 Mar 28:10.1007/s12021-022-09572-9. doi: 10.1007/s12021-022-09572-9. Epub ahead of print. PMID: 35347570; PMCID: PMC9515245. by Singh NM, Harrod JB, Subramanian S, Robinson M, Chang K, Cetin-Karayumak S, et al.
  
• Insomnia and morning motor vehicle accidents: A decision analysis of the risk of hypnotics versus the risk of untreated insomnia. Journal of Clinical Psychopharmacology. 2014 Jun;34(3):400-402. PMCID: PMC6794095. by Bianchi MT, Westover MB.
  
• Large-Scale Automated Sleep Staging. Sleep. 2017 Oct 1;40(10). doi: 10.1093/sleep/zsx139. PMCID: PMC6251659. by Sun H, Jian J, Goparaju B, Huang GB, Sourina O, Bianchi MT, et al.
  
• Night-to-Night Variability of Sleep Electroencephalography-Based Brain Age Measurements. Clinical Neurophysiology. 2020 Oct 29;132(1):1-12. doi: 10.1016/j.clinph.2020.09.029. Epub ahead of print. PMCID: PMC7855943. by Hogan J, Sun H, Thomas RT, Westover MB.
  
• Optimal Spindle Detection Parameters for Predicting Cognitive Performance. Sleep. 2022 Jan 4:zsac001. doi: 10.1093/sleep/zsac001. Epub ahead of print. PMCID: PMC8996023. by Adra N, Sun H, Ganglberger W, Ye EM, Dümmer LW, Tesh RA, et al.
  
• Power Law versus Exponential State Transition Dynamics: Application to Sleep-Wake Architecture. PLoSONE 5(12): e14204. Dec. 2, 2010. PMCID: PMC2996311. by Chu-Shore J, Westover MB, Bianchi MT
  
• Sleep Apnea and Respiratory Anomaly Detection from a Wearable Band and Oxygen Saturation. Sleep and Breathing. 2021 Aug 18. doi: 10.1007/s11325-021-02465-2. Online ahead of print. PMCID: PMC8854446. by Ganglberger W, Bucklin AA, Tesh R, Cardoso MDS, Sun H, Leone M, , et al.
  
• Sleep EEG-based Brain Age Index is a Biomarker for Dementia. JAMA Network Open. 2020 Sep 1;3(9):e2017357. doi: 10.1001/jamanetworkopen.2020.17357. PMID: 32986106; PMCID: PMC7522697. by Ye E, Sun H, Leone MJ, Paixao L, Thomas RJ, Lam AD, et al.
  
• Sleep Staging from Electrocardiography and Respiration with Deep Learning. SLEEP. Sleep. 2020 Jul 13;43(7):zsz306. doi: 10.1093/sleep/zsz306. PMCID: PMC7355395. by Sun H, Ganglberger W, Panneerselvam E, Leone MJ, Quadri SA, Goparaju B, et al.
  
• The Challenge of Undiagnosed Sleep Apnea in Low-Risk Populations: A Decision Analysis. Military Medicine 2014 Aug;179(8S):47-54. PMCID: PMC6788752. by Bianchi MT, Hershman S, Bahadoran M, Ferguson M, Westover MB.
  
• The Impact of Body Posture and Sleep Stages on Sleep Apnea Severity in Adults. Journal of Clinical Sleep Medicine. 2012 Dec 15;8(6):655-66A. PMCID: PMC3501662. by Eiseman NA, Westover MB, Ellenbogen JM, Bianchi MT
  
• The sleep and wake electroencephalogram over the lifespan. Neurobiol Aging. 2023 Jan 19;124:60-70. doi: 10.1016/j.neurobiolaging.2023.01.006. Epub ahead of print. PMID: 36739622. by Sun H, Ye E, Paixao L, Ganglberger W, Chu CJ, Zhang C, et al.
  

The Cancer Genome Atlas

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TCGA Cancers Selected for Study by National Cancer Institute
  
• Using TCGA Data, Resources, and Materials by National Cancer Institute
  

Publications

• "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.
  
• A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples by Han Chen, Chunyan Li, et al.
  
• An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics by Jianfang Liu, Tara Lichtenberg, et al.
  
• 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.
  
• Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas by Yang Liu, Nilay S. Sethi, et al.
  
• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients by André Kahles, Kjong-Van Lehmann, et al.
  
• Comprehensive Characterization of Cancer Driver Genes and Mutations by Matthew H. Bailey, Collin Tokheim, et al.
  
• Genomic and Functional Approaches to Understanding Cancer Aneuploidy by Alison M. Taylor, Juliann Shih, et al.
  
• Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas by Theo A. Knijnenburg, Linghua Wang, et al.
  
• Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas by Joshua D. Campbell, Christina Yau, et al.
  
• Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types by Zhongqi Ge, Jake S. Leighton, et al.
  
• Machine Learning Detects Pan-Cancer Ras Pathway Activation in The Cancer Genome Atlas by Gregory P. Way, Francisco Sanchez-Vega, et al.
  
• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation by Tathiane M. Malta, Artem Sokolov, et al.
  
• Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers by Xinxin Peng, Zhongyuan Chen, et al.
  
• Oncogenic Signaling Pathways in The Cancer Genome Atlas by Francisco Sanchez-Vega, Marco Mina, et al.
  
• Pan-Cancer Alterations of the MYC Oncogene and its Proximal Network Across The Cancer Genome Atlas by Franz X. Schaub, Varsha Dhankani, et al.
  
• Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context by Hua-Sheng Chiu, Sonal Somvanshi, et al.
  
• Pathogenic Germline Variants in 10,389 Adult Cancers by Kuan-lin Huang, R. Jay Mashl, et al.
  
• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines by Kyle Ellrott, Matthew H. Bailey, et al.
  
• Spatial Organization And Molecular Correlation Of Tumor-Infiltrating Lymphocytes Using Deep Learning On Pathology Images by Joel Saltz, Rajarsi Gupta, et al.
  
• The chromatin accessibility landscape of primary human cancers by M. Ryan Corces, Jeffrey M. Granja, et al.
  
• The Immune Landscape of Cancer by Vésteinn Thorsson, David L. Gibbs, et al.
  

Foldingathome COVID-19 Datasets

Tutorials

• Folding@home COVID-19 efforts by Folding@home Consortium
  

Tools & Applications

• SARS-CoV-2 spike RBD with N501Y mutation bound to human ACE2 (953.7 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 COVID Moonshot absolute free energy calculations by The Voelz lab at Temple University
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• SARS-CoV-2 spike RBD (with glycosylation) (1.8 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD (without glycosylation) (1.9 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• 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
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S2H97 (623.7 us) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD bound to monoclonal antibody S309 (1.1 ms) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337A mutation bound to monoclonal antibody S309 (907.0 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  
• SARS-CoV-2 spike RBD with P337L mutation bound to monoclonal antibody S309 (923.2 µs) by The Chodera lab at the Memorial Sloan Kettering Cancer Center
  

Publications

• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity by Emma C. Thomson, Laura E, Rosen, James G. Shepherd, et al.
  
• SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape by Tyler N. Starr, Nadine Czudnochowski, Zhuoming Liu, et al.
  
• 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
  

Therapeutically Applicable Research to Generate Effective Treatments (TARGET)

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TARGET data matrix by National Cancer Institute
  

Publications

• A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor by Gadd S, Huff V, Walz AL, et al.
  
• Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia by Yang JJ, Cheng C, Devidas M, et al.
  
• 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.
  
• CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AM by Maxson JE, Ries RE, Wang YC, et al.
  
• 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.
  
• 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.
  
• 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.
  
• Genomics in childhood acute myeloid leukemia comes of age by Brunner AM, Graubert TA.
  
• 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.
  
• MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia by Lim EL, Trinh DL, Ries RE, et al.
  
• MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours by Perlman EJ, Gadd S, Arold ST, et al.
  
• Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors by Walz AL, Ooms A, Gadd S, et al.
  
• Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations by Eleveld TF, Oldridge DA, Bernard V, Koster J, et al.
  
• 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.
  
• TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney by Gooskens SL, Gadd S, Guidry Auvil JM, et al.
  
• 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.
  
• The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia by Yu Liu, John Easton, Ying Shao, et al.
  
• 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.
  

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5, 3.7, 4.0, and 4.2

Tutorials

• DRAGEN Quick Start on AWS by AWS Quick Start Team
  

Tools & Applications

• DRAGEN 3.5.7b Software Release Notes by Illumina Inc.
  
• DRAGEN 3.7.5 Software Release Notes by Illumina Inc.
  
• DRAGEN on BaseSpace Sequence Hub by Illumina Inc.
  
• DRAGEN v4.0.3 Software Release Notes by Illumina Inc.
  
• DRAGEN v4.2.4 Software Release Notes by Illumina Inc.
  
• Illumina Connected Analytics by Illumina Inc.
  
• Illumina Connected Analytics User Guide by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v3.5 User Guide by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v3.7 Online Help by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v4.0 Online Help by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v4.2 Online Help by Illumina Inc.
  
• Nirvana Documentation by Illumina Inc.
  

Publications

• Accurate and efficient calling of small and large variants from popgen datasets using the DRAGEN Bio-IT Platform by Illumina Inc. (2021)
  
• Data solution empowering population genomics by Illumina Inc. (2021)
  
• Demystifying the versions of GRCh38/hg38 reference genomes, how they are used in DRAGEN and their impact on accuracy by Illumina Inc. (2021)
  
• DRAGEN Sets New Standard for Data Accuracy in PrecisionFDA Benchmark Data. Optimizing Variant Calling Performance with Illumina Machine Learning and DRAGEN Graph by Illumina Inc. (2022)
  
• DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes by Illumina Inc. (2020)
  
• Genotyping variants at population scale using DRAGEN gVCF Genotyper by Illumina Inc. (2023)
  
• Overcoming high homology to detect variation in CYP21A2 with whole-genome sequencing in DRAGEN by Illumina Inc. (2023)
  
• precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions (Preprint) by Olson et al (2020)
  
• Unveiling Illumina Connected Annotations: A breakthrough in genomic annotation by Illumina Inc. (2024)
  

Allen Cell Imaging Collections

Tutorials

• Download and train label-free models by Greg Johnson
  
• Integrating single-cell sequencing and nuclear imaging data by Chengxiang Qiu and William Noble
  

Tools & Applications

• AICS Volume Viewer by Dan Toloudis
  
• AICSImageIO by Matthew Bowden, Jackson Brown, Jamie Sherman, Dan Toloudis
  
• Allen Cell Feature Explorer by Allen Institute for Cell Science
  
• Allen Cell Structure Segmenter by Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski
  
• Integrated Mitotic Stem Cell by Allen Institute for Cell Science
  
• Pytorch 3D Integrated Cell by Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar
  
• Visual Guide to Human Cells by Allen Institute for Cell Science
  

Publications

• 4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics by Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot, Neda Bagheri & Graham T. Johnson
  
• A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes by Tanya Grancharova*, Kaytlyn A. Gerbin*, Alexander B. Rosenberg, Charles M. Roco, Joy E.Arakaki , Colette M. DeLizo, Stephanie Q. Dinh, Rory M. Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig & Ruwanthi N. Gunawardane
  
• A deep generative model of 3D single-cell organization by Rory M. Donovan-Maiye, Jackson M. Brown, Caleb K. Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg & Gregory R. Johnson
  
• A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs) by Caroline Hookway*, Antoine Borensztejn*, Leigh K. Harris*, Sara Carlson, Gokhan Dalgin, Suraj Mishra, Nivedita Nivedita, Ellen M. Adams, Tiffany Barszczewski, Julie C. Dixon, Jacqueline H. Edmonds, Erik A. Ehlers, Alexandra J. Ferrante, Margaret A. Fuqua, Philip Garrison, Janani Gopalan, Benjamin W. Gregor, Maxwell J. Hedayati, Kyle N. Klein, Chantelle L. Leveille, Sean L. Meharry, Haley S. Morris, Gouthamrajan Nadarajan, Sandra A. Oluoch, Serge E. Parent, Amber Phan, Brock Roberts, Emmanuel E. Sanchez, M. Filip Sluzewski, Lev S. Snyder, Derek J. Thirstrup, John Paul Thottam, Julia R. Torvi, Gaea Turman, Matheus P. Viana, Lyndsay Wilhelm, Chamari S. Wijesooriya, Jie Yao, Julie A. Theriot, Susanne M. Rafelski & Ruwanthi N. Gunawardane
  
• Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy by Benjamin W. Gregor*, Mackenzie E. Coston*, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane & Nathalie Gaudreault
  
• Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes by Kaytlyn A. Gerbin*, Tanya Grancharova*, Rory M. Donovan-Maiye*, Melissa C. Hendershott*, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Q. Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Filip Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo A. Knijnenburg, Susanne M. Rafelski, Julie A. Theriot & Ruwanthi N. Gunawardane
  
• Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories by Julie C. Dixon*, Christopher L. Frick*, Chantelle L. Leveille*, Philip Garrison, Peyton A. Lee, Saurabh S. Mogre, Benjamin Morris, Nivedita Nivedita, Ritvik Vasan, Jianxu Chen, Cameron L. Fraser, Clare R. Gamlin, Leigh K. Harris, Melissa C. Hendershott, Graham T. Johnson, Kyle N. Klein, Sandra A. Oluoch, Derek J. Thirstrup, M. Filip Sluzewski, Lyndsay Wilhelm, Ruian Yang, Daniel M. Toloudis, Matheus P. Viana, Julie A. Theriot & Susanne M. Rafelski
  
• Integrated intracellular organization and its variations in human iPS cells 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
  
• Interpretable representation learning for 3D multi-piece intracellular structures using point clouds by Ritvik Vasan, Alexandra J. Ferrante, Antoine Borensztejn, Christopher L. Frick, Nathalie Gaudreault, Saurabh S. Mogre, Benjamin Morris, Guilherme G. Pires, Susanne M. Rafelski, Julie A. Theriot & Matheus P. Viana
  
• 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
  
• Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization by Brock Roberts*, Amanda Haupt*, Andrew Tucker, Tanya Grancharova, Joy Arakaki, Margaret A. Fuqua, Angelique Nelson, Caroline Hookway, Susan A. Ludmann, Irina A. Mueller, Ruian Yang, Rick Horwitz, Susanne M. Rafelski & Ruwanthi N. Gunawardane
  

CZ CELLxGENE Discover Census

Tutorials

• Computing on the cell by gene matrix using online (incremental) algorithms by CZI
  
  
• Experimental Highly Variable Genes API by CZI
  
  
• Exploring all data from a tissue by CZI
  
  
• Exploring pre-calculated summary cell counts by CZI
  
  
• Exploring the Census Datasets table by CZI
  
  
• Genes measured in each cell (dataset presence matrix) by CZI
  
  
• Integrating multi-dataset slices of data by CZI
  
  
• Learning about the CZ CELLxGENE Census by CZI
  
  
• Normalizing full-length gene sequencing data by CZI
  
  
• Out-of-core (incremental) mean and variance calculation by CZI
  
  
• Querying and fetching the single-cell data and cell/gene metadata. by CZI
  
  
• Querying data using the gget cellxgene module by CZI
  
  
• Summarizing cell and gene metadata by CZI
  
  
• Training a PyTorch Model by CZI
  
  
• Understanding and filtering out duplicate cells by CZI
  
  

Tools & Applications

• Census Python API by CZI
  
• Census R API by CZI
  

Publications

• CZ CELLxGENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data by CZI Single-Cell Biology et al.
  
• scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI. by Haotian Cui, et al.
  

Gabriella Miller Kids First Pediatric Research Program (Kids First)

Tools & Applications

• CAVATICA by Seven Bridges Genomics
  
• Kids First DRC Portal by Kids First DRC
  
• Kids First DRC Source Code by Kids First DRC
  
• PedcBioPortal by cBioPortal
  

Publications

• 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.
  
• Decreased ACKR3 (CXCR7) function causes oculomotor synkinesis in mice and humans. by Mary C Whitman, Noriko Miyake, et al.
  
• 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.
  
• Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers. by Fengqi Chang, Fumin Lin, et al.
  
• Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. by Allison H Seiden, Felix Richter, et al.
  
• 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.
  
• Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. by Madison R Bishop, Kimberly K Diaz Perez, et al.
  
• Genomic Analyses Implicate Noncoding De Novo Variants in Congenital Heart Disease. by Felix Richter, Sarah U Morton, et al.
  
• Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. by Laura Egolf, Zalman Vaksman, et al.
  
• Germline microsatellite genotypes differentiate children with medulloblastoma. by Samuel Rivero-Hinojosa, Nicholas Kinney, et al.
  
• 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.
  
• MAGEL2-Related Disorders: A study and case series. by Jameson Patak, James Gilfert, et al.
  
• Phenotype delineation of ZNF462 related syndrome. by Paul Kruszka, Tommy Hu, et al.
  
• The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. by Deanne M Taylor, Bruce J Aronow, et al.
  
• 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.
  

Cell Painting Gallery

Tutorials

• Cell Painting wiki by Multiple Authors
  
• Center for Open Bioimage Analysis (COBA) YouTube Channel - video tutorials of CellProfiler and other softwares by Multiple Authors
  
• Image-based Profiling Handbook - for processing image-based profiling datasets using CellProfiler and pycytominer by Multiple Authors
  
• Image-based profiling introductory exercise - data and an exercise on exploring image-based profiles, including understanding the various data levels by Beth Cimini
  
• Scientific Community Image Forum - for software-oriented aspects of scientific imaging including analysis, processing, and acquisition by Multiple Authors
  

Tools & Applications

• Accelerating Drug Discovery with high-throughput Cell Painting on AWS by Chris Kaspar
  
• Deep Profiler - Morphological profiling using deep learning by Multiple Authors
  
• Distributed CellProfiler - Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure by Multiple Authors
  
• Image-based Profiling Recipe by Multiple Authors
  
• Pycytominer - Data processing functions for profiling perturbations by Multiple Authors
  

Publications

• A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay by Bray M-A, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancik V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, & Carpenter AE
  
• Cell Painting predicts impact of lung cancer variants by Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, & Singh S
  
• Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes by Bray M-A, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, & Carpenter AE
  
• Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects by Singh S, Wu X, Ljosa V, Bray M-A, Piccioni F, Root DE, Doench JG, Boehm JS, & Carpenter AE
  
• Multiplex Cytological Profiling Assay to Measure Diverse Cellular States by Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF
  
• Systematic morphological profiling of human gene and allele function via Cell Painting by Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, & Carpenter AE
  
• Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling by Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, BodycombeNE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSK, Duvall JR, Wilson JA, Bittker JA, Dancik V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, & Clemons PA
  

Genome Aggregation Database (gnomAD)

Tools & Applications

• gnomAD quality control GitHub repository by gnomAD Production Team
  
• Hail by Hail Team
  
• Hail utilities for gnomAD by gnomAD Production Team
  

Publications

• A genomic mutational constraint map using variation in 76,156 human genomes. Nature 625, 92–100 (2024) by Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., Poterba, T., Wilson, M. W., Tarasova, Y., Phu, W., Yohannes, M. T., Koenig, Z., Farjoun, Y., Banks, E., Donnelly, S., Gabriel, S., Gupta, N., Ferriera, S., Tolonen, C., Novod, S., Bergelson, L., Roazen, D., Ruano-Rubio, V., Covarrubias, M., Llanwarne, C., Petrillo, N., Wade, G., Jeandet, T., Munshi, R., Tibbetts, K., gnomAD Project Consortium, O’Donnell-Luria, A., Solomonson, M., Seed, C., Martin, A. R., Talkowski, M. E., Rehm, H. L., Daly, M. J., Tiao, G., Neale, B. M., MacArthur, D. G. & Karczewski, K. J.
  
• 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.
  
• Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016) by Lek, M., Karczewski, K., Minikel, E. et al.
  
• 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.
  
• 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.
  
• gnomAD v2.1 by Laurent Francioli, Grace Tiao, Konrad Karczewski, Matthew Solomonson, Nick Watts
  
• gnomAD v3.0 by Laurent Francioli, Daniel MacArthur
  
• 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.
  
• 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.
  
• 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.
  
• 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.
  
• 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.
  

The Singapore Nanopore Expression Data Set

Tutorials

• Accessing the SG-NEx dataset on AWS by Ying Chen
  
• Basecalling and analysing SG-NEx samples in S/BLOW5 format by Hasindu Gamaarachchi
  
• Differential RNA modification analysis tutorial with xPore by Yu Song Chuah
  
• Performing transcript discovery and quantification with Bambu by Min Hao Ling
  
• RNA modification analysis tutorial with m6Anet by Yu Song Chuah
  

Tools & Applications

• Bambu: Transcript discovery and quantification using long read RNA-Seq data by Ying Chen, Andre Sim et al.
  
• JAFFAL: Detection of fusion genes from long read RNA-Seq data by Nadia M Davidson et al.
  
• m6Anet: Identification of m6A from a single direct RNA-Seq sample by Christopher Hendra et al.
  
• nf-core/nanoseq: A nanopore DNA and RNA-Seq demultiplexing, QC, alignment and analysis pipeline by Chelsea Sawyer et al.
  
• xPore: Identification of differential RNA modification from direct RNA-Seq data by Ploy Pratanwanich et al.
  

Publications

• A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. by Ying Chen et al.
  
• Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. by Yuk Kei Wan et al.
  
• Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. by Christopher Hendra et al.
  
• Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. by Ploy N Pratanwanich et al.
  
• JAFFAL: Detecting fusion genes with long read transcriptome sequencing. by Nadia M Davidson et al.
  

Fly Brain Anatomy: FlyLight Gen1 and Split-GAL4 Imagery

Tutorials

• File Operations on AWS S3 by Rob Svirskas
  
• Scaling Neuroscience Research on AWS by Konrad Rokicki
  AWS LambdaAWS AppSyncAmazon DynamoDBAWS Step Functions
• Tutorial for neuronbridger (R API) by Alexander Bates
  
• Using Imagery on AWS S3 by Rob Svirskas
  

Tools & Applications

• Color Depth Search Fiji Plugin by Hideo Otsuna
  
• Fly Light Split-GAL4 Driver Collection by Rob Svirskas
  
• FlyLight Project Website by Geoffrey Meissner
  
• NeuronBridge by Jody Clements, Rob Svirskas, Hideo Otsuna, Cristian Goina, Konrad Rokicki
  

Publications

• A GAL4-Driver Line Resource for Drosophila Neurobiology by Arnim Jenett, Gerald M Rubin, Teri-TB Ngo, David Shepherd, Christine Murphy, Heather Dionne, Barret D Pfeiffer, Amanda Cavallaro, Donald Hall, Jennifer Jeter, Nirmala Iyer, Dona Fetter, Joanna H Hausenfluck, Hanchuan Peng, Eric T Trautman, Robert R Svirskas, Eugene W Myers, Zbigniew R Iwinski, Yoshinori Aso, Gina M DePasquale, Adrianne Enos, Phuson Hulamm, Shing Chun Benny Lam, Hsing-Hsi Li, Todd R Laverty, Fuhui Long, Lei Qu, Sean D Murphy, Konrad Rokicki, Todd Safford, Kshiti Shaw, Julie H Simpson, Allison Sowell, Susana Tae, Yang Yu, Christopher T Zugates
  
• An image resource of subdivided Drosophila GAL4-driver expression patterns for neuron-level searches by Geoffrey W Meissner, Zachary Dorman, Aljoscha Nern, Kaitlyn Forster, Theresa Gibney, Jennifer Jeter, Lauren Johnson, Yisheng He, Kelley Lee, Brian Melton, Brianna Yarbrough, Jody Clements, Cristian Goina, Hideo Otsuna, Konrad Rokicki, Robert R Svirskas, Yoshinori Aso, Gwyneth M Card, Barry J Dickson, Erica Ehrhardt, Jens Goldammer, Masayoshi Ito, Wyatt Korff, Ryo Minegishi, Shigehiro Namiki, Gerald M Rubin, Gabriella Sterne, Tanya Wolff, Oz Malkesman, FlyLight Project Team
  
• An unbiased template of the Drosophila brain and ventral nerve cord by John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
  
• Color depth MIP mask search: a new tool to expedite Split-GAL4 creation by Hideo Otsuna, Masayoshi Ito, Takashi Kawase
  
• The neuronal architecture of the mushroom body provides a logic for associative learning by Yoshinori Aso, Daisuke Hattori, Yang Yu, Rebecca M Johnston, Nirmala A Iyer, Teri-TB Ngo, Heather Dionne, LF Abbott, Richard Axel, Hiromu Tanimoto, Gerald M Rubin
  

International Neuroimaging Data-Sharing Initiative (INDI)

Tutorials

• Downloading FCP-INDI Neuroimaging Data from Amazon S3 by INDI
  

Tools & Applications

• Configurable Pipeline for the Analysis of Connectomes (C-PAC) by [INDI C-PAC Team](https://fcp-indi.github.io/)
  

Publications

• Accelerating the Evolution of Nonhuman Primate Neuroimaging by M.P. Milham, C. Petkov
  
• An Open Resource for Non-human Primate Imaging by M.P. Milham, L. Ai, ..., C.E. Schroeder
  
• An open resource for transdiagnostic research in pediatric mental health and learning disorders by L.M. Alexander, J. Escalera, ..., M.P. Milham
  
• Assessment of the impact of shared brain imaging data on the scientific literature by M.P. Milham, R.C. Craddock, ..., A. Klein
  
• 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
  
• Making data sharing work: The FCP/INDI experience by M. Mennes, B.B. Biswal, F.X. Castellanos, M.P. Milham
  
• 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
  
• 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
  
• 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
  

Garvan Institute Long Read Sequencing Benchmark Data

Tutorials

• Directly processing on an s3fs mount by Hasindu Gamaarachchi
  
• Fetching subsets with slow5curl and samtools by Bonson Wong
  

Tools & Applications

• buttery-eel: The buttery eel - a slow5 guppy basecaller wrapper by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
  
• Slow5curl: library and tool for accessing remote BLOW5 files. by Wong, B., et al.
  
• Slow5lib: toolkit slow5lib is a software library for reading & writing SLOW5 files. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
  
• Slow5tools: toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
  

Publications

• Accelerated nanopore basecalling with SLOW5 data format. by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
  
• Fast nanopore sequencing data analysis with SLOW5. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
  
• Flexible and efficient handling of nanopore sequencing signal data with slow5tools. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
  

Open NeuroData

Tutorials

• Download by Benjamin Falk
  
• Visualization using Neuroglancer by Benjamin Falk
  

Tools & Applications

• CloudVolume by William Silversmith
  
• Igneous by William Silversmith
  
• Neuroglancer by Jeremy Maitin-Shepard
  

Publications

• 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
  
• From cosmos to connectomes: The evolution of data-intensive science by R. Burns, J. T. Vogelstein, and A. S. Szalay
  
• 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.
  
• 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
  

PubSeq - Public Sequence Resource

Tutorials

• PubSeq Documentation by PubSeq development team
  
• PubSeq FAQ by PubSeq development team
  
• Query metadata by PubSeq development team
  
• REST API by PubSeq development team
  
• Submitting a sequence by PubSeq development team
  

Tools & Applications

• Source code for (meta)data uploader by PubSeq development team
  
• Source code for CWL workflows by PubSeq development team
  
• Source code for website by PubSeq development team
  

Publications

• Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.
  

Cancer Cell Line Encyclopedia (CCLE)

Tools & Applications

• Broad Institute Cancer Cell Line Encyclopedia by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• Genomic Data Commons by National Cancer Institute
  
• ISB CGC BigQuery tables by Institute for Systems Biology
  

Publications

• Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, M., Huang F. et al.
  
• Pharmacogenomic agreement between two cancer cell line data sets by The Cancer Cell Line Encyclopedia Consortium & The Genomics of Drug Sensitivity in Cancer Consortium
  
• The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity by Barretina Caponigro Stransky et al.
  
• The landscape of cancer cell line metabolism by Li, H. et al.
  

IBL Neuropixels Brainwide Map on AWS

Tutorials

• Download the public datasets by IBL Data Architecture Working Group
  
• Example analysis of the brain-wide map dataset by IBL Data Architecture Working Group
  
• Find data associated with a release or publication by IBL Data Architecture Working Group
  
• Introduction to IBL and the brain-wide map dataset by IBL Data Architecture Working Group
  
• Loading Data by IBL Data Architecture Working Group
  
• Using IBL data with ONE by IBL Data Architecture Working Group
  

Tools & Applications

• Data Explorer by IBL Data Architecture Working Group
  
• ONE-api on pypi.python.org - python API to query and download neurophysiology data by IBL Data Architecture Working Group
  

Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET)

Tutorials

• Finding and Downloading TaRGET II Data files by TaRGET-DCC
  

Tools & Applications

• Visualize TaRGET II data with WashU Epigenome Browser by WashU Epigenome Browser
  

Publications

• Comparison of differential accessibility analysis strategies for ATAC-seq data by Gontarz P, Fu S, Xing X, Liu S, Miao B et.al.
  
• Environmental Determinants of cardiovasular disease: lessons learned from air pollution by Al-Kindi SG, Brook RD, Biswal S, Rajagopalan S.
  
• Epigenetic biomarkers and preterm birth by Park B, Khanam R, Vinayachandran V, et.al.
  
• Metabolic effects of air pollution exposure and reversibility by Rajagopalan S, Park B, Palanivel R, et al.
  
• The NIEHS TaRGET II Consortium and environmental epigenomics by Wang, T., Pehrsson, E., Purushotham, D. et al.
  
• The role of environmental exposures and the epigenome in health and disease. by Perera BPU, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC.
  

Clinical Proteomic Tumor Analysis Consortium 2 (CPTAC-2)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• 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
  
• 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
  
• 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
  

ICGC on AWS

Tutorials

• AWS Pancancer Workflow Launcher by Solomon Shorser
  

Publications

• Analyses of non-coding somatic drivers in 2,693 cancer whole genomes by Rheinbay et al (2020)
  
• Genomic basis of RNA alterations in cancer by PCAWG Transcriptome Core Group et al. (2020)
  
• Pan-cancer analysis of whole genomes by The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020)
  
• Patterns of somatic structural variation in human cancer genomes by Li et al. (2020)
  
• The evolutionary history of 2,658 cancers by Gerstung et al (2020)
  
• The repertoire of mutational signatures in human cancer by Alexandrov et al (2020)
  

BossDB Open Neuroimagery Datasets

Tutorials

• Data access and download by Jordan Matelsky
  

Tools & Applications

• bossDB by bossDB Team
  
• CloudVolume by Seung Lab
  

Publications

• 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
  
• intern: Integrated Toolkit for Extensible and Reproducible Neuroscience by Jordan K Matelsky, Luis Rodriguez, Daniel Xenes, Timothy Gion, Robert Hider Jr., Brock Wester, William Gray-Roncal
  
• The Block Object Storage Service (bossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery by Robert Hider Jr., Dean M. Kleissas, Derek Pryor, Timothy Gion, Luis Rodriguez, Jordan Matelsky, William Gray-Roncal, Brock Wester
  

Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• 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
  
• 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
  

IBL Neuropixels Reproducible Ephys Data on AWS

Tutorials

• Download the public datasets by IBL Data Architecture Working Group
  
• Find data associated with a release or publication by IBL Data Architecture Working Group
  
• Loading Data by IBL Data Architecture Working Group
  

Tools & Applications

• Data Explorer by IBL Data Architecture Working Group
  
• ONE-api on pypi.python.org - python API to query and download neurophysiology data by IBL Data Architecture Working Group
  

Publications

• Reproducibility of in-vivo electrophysiological measurements in mice by International Brain Laboratory et al.
  

NYU Langone & FAIR FastMRI Dataset

Tutorials

• FastMRI Tutorial (Jupyter Notebook) by Tullie Murrell
  
• How to Get Started Working with the FastMRI Dataset (and why you should!) by Kevin Hodges
  

Publications

• Advancing machine learning for MR image reconstruction with an open competition:Overview of the 2019 fastMRI challenge by Knoll et al (2020)
  
• Assessment of the generalization of learned image reconstruction and the potential for transfer learning. by Knoll et al (2019)
  
• Deep Learning Methods for Parallel Magnetic Resonance Image Reconstruction by Knoll et al (2019)
  
• fastMRI:An Open Dataset and Benchmarks for Accelerated MRI by Zbontar et al (2019)
  

Open Bioinformatics Reference Data for Galaxy

Tutorials

• Using Open Bio Ref Data with Galaxy and Bioconductor by Enis Afgan, Alexandru Mahmoud, Nuwan Goonasekera
  

Tools & Applications

• Bioconductor by Bioconductor Project
  
• Galaxy by Galaxy Project
  

Publications

• Accessible, curated metagenomic data through ExperimentHub by Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, and Levi Waldron
  
• TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages by Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
  
• Wrangling Galaxy's reference data by Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko
  

Serratus: Ultra-deep Search for Novel Viruses - Versioned Data Release

Tools & Applications

• Serratus Explorer by Serratus Team
  
• Tantalus: An R Package for exploration of Serratus data by Serratus Team
  

Publications

• coronaSPAdes. From biosynthetic gene clusters to RNA viral assemblies by Meleshko D., Hajirasouliha I., and Korobeynikov A. (2021)
  
• Diversification of mammalian deltaviruses by host shifting by Bergner L.M., Orton R.J., et al (2021)
  
• Petabase-scale sequence alignment catalyses viral discovery by Edgar R., Taylor J., Lin V., et al (2021)
  
• Ribovirus classification by a polymerase barcode sequence by Babaian A., and Edgar R. (2021)
  

3000 Rice Genomes Project

Tools & Applications

• RiceGalaxy by International Rice Research Institute
  

Publications

• Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study by Meng B et al (2022)
  
• Rice Galaxy: an open resource for plant science by Juanillas V et al (2019)
  
• Structural variants in 3000 rice genomes by Fuentes RR et al (2019)
  
• Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice by Chen J et al (2019)
  

Automated Segmentation of Intracellular Substructures in Electron Microscopy (ASEM) on AWS

Tutorials

• Data layout and how to view by kirchhausenlab
  
• How to use models by kirchhausenlab
  

Tools & Applications

• ASEM Colab Notebook (Interactive Demo) by Patrick Stock
  
• TK Lab Data Explorer by Patrick Stock
  

Publications

• Deep neural network automated segmentation of cellular structures in volume electron microscopy by Benjamin Gallusser, Giorgio Maltese, Giuseppe Di Caprio, Tegy John Vadakkan, Anwesha Sanyal, Elliott Somerville, Mihir Sahasrabudhe, Justin O’Connor, Martin Weigert, Tom Kirchhausen
  

CAncer MEtastases in LYmph nOdes challeNge (CAMELYON) Dataset

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• CAMELYON Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Publications

• 1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset by Geert Litjens, et al.
  
• Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer by Babak Ehteshami Bejnordi, et al.
  
• From Detection of Individual Metastases to Classification of Lymph Node Status at the Patient Level: The CAMELYON17 Challenge by Peter Bandi, et al.
  

CoMMpass from the Multiple Myeloma Research Foundation

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• "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
  
• "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.
  
• "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
  
• "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
  

IBL Behavioral Data on AWS

Tutorials

• Download the public data via ONE by IBL Data Architecture Working Group
  
• Find data associated with a release or publication by IBL Data Architecture Working Group
  
• Loading Data by IBL Data Architecture Working Group
  

Tools & Applications

• ONE-api on pypi.python.org - python API to query and download neurophysiology data by IBL Data Architecture Working Group
  

Publications

• Standardized and reproducible measurement of decision-making in mice by International Brain Laboratory et al.
  

Logan Unitigs and Contigs of the Sequence Read Archive (SRA) on AWS

Tutorials

• Downloading unitigs of several accessions by Rayan Chikhi
  
• Downloading, mapping many contigs to a gene of interest by Rayan Chikhi
  
• Search for a k-mer of interest inside an unitigs accession by Rayan Chikhi
  

Tools & Applications

• Minia 3 by Rayan Chikhi
  
• Open Virome by Artem Babaian
  

MONKEY

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• MONKEY Challenge by Computational Pathology Group Radboudumc, Nijmegen
  
• MONKEY challenge tutorials by Computational Pathology Group Radboudumc, Nijmegen
  
• Structured description of the MONKEY Challenge by Linda Studer, Dominique van Midden, Fazael Ayatollahi, Jeroen van der Laak
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

NIH NCBI Sequence Read Archive (SRA) on AWS

Tutorials

• Access SRA data using Amazon Web Services (AWS) by NCBI SRA
  
• Get started with the SRA and Amazon Athena by NCBI SRA
  
• SRA in the Cloud by NCBI SRA
  

Tools & Applications

• SRA Toolkit by NCBI SRA
  

Publications

• The Sequence Read Archive by Leinonen et al (2011)
  

The Human Connectome Project

Tutorials

• Exploring the Human Connectom by The Human Connectome Project
  

Tools & Applications

• The Human Connectome Workbench by The Human Connectome Project
  

Publications

• The Human Connectome Project: A retrospective by Elam JS, Glasser MF, Harms MP, Sotiropoulos SN, Andersson JL, Burgess GC, Curtiss SW, et al.
  
• The minimal preprocessing pipelines for the Human Connectome Project by Glasser MF, Sotiropoulos SN, Wilson JA, Coalson TS, Fischl B, Andersson JL, Xu J, Jbabdi S, et al.
  
• The WU-Minn Human Connectome Project: an overview. by Van Essen DC, Smith SM, Barch DM, Behrens TEJ, Yacoub E, Ugurbil, K, and the WU-Minn HCP Consortium.
  

Basic Local Alignment Sequences Tool (BLAST) Databases

Tools & Applications

• BLAST on the Cloud with NCBI’s ElasticBLAST by Sixing Huang
  
• BLAST+ Docker by NCBI BLAST
  

Publications

• BLAST+: Architecture and Applications by Christiam Camacho 1 , George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden
  
• 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
  

Encyclopedia of DNA Elements (ENCODE)

Tutorials

• ENCODE CTCF ChIP-seq data correlation across different cell types by Paul Sud
  
• Exploring ENCODE data from EC2 with Jupyter notebook by Keenan Graham
  
• Ingesting ENCODE data into TileDB with S3 backend by Otto Jolanki
  

Publications

• New developments on the Encyclopedia of DNA Elements (ENCODE) data portal by Luo et al 2020
  

Genome in a Bottle on AWS

Tools & Applications

• GA4GH Benchmarking Tools by GA4GH Benchmarking Team
  
• The Genome in a Bottle Github Project by Genome In A Bottle Consortium
  

Publications

• Extensive sequencing of seven human genomes to characterize benchmark reference materials by Zook J et al (2016)
  
• High-coverage, long-read sequencing of Han Chinese trio reference samples by Wang Y et al (2019)
  

Molecular Profiling to Predict Response to Treatment (phs001965)

Tools & Applications

• Childhood Cancer Data Initiative Data Catalog by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  

Publications

• Finding the way to Wilms tumor by comparing the primary and relapse tumor samples by Filippo Spreafico, Sara Ciceri, et al.
  
• Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study by Samantha Gadd, Vicki Huff, et al.
  

Mouse Brain Anatomy: MouseLight Imagery

Tools & Applications

• HortaCloud by David Schauder, Donald J. Olbris, Jody Clements, Cristian Goina, Robert R. Svirskas, Konrad Rokicki
  
• MouseLight NeuronBrowser by Tiago A. Ferreira, Jayaram Chandrashekar
  
• MouseLight Project Website by Tiago A. Ferreira, Jayaram Chandrashekar
  

Publications

• Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain by Johan Winnubst, Erhan Bas, Tiago A. Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Ben J. Arthur, Christopher Bruns, Konrad Rokicki, David Schauder, Donald J. Olbris, Sean D. Murphy, David G. Ackerman, Cameron Arshadi, Perry Baldwin, Regina Blake, Ahmad Elsayed, Mashtura Hasan, Daniel Ramirez, Bruno Dos Santos, Monet Weldon, Amina Zafar, Joshua T. Dudman, Charles R. Gerfen, Adam W. Hantman, Wyatt Korff, Scott M. Sternson, Nelson Spruston, Karel Svoboda, Jayaram Chandrashekar
  

OpenCell on AWS

Tools & Applications

• cytoself (an unsupervised ML model to quantify localization patterns) by Hirofumi Kobayashi, Keith C. Cheveralls, Manuel D. Leonetti, Loic A. Royer
  
• OpenCell web portal by OpenCell team
  

Publications

• OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization by Nathan H. Cho, Keith C. Cheveralls, Andreas-David Brunner, Kibeom Kim, André C. Michaelis, Preethi Raghavan, et al.
  
• Self-Supervised Deep-Learning Encodes High-Resolution Features of Protein Subcellular Localization by Hirofumi Kobayashi, Keith C. Cheveralls, Manuel D. Leonetti, Loic A. Royer
  

Refgenie reference genome assets

Tutorials

• Basic Refgenie tutorial by Nathan Sheffield
  

Tools & Applications

• Pipeline for ATAC-seq data analysis by Jason Smith and Nathan Sheffield
  
• Pipeline for PRO-seq data analysis by Jason Smith and Nathan Sheffield
  

Publications

• Refgenie: a reference genome resource manager by Michał Stolarczyk, Vincent P Reuter, Jason P Smith, Neal E Magee, Nathan C Sheffield
  

Synthea synthetic patient generator data in OMOP Common Data Model

Tutorials

• Create data science environments on AWS for health analysis using OHDSI by James Wiggins
  AWS CloudFormationAmazon EC2Amazon RDS
• Map clinical notes to the OMOP Common Data Model and healthcare ontologies using Amazon Comprehend Medical by James Wiggins
  Amazon ComprehendAWS CloudFormationAmazon EC2Amazon RDS
• Predict patient health outcomes using OHDSI and machine learning on AWS by James Wiggins
  AWS CloudFormationAmazon EC2Amazon RDS

Tools & Applications

• OHDSIonAWS by James Wiggins
  

UK Biobank Linkage Disequilibrium Matrices

Tutorials

• PolyFun Wiki by Omer Weissbrod
  

Tools & Applications

• PolyFun and PolyPred software by Omer Weissbrod
  

Publications

• Functionally informed fine-mapping and polygenic localization of complex trait heritability by Weissbrod et al.
  
• Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores by Weissbrod et al.
  

UK Biobank Pan-Ancestry Summary Statistics

Tutorials

• Hail Tutorials by Hail Team
  

Tools & Applications

• Hail by Hail Team
  
• Hail on AWS Quick Start by Amazon Web Services and PrivoIT
  

Publications

• Pan-ancestry genetic analysis of the UK Biobank by Pan UKBB Team
  

Allen Ivy Glioblastoma Atlas

Tutorials

• Accessing Ivy Glioblastoma Atlas Project data by Allen Institute for Brain Science
  

Tools & Applications

• Ivy Glioblastoma Atlas Project by Allen Institute for Brain Science
  

Publications

• An anatomic transcriptional atlas of human glioblastoma by Ralph Puchalski, et al.
  

Allen Mouse Brain Atlas

Tutorials

• Accessing Allen Mouse Brain Atlas data by Allen Institute for Brain Science
  

Tools & Applications

• Allen Mouse Brain Atlas by Allen Institute for Brain Science
  

Publications

• Genome-wide atlas of gene expression in the adult mouse brain by Ed Lein, et al.
  

Beat Acute Myeloid Leukemia (AML) 1.0

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms by Zhang H, Savage S, Schultz AR, Bottomly D, White L, Segerdell E, et al.
  
• Functional Genomic Landscape of Acute Myeloid Leukemia by Jeffrey W. Tyner, Cristina E. Tognon, Dan Bottomly et al.
  

Broad Genome References

Tutorials

• Using Amazon FSx for Lustre for Genomics Workflows on AWS by W. Lee Pang
  AWS BatchAmazon FSx

Tools & Applications

• Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang
  

Publications

• Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA by Willey J. C., Morrison T. B., Austermiller B., Crawford E. E., et al (2021)
  

COBRA

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• COBRA Tools & Labels by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

COVID-19 Harmonized Data

Tutorials

• How Talend is joining the fight against COVID-19 by Thomas Bennett
  

Tools & Applications

• Stitch COVID-19 Integration by Jeff Huth
  
• Tap COVID-19 Python by Jeff Huth
  

Cell Organelle Segmentation in Electron Microscopy (COSEM) on AWS

Publications

• Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. by David P. Hoffman, 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
  
• 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.
  
• Whole-cell organelle segmentation in volume electron microscopy by Lisa Heinrich, Davis Bennett, David Ackerman, Woohyun Park, Jon Bogovic, Nils Eckstein, et al.
  

Clinical Trial Sequencing Project - Diffuse Large B-Cell Lymphoma

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• 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
  
• 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.
  

Distributed Archives for Neurophysiology Data Integration (DANDI)

Tools & Applications

• DANDI JupyterHub Interface by DANDI Project
  
• DANDI Shell Interface by DANDI Project
  
• DANDI Web Interface by DANDI Project
  

Exceptional Responders Initiative

Tools & Applications

• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  

Publications

• The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study by Barbara A. Conley, Lou Staudt, et al.
  

Foundation Medicine Adult Cancer Clinical Dataset (FM-AD)

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• 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
  
• 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
  

Golden Retriever Lifetime Study: Whole genome genotyping of Golden Retrievers on Axiom HD Arrays

Tutorials

• GRLS GWAS Tutorial by Tamer Mansour
  

Publications

• Cohort profile: The Golden Retriever Lifetime Study (GRLS) by Julia Labadie, Brenna Swafford, Mara DePena, Kathy Tietje, Rodney Page, Janet Patterson-Kane
  
• The Golden Retriever Lifetime Study: establishing an observational cohort study with translational relevance for human health by Michael K. Guy, Rodney L. Page, Wayne A. Jensen, Patricia N. Olson, J. David Haworth, Erin E. Searfoss, and Diane E. Brown
  

I-CARE:International Cardiac Arrest REsearch consortium Electroencephalography Database

Tools & Applications

• WFDB Software Package by Moody, G., Pollard, T., & Moody, B.
  

Publications

• I-CARE:International Cardiac Arrest REsearch consortium Electroencephalography Database by Amorim E, Zheng WL, Ghassemi MM, Aghaeeaval M, Kandhare P, Karukonda V, et al.
  
• The International Cardiac Arrest Research (I-CARE) Consortium Electroencephalography Database by Amorim E, Zheng WL, Ghassemi MM, Aghaeeaval M, Kandhare P, Karukonda V, et al.
  

Kraken2 NCBI RefSeq Complete V205 database on AWS

Tutorials

• Using an Amazon Machine Image for analysing samples with Kraken2 by Robyn Wright
  Amazon EC2

Tools & Applications

• Kraken2 by Derrick Wood, Jennifer Lu and Ben Langmead
  

Publications

• From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools by Robyn J. Wright, Andre M. Comeau and Morgan G.I. Langille
  

MIMIC-III (‘Medical Information Mart for Intensive Care’)

Tutorials

• Building predictive disease models using Amazon SageMaker with Amazon HealthLake normalized data by Ujjwal Ratan, Nihir Chadderwala, and Parminder Bhatia
  AWS GlueAWS HealthLakeAmazon SageMaker
• Perform biomedical informatics without a database using MIMIC-III data and Amazon Athena by James Wiggins, Alistair Johnson
  Amazon AthenaAWS Glue

Tools & Applications

• MIMIC-code GitHub repository by Alistair Johnson
  

Medical Segmentation Decathlon

Tutorials

• Pytorch-Integrated MSD Data Loader by MONAI Development Team
  

Tools & Applications

• MONAI: Getting Started by MONAI Development Team
  

Publications

• A large annotated medical image dataset for the development and evaluation of segmentation algorithms by Simpson A. L., Antonelli M., Bakas S., Bilello M., Farahana K., van Ginneken B., et al
  

NASA Space Biology Open Science Data Repository (OSDR)

Publications

• Advancing the Integration of Biosciences Data Sharing to Further Enable Space Exploration by Ryan T. Scott, Kirill Grigorev, Graham Mackintosh, Samrawit G. Gebre, Christopher E. Mason, Martha E. Del Alto, Sylvain V. Costes
  
• GeneLab: Omics database for spaceflight experiments by Shayoni Ray, Samrawit Gebre, Homer Fogle, Daniel C Berrios, Peter B Tran, Jonathan M Galazka, Sylvain V Costes
  
• NASA GeneLab: interfaces for the exploration of space omics data by Daniel C Berrios, Jonathan Galazka, Kirill Grigorev, Samrawit Gebre, Sylvain V Costes
  

National Cancer Institute Imaging Data Commons (IDC) Collections

Tutorials

• IDC "Getting started" tutorial series by Imaging Data Commons team
  

Tools & Applications

• IDC Portal by Imaging Data Commons team
  

Publications

• NCI Imaging Data Commons by Fedorov A, Longabaugh W, Pot D, Clunie D, Pieper S, Aerts H, et al.
  

Open VLF: Scientific Open Data Initiative for CRAAM's SAVNET and AWESOME VLF Data.

Tools & Applications

• All source code, program utilities, and file layouts. by Kauffmann, DHV; Santiago, LS; Oliveira, R de.
  
• Open VLF platform by CRAAM
  

Publications

• Open VLF: Scientific Open Data Initiative for CRAAM's SAVNET and AWESOME VLF Data (2023). by Kauffmann, DHV; Santiago, LS; Raulin, JP; Correia, E; Oliveira, R de.
  

OpenProteinSet

Tutorials

• Run inference at scale for OpenFold, a PyTorch-based protein folding ML model, using Amazon EKS by Shubha Kumbadakone, Ankur Srivastava, and Sachin Kadyan
  Amazon EKSAmazon FSx

Publications

• OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization by Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J, et al
  
• OpenProteinSet: Training data for structural biology at scale by Ahdritz, Gustaf; Bouatta, Nazim; Kadyan, Sachin; Jarosch, Lukas; Berenberg, Daniel; Fisk, Ian, et al
  

QIIME 2 Tutorial Data

Tutorials

• Developing with QIIME 2 by Caporaso and Bolyen
  
• QIIME 2 User Documentation (currently being replaced by *Using QIIME 2*) by The QIIME 2 Development Team
  
• Using QIIME 2 by Caporaso Lab
  

SPaRCNet data:Seizures, Rhythmic and Periodic Patterns in ICU Electroencephalography

Tools & Applications

• IIIC-SPaRCNet Github Repository by Brain Data Science Platform (BDSP)
  

Publications

• Development of Expert-Level Classification of Seizures and Rhythmic and Periodic Patterns During EEG Interpretation by Jing J, Ge W, Hong S, Fernandes MB, Lin Z, Yang C et al., et al.
  
• SPaRCNet data:Seizures, Rhythmic and Periodic Patterns in ICU Electroencephalography by Jing, J., Ge, W., Struck, A. F., Fernandes, M., Hong, S., An, S., et al.
  

STOIC2021 Training

Tools & Applications

• STOIC2021 Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Publications

• How Well Do Self-Supervised Models Transfer to Medical Imaging? by Anton J, Castelli L, Chan MF, Outthers M, Tang WH, Cheung V, et al.
  
• Study of Thoracic CT in COVID-19: The STOIC Project by Revel MP, Boussouar S, de Margerie-Mellon C, Saab I, Lapotre T, Mompoint D, et al.
  

The Human Microbiome Project

Publications

• 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
  
• 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.
  
• The Human Microbiome Project by Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon
  

Variant Effect Predictor (VEP) and the Loss-Of-Function Transcript Effect Estimator (LOFTEE) Plugin

Tools & Applications

• Hail by Neale Lab
  
• Loss-Of-Function Transcript Effect Estimator (LOFTEE) by Konrad Karczewski
  
• Variant Effect Predictor (VEP) by Ensembl
  

VirtualFlow Ligand Libraries

Tutorials

• VirtualFlow tutorial by Christoph Gorgulla
  

Tools & Applications

• VirtualFlow for Virtual Screening (VFVS) Module on GitHub by Christoph Gorgulla
  

Publications

• VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules by Christoph Gorgulla, AkshatKumar Nigam, Matt Koop, Süleyman Selim Çınaroğlu, Christopher Secker, Mohammad Haddadnia, Abhishek Kumar, Yehor Malets, Alexander Hasson, Roni Levin-Konigsberg, Dmitry Radchenko, Aditya Kumar, Minko Gehev, Pierre-Yves Aquilanti, Henry Gabb, Amr Alhossary, Gerhard Wagner, Al, Yurii S. Moroz, Konstantin Fackeldey, Haribabu Arthanari
  

4D Nucleome (4DN)

Tutorials

• Finding and Downloading 4DN Data files by 4DN-DCIC
  
• Using jupyterhub on the 4DN data portal by 4DN-DCIC
  

Africa Soil Information Service (AfSIS) Soil Chemistry

Tutorials

• AfSIS Soil Chemistry - Usage Tutorial by QED
  

Publications

• Goalkeepers 2018, Soil - The Big Data Beneath Your Feet by QED
  

Allen Institute for Brain Science - Synaptic Physiology Public Data Set

Tools & Applications

• aisynphys python package for accessing synaptic physiology data by Campagnola L., Seeman S., et al.
  

Publications

• Local connectivity and synaptic dynamics in mouse and human neocortex by Campagnola L., Seeman S., et al.
  

Allen Institute for Neural Dynamics - Extracellular Electrophysiology Compression Benchmark

Tutorials

• AIND ephys compression benchmark data by David Feng, Alessio Buccino
  

Publications

• Compression strategies for large-scale electrophysiology data by Alessio P. Buccino, Olivier Winter, David Bryant, David Feng, Karel Svoboda, Joshua H. Siegle.
  

Biodiversity Heritage Library Metadata and Page Images

Tools & Applications

• BHLIndex by Global Names
  
• BioStor by Roderic Page
  

Publications

• AI models are getting better and better at reading handwriting, but how can we find handwritten text to begin with? by Mike Trizna, JJ Dearborn
  
• Understanding BHL Through Metadata: Patterns of Bio-Diverse Knowledge Production by Lidia Ponce de la Vega
  
• Unearthing the Past for a Sustainable Future: Extracting and transforming data in the Biodiversity Heritage Library for climate action by Dearborn J, Lichtenberg M, Richard J, deVeer J, Trizna M, Mika K
  

Biological and Physical Sciences (BPS) Microscopy Benchmark Training Dataset

Publications

• Dose, LET and Strain Dependence of Radiation-Induced 53BP1 Foci in 15 Mouse Strains Ex Vivo Introducing Novel DNA Damage Metrics by Sébastien Penninckx, Egle Cekanaviciute, Charlotte Degorre, Elodie Guiet, Louise Viger, Stéphane Lucasb, Sylvain V. Costes
  
• NASA SMD AI Workshop Report by SMD Artificial Intelligence (AI) Initiative
  

Biological and Physical Sciences (BPS) RNA Sequencing Benchmark Training Dataset

Publications

• Adversarial generation of gene expression data by Ramon Viñas, Helena Andrés-Terré, Pietro Liò, Kevin Bryson
  
• NASA SMD AI Workshop Report by SMD Artificial Intelligence (AI) Initiative
  

COVID-19 Data Lake

Tutorials

• A public data lake for analysis of COVID-19 data by AWS Data Lake Team
  AWS GlueAmazon AthenaAmazon ComprehendAmazon KendraAmazon QuickSight
• Exploring the public AWS COVID-19 data lake by AWS Data Lake Team
  Amazon AthenaAWS GlueAmazon SageMaker
• How to use SQL to query data in S3 Bucket with Amazon Athena and AWS SDK for .NET by AWS ProServe US West Applications Team
  Amazon AthenaAWS GlueAmazon S3AWS CloudFormation

Tools & Applications

• CloudFormation template for Glue Catalog table definitions by AWS Data Lake Team
  
• Explore the COVID-19 data lake public S3 bucket by AWS Data Lake Team
  

Cancer Genome Characterization Initiatives - Burkitt Lymphoma, HIV+ Cervical Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma by Grande B. M., Gerhard D. S., Jiang A., Griner N. B., Abramson J. S., Alexander T. B., et al.
  

Cell Painting Image Collection

Tools & Applications

• Accelerating Drug Discovery with high-throughput Cell Painting on AWS by Chris Kaspar
  

Publications

• Example submission for the 2018 CytoData Hackathon (in R and Python) by Juan Caicedo, Tim Becker
  

Cloud Indexes for Bowtie, Kraken, HISAT, and Centrifuge

Tutorials

• Table of contents for tutorials for constituent tools by Ben Langmead
  

Publications

• Reducing reference bias using multiple population reference genomes by Chen et al (2020)
  

CryoET Data Portal

Tutorials

• Downloading data via the AWS CLI by CZI
  
• Examples of working with the portal API by CZI
  
• Predicting sample boundaries by CZI
  

Tools & Applications

• Python API for CryoET Data Portal by CZI
  

Publications

• Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites by Mahrukh Usmani, et al.
  

DNAStack COVID19 SRA Data

Tutorials

• Viral lineage assignment by Heather Ward
  AWS BatchAmazon EC2Amazon S3

Tools & Applications

• Viral AI by DNAstack
  

EMory BrEast Imaging Dataset (EMBED)

Tutorials

• Sample Notebook by Emory-HITI
  

Publications

• The EMory BrEast imaging Dataset (EMBED): A Racially Diverse, Granular Dataset of 3.4M Screening and Diagnostic Mammograms by Jiwoong J. Jeong, Brianna L. Vey, Ananth Reddy, Thomas Kim, Thiago Santos, Ramon Correa, Raman Dutt, Marina Mosunjac, Gabriela Oprea-Ilies, Geoffrey Smith, Minjae Woo, Christopher R. McAdams, Mary S. Newell, Imon Banerjee, Judy Gichoya, Hari Trivedi
  

Emory Knee Radiograph (MRKR) dataset

Tutorials

• Example Notebook by Emory-HITI
  

Publications

• Emory Knee Radiograph Dataset by Brandon Price, Jason Adleberg, Kaesha Thomas, Zach Zaiman, Aawez Mansuri, Beatrice Brown-Mulry, Chima Okecheukwu, Judy Gichoya, Hari Trivedi.
  

GATK Structural Variation (SV) Data

Tutorials

• AWS Setup & Execution by Goldfinch Bio and Loka Inc.
  

Tools & Applications

• Structural Variant Analysis on AWS with Amazon FSx for Lustre by Goldfinch Bio and Loka Inc.
  

Genomic Characterization of Metastatic Castration Resistant Prostate Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic characterization of metastatic castration-resistant prostate cancer patients undergoing PSMA radioligand therapy: A single-center experience by Swayamjeet Satapathy, Chandan K Das, et al.
  

Harvard Electroencephalography Database

Tools & Applications

• Harvard-EEG-Database-Tools by Brain Data Science Platform (BDSP)
  

Publications

• Harvard Electroencephalography Database by Zafar, S., Loddenkemper, T., Lee, J. W., Cole, A., Goldenholz, D., Peters, J., et al.
  

Harvard-Emory ECG Database

Tools & Applications

• WFDB Software Package by Moody, G., Pollard, T., & Moody, B.
  

Publications

• Harvard Electroencephalography Database by Moura Junior, V.; Reyna, M.; Hong, S.; Gupta, A.; Ghanta, M.; Sameni, R., et al.
  

Hecatomb Databases

Tutorials

• The Hecatomb Tutorial by Michael Roach
  

Publications

• No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study by Michael Roach,Adrian Cantu,Melissa Krizia Vieri,Matthew Cotten,Paul Kellam,My Phan,Lia van der Hoek,Michel Mandro,Floribert Tepage,Germain Mambandu,Gisele Musinya,Anne Laudisoit,Robert Colebunders,Robert Edwards, John L. Mokili
  

Indexes for Kaiju

Tutorials

• Quickstart Tutorial for downloading the index files and running Kaiju. by Peter Menzel
  

Publications

• Fast and sensitive taxonomic classification for metagenomics with Kaiju by Peter Menzel et al (2016)
  

Integrative Analysis of Lung Adenocarcinoma in Environment and Genetics Lung cancer Etiology (Phase 2)

Tools & Applications

• EAGLE - Environment And Genetics in Lung cancer Etiology by National Cancer Institute Division of Cancer Epidemiology and Genetics
  
• Genomic Data Commons by National Cancer Institute
  

LEarning biOchemical Prostate cAncer Recurrence from histopathology sliDes challenge (LEOPARD) Dataset

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• LEOPARD Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

NIH NCBI PubMed Central (PMC) Article Datasets - Full-Text Biomedical and Life Sciences Journal Articles on AWS

Tutorials

• Accessing PMC Article Datasets Using Amazon Web Services by NCBI PMC
  

Tools & Applications

• Extracting insights from PubMed articles using Amazon Q Business by Bharath Gunapati and Stefan Mationg
  

National Cancer Institute Center for Cancer Research - Diffuse Large B Cell Lymphoma (DLBCL) Genomics and Expression

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., et al.
  

OpenCRAVAT

Tutorials

• Changing the OpenCRAVAT store url by Kyle Moad
  

Tools & Applications

• OpenCRAVAT by Karchinlab
  

Oregon Health & Science University Chronic Neutrophilic Leukemia Dataset

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic landscape of neutrophilic leukemias of ambiguous diagnosis by Zhang H, Wilmot B, Bottomly D et al.
  

Pancreatic Cancer Organoid Profiling

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer by Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville TD, et al.
  

Protein Data Bank 3D Structural Biology Data

Publications

• Announcing the worldwide Protein Data Bank by Berman, H., Henrick, K. & Nakamura, H.
  
• Protein Data Bank: the single global archive for 3D macromolecular structure data by wwPDB consortium
  

REDASA COVID-19 Open Data

Tools & Applications

• Curadr - Curation Platform by REDASA Consortium, Imperial College London
  

Publications

• Using a Secure, Continually Updating, Web Source Processing Pipeline to Support the Real-Time Data Synthesis and Analysis of Scientific Literature: Development and Validation Study by Uddhav Vaghela, Simon Rabinowicz, Paris Bratsos, Guy Martin, Epameinondas Fritzilas, et al.
  

Reference data for HiFi human WGS

Tutorials

• PacBio WGS Variant Pipeline README by Pacific Biosciences of California, Inc
  

Tools & Applications

• Consolidated analysis with the PacBio WGS Variant Pipeline by Pacific Biosciences of California, Inc
  

Sounds of Central African landscapes

Publications

• Listen to the rainforest chorus that's helping scientists protect African elephants by Amazon Staff
  
• You can now hear rainforest sounds worldwide-here's why that matters by Rachel Fobar
  

TIGER Training

Tools & Applications

• TIGER Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

UniProt

Tutorials

• Exploring the UniProt protein knowledgebase with AWS Open Data and Amazon Neptune by Eric Greene, Rafa Xu, Yuan Shi (AWS)
  Amazon Neptune
• UniProt SPARQL by Swiss-Prot Group at SIB Swiss Institute of Bioinformatics
  

1000 Genomes

Publications

• Exploratory data analysis of genomic datasets using ADAM and Mango with Apache Spark on Amazon EMR by Alyssa Marrow
  

Allen Brain Observatory - Visual Coding AWS Public Data Set

Tutorials

• Use the Allen Brain Observatory – Visual Coding on AWS by Nika Keller, David Feng
  

Allen Institute for Neural Dynamics - Mouse Neuroanatomy and Physiology Data

Tutorials

• AIND Open Data Access by David Feng, Saskia de Vries
  

CIViC (Clinical Interpretation of Variants in Cancer)

Publications

• CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer by Malachi Griffith
  

CMS 2008-2010 Data Entrepreneurs’ Synthetic Public Use File (DE-SynPUF) in OMOP Common Data Model

Tutorials

• Create data science environments on AWS for health analysis using OHDSI by James Wiggins
  AWS CloudFormationAmazon EC2Amazon RDS
• Map clinical notes to the OMOP Common Data Model and healthcare ontologies using Amazon Comprehend Medical by James Wiggins
  Amazon ComprehendAWS CloudFormationAmazon EC2Amazon RDS
• Predict patient health outcomes using OHDSI and machine learning on AWS by James Wiggins
  AWS CloudFormationAmazon EC2Amazon RDS

Tools & Applications

• OHDSIonAWS by James Wiggins
  

COVID-19 Genome Sequence Dataset

Tools & Applications

• Download SRA sequence data using Amazon Web Services (AWS) by NCBI SRA
  

COVID-19 Open Research Dataset (CORD-19)

Tools & Applications

• COVID-19 Open Research Dataset Challenge (CORD-19) by Kaggle
  

Conformational Space of Short Peptides

Tutorials

• Intro to Conformational Space of Short Peptides by Sebastian Bassi and Virginia Gonzalez
  

GATK Test Data

Tools & Applications

• Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang
  

Global Biodiversity Information Facility (GBIF) Species Occurrences

Tutorials

• GBIF and Apache-Spark on AWS tutorial by John Waller
  Amazon EMR

Human Cancer Models Initiative (HCMI) Cancer Model Development Center

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Human PanGenomics Project

Publications

• Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes by Shafin et al (2020)
  

NYUMets Brain Dataset

Publications

• Longitudinal deep neural networks for assessing metastatic brain cancer on a massive open benchmark. by Link et al (2023)
  

Ohio State Cardiac MRI Raw Data (OCMR)

Tutorials

• OCMR Tutorial by Chong Chen
  

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

• ONT Dataset Tutorials by EPI2MELabs
  

RSNA Abdominal Trauma Detection (RSNA-ABT)

Publications

• The RSNA Abdominal Traumatic Injury CT (RATIC) Dataset by Rudie, Jeffrey D.
  

RSNA Cervical Spine Fracture Detection (RSNA-CSF) Dataset

Publications

• The RSNA Cervical Spine Fracture CT Dataset by Ming, Hui Lin
  

RSNA Intracranial Hemorrhage Detection

Publications

• Construction of a Machine Learning Dataset through Collaboration: The RSNA 2019 Brain CT Hemorrhage Challenge by Rudie, Jeffrey D.
  

RSNA Pulmonary Embolism Detection

Publications

• The RSNA Pulmonary Embolism CT Dataset by Colak, Errol
  

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD)

Tools & Applications

• Seattle Alzheimer’s Disease Brain Cell Atlas by Lein, E et al.
  

Synthea Coherent Data Set

Publications

• The “Coherent Data Set”: Combining Patient Data and Imaging in a Comprehensive Synthetic Health Record. by Walonoski J, Hall D, Bates KM, Farris MH, Dagher J, Downs ME, Sivek RT, Wellner B, Gregorowicz A, Hadley M, Campion FX, Levine L, Wacome K, Emmer G, Kemmer A, Malik M, Hughes J, Granger E, Russell S.
  

Tabula Muris

Publications

• Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. by Tabula Muris Consortium (2019)
  

Tabula Muris Senis

Tutorials

• Fast queries of scRNAseq datasets with Amazon Athena by Andrew Ang, James Golden, Lisa McFerrin, and Lee Pang
  Amazon AthenaAWS Glue

Tabula Sapiens

Publications

• The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans by The Tabula Sapiens Consortium, Stephen R Quake
  

UK Biobank Pharma Proteomics Project (UKB-PPP)

Publications

• Plasma proteomic associations with genetics and health in the UK Biobank by Sun B, Chiou J, Traylor M, Benner C, Hsu Y, Richardson T, et al
  

VitalDB

Publications

• VitalDB, a high-fidelity multi-parameter vital signs database in surgical patients by Hyung-Chul Lee, Yoonsang Park, Soo Bin Yoon, Seong Mi Yang, Dongnyeok Park, and Chul-Woo Jung
  

ZINC Database

Publications

• ZINC Database by John Irwin
  

iHART Whole Genome Sequencing Data Set

Publications

• Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks by Ruzzo et al. (2020)
  

recount3

Tutorials

• recount3 quick start guide by Leonardo Collado-Torres
  

Baby Open Brains (BOBs) Repository on AWS

Tutorials

• Downloading BOBs Repository Data from Amazon S3 Bucket by Lucille A. Moore
  

Tools & Applications

• BIBsnet by Timothy J. Hendrickson et al.
  

Publications

• BIBSNet: A Deep Learning Baby Image Brain Segmentation Network for MRI Scans by Timothy J. Hendrickson et al.
  

GenomeKit genomic data

Tutorials

• Quickstart by Deep Genomics
  

Tools & Applications

• An RNA foundation model enables discovery of disease mechanisms and candidate therapeutics by Albi Celaj, Alice Jiexin Gao, Tammy T.Y. Lau, Erle M. Holgersen, Alston Lo, Varun Lodaya, Christopher B. Cole, Robert E. Denroche, Carl Spickett, Omar Wagih, Pedro O. Pinheiro, Parth Vora, Pedrum Mohammadi-Shemirani, Steve Chan, Zach Nussbaum, Xi Zhang, Helen Zhu, Easwaran Ramamurthy, Bhargav Kanuparthi, Michael Iacocca, Diane Ly, Ken Kron, Marta Verby, Kahlin Cheung-Ong, Zvi Shalev, Brandon Vaz, Sakshi Bhargava, Farhan Yusuf, Sharon Samuel, Sabriyeh Alibai, Zahra Baghestani, Xinwen He, Kirsten Krastel, Oladipo Oladapo, Amrudha Mohan, Arathi Shanavas, Magdalena Bugno, Jovanka Bogojeski, Frank Schmitges, Carolyn Kim, Solomon Grant, Rachana Jayaraman, Tehmina Masud, Amit Deshwar, Shreshth Gandhi, Brendan J. Frey
  

NASA SOTERIA Simulation Testbed Data

Tools & Applications

• Python Processing Code by Tyler Fettrow
  

Publications

• SOTERIA Simulation - Experimental Methods, Data Processing, and Data Quality by Tyler Fettrow, Chad Stephens, Lance Prinzel, Jon Holbrook, Sepher Bastami, Michael Stewart, Kathryn Ballard, Daniel Kiggins
  

Platinum Pedigree

Publications

• A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree by Porubsky et. al.
  
• The Platinum Pedigree: A long-read benchmark for genetic variants by Kronenberg et. al.
  

AWS iGenomes

Tools & Applications

• nf-core analysis pipelines by Phil Ewels
  

Boltz-1 Training Data

Publications

• Boltz-1: Democratizing Biomolecular Interaction Modeling by J Wohlwend, G Corso, S Passaro, M Reveiz, K Leidal, W Swiderski, T Portnoi, I Chinn, J Silterra, T Jaakkola, R Barzilay
  

Google Brain Genomics Sequencing Dataset for Benchmarking and Development

Publications

• An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development by Baid G., Nattestad M., Kolesnikov A., Goel S., Yang H., Chang P., and Carroll A (2020)