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1. Full Text Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
by Ewing, Adam D and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P'Ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and Kellen, Michael R and Norman, Thea C and Haussler, David and Friend, Stephen H and Stolovitzky, Gustavo and Margolin, Adam A and Stuart, Joshua M and Boutros, Paul C and ICGC-TCGA Dream Somatic Mutation and ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants
Nature methods, ISSN 1548-7091, 06/2015, Volume 12, Issue 7, pp. 623 - 630
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Crowdsourcing | Algorithms | Neoplasms - genetics | Humans | Benchmarking | Polymorphism, Single Nucleotide | Genome | Care and treatment | Analysis | Genomes | Aberration | Research | Simulation methods | Cancer | Index Medicus
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2. Full Text Enabling transparent and collaborative computational analysis of 12 tumor types within the Cancer Genome Atlas
by Omberg, Larsson and Ellrott, Kyle and Yuan, Yuan and Kandoth, Cyriac and Wong, Chris and Kellen, Michael R and Friend, Stephen H and Stuart, Josh and Liang, Han and Margolin, Adam A
Nature genetics, ISSN 1061-4036, 10/2013, Volume 45, Issue 10, pp. 1121 - 1126
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Reproducibility of Results | Neoplasms - genetics | Humans | Cooperative Behavior | Neoplasms - classification | Genome | Neoplasms - pathology | Genetic aspects | Research | Pancreatic cancer | Risk factors | Cancer | Biomedical research | Research & development--R&D | Collaboration | DNA methylation | Software | Models | Genomes | Mutation | Comparative analysis | Gene expression | Programming languages | Index Medicus
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3. Full Text TumorMap: Exploring the molecular similarities of cancer samples in an interactive portal
by Newton, Yulia and Novak, Adam M and Swatloski, Teresa and McColl, Duncan C and Chopra, Sahil and Graim, Kiley and Weinstein, Alana S and Baertsch, Robert and Salama, Sofie R and Ellrott, Kyle and Chopra, Manu and Goldstein, Theodore C and Haussler, David and Morozova, Olena and Stuart, Joshua M
Cancer research (Chicago, Ill.), ISSN 0008-5472, 11/2017, Volume 77, Issue 21, pp. e111 - e114
Life Sciences & Biomedicine | Oncology | Science & Technology | User-Computer Interface | Computational Biology - methods | Genetic Predisposition to Disease - genetics | Reproducibility of Results | Gene Regulatory Networks - genetics | Humans | Genome, Human - genetics | Neoplasms - genetics | Chromosome Mapping - methods | Software | Mutation | Genomics - methods | Neoplasms - pathology | Maps | Statistical analysis | Similarity | Interrogation | Browsing | Computer applications | Genomes | Statistical methods | Gene mapping | Cancer | Index Medicus
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4. Full Text Abstract 926: Multi-Center Mutation Calling in Multiple Cancers: The MC3 Project
by Ellrott, Kyle and Bailey, Mathew and Saksena, Gordon and Covington, Kyle and Kandoth, Cyriac and Stewart, Chip and McLellan, Michael and Sofia, Heidi and Hutter, Carolyn and Getz, Gad and Wheeler, David and Ding, Li
Cancer research (Chicago, Ill.), ISSN 0008-5472, 07/2018, Volume 78, Issue 13 Supplement, pp. 926 - 926
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5. Full Text neoepiscope improves neoepitope prediction with multivariant phasing
by Wood, Mary A and Nguyen, Austin and Struck, Adam J and Ellrott, Kyle and Nellore, Abhinav and Thompson, Reid F
Bioinformatics, ISSN 1367-4803, 02/2020, Volume 36, Issue 3, pp. 713 - 720
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Index Medicus
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6. Full Text Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges
by Ellrott, Kyle and Buchanan, Alex and Creason, Allison and Mason, Michael and Schaffter, Thomas and Hoff, Bruce and Eddy, James and Chilton, John M and Yu, Thomas and Stuart, Joshua M and Saez-Rodriguez, Julio and Stolovitzky, Gustavo and Boutros, Paul C and Guinney, Justin
Genome Biology, ISSN 1474-7596, 09/2019, Volume 20, Issue 1, pp. 195 - 195
Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Benchmarking | Reproducibility of Results | Algorithms | Models, Biological | Information Dissemination | Medical research | Cloud computing | Biomedical research | Self evaluation | Mammography | Breast cancer | Gene expression | Computer programs | Deep learning | Datasets | Problems | Information sharing | Index Medicus
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7. Full Text The UCSC cancer genomics browser: Update 2013
by Goldman, Mary and Craft, Brian and Swatloski, Teresa and Ellrott, Kyle and Cline, Melissa and Diekhans, Mark and Ma, Singer and Wilks, Chris and Stuart, Josh and Haussler, David and Zhu, Jingchun
Nucleic acids research, ISSN 0305-1048, 01/2013, Volume 41, Issue 1, pp. D949 - D954
Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Cell Line, Tumor | Databases, Genetic | Internet | Neoplasms - genetics | Genomics | Humans | Index Medicus
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8. Full Text Population-level distribution and putative immunogenicity of cancer neoepitopes
by Wood, Mary A and Paralkar, Mayur and Paralkar, Mihir P and Nguyen, Austin and Struck, Adam J and Ellrott, Kyle and Margolin, Adam and Nellore, Abhinav and Thompson, Reid F
BMC cancer, ISSN 1471-2407, 04/2018, Volume 18, Issue 1, pp. 414 - 414
Neoantigens | Immunogenicity | Neoepitopes | Immunotherapy | TCGA | Life Sciences & Biomedicine | Oncology | Science & Technology | Amino Acid Sequence | Antigens, Neoplasm - genetics | Epitope Mapping | Peptides - chemistry | Antigens, Neoplasm - immunology | Humans | Peptides - immunology | Peptides - genetics | Epitopes - genetics | Epitopes - immunology | Neoplasms - therapy | Neoplasms - genetics | Neoplasms - immunology | Alleles | ROC Curve | Epitopes - chemistry | Genomics - methods | Care and treatment | Usage | Immune response | Analysis | Genetic aspects | Research | Cancer | Medical research | Peptides | Genomics | Melanoma | Medicine, Experimental | Antigenic determinants | Protein binding | Index Medicus
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9. Full Text The cancer genome atlas pan-cancer analysis project
by Sander, Chris and Davis, Caleb and Drummond, Jennifer and Wheeler, David and Balasundaram, Miruna and Guin, Ranabir and Robertson, A Gordon and Thiessen, Nina and Cherniack, Andrew D and Freeman, Samuel S and Jung, Joonil and Meyerson, Matthew and Pedamallu, Chandra Sekhar and Lander, Eric S and Luquette, Lovelace J and Santoso, Netty and Xi, Ruibin and Xu, Andrew W and Parker, Joel S and Silva, Grace O and Waring, Scot and Bodenheimer, Tom and Mose, Lisle E and Cibulskis, Kristian and Zhang, Jianhua and Sougnez, Carrie and Wang, Min and Doddapaneni, Harsha Vardhan and Gunaratne, Preethi and Han, Yi and Kovar, Christie and Reid, Jeffrey and Lin, Pei and Stojanov, Petar and Zou, Lihua and Stewart, Chip and Kreisberg, Richard and Miller, Michael and Reynolds, Sheila M and Amin, Samirkumar and Wu, Chang-Jiun and Aldape, Kenneth and Broom, Bradley and Han, Leng and Lerner, Seth and Melott, James and Wong, Andrew and Yang, Yang and Yoshihara, Kosuke and Yuan, Yuan and Yung, Alfred K and Gross, Benjamin and Kahles, Andre and Lehmann, Kjong-Van and Ramirez, Ricardo and Rätsch, Gunnar and Shen, Ronglai and Sumer, S Onur and Spellman, Paul and Benz, Christopher and Paull, Evan and Sokolov, Artem and Hamilton, Stanley R and Abbott, Scott and Delehaunty, Kim and Kandoth, Cyriac and Ley, Timothy J and Lin, Ling and Lu, Charles and Magrini, Vincent J and Mardis, Elaine R and O'Laughlin, Michelle and Pohl, Craig and Wendl, Michael C and Wylie, Todd and Burton, Robert and Jensen, Mark A and Pihl, Todd and Pot, David and Wan, Yunhu and Gastier-Foster, Julie M and Helsel, Carmen and Leraas, Kristen M and Lichtenberg, Tara M and Sharpe, Samantha and Davidsen, Tanja and Eley, Greg and Staudt, Louis and Raphael, Benjamin J and Leiserson, Mark D.M and Noushmehr, Houtan and Wolf, Denise and Anastassiou, Dimitris and Yang, Tai-Hsien Ou and Lopez-Bigas, Nuria and Li, Wei and Hamilton, Mark and McGuire, Sean and Nelander, Sven and Kling, Teresia and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and The Cancer Genome Atlas Research Network and Department of Mathematical Sciences, Mathematical Statistics and Naturvetenskapliga fakulteten and Institutionen för matematiska vetenskaper, matematisk statistik and Faculty of Sciences and Göteborgs universitet and Gothenburg University
Nature genetics, ISSN 1061-4036, 10/2013, Volume 45, Issue 10, pp. 1113 - 1120
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Gene Expression Profiling | Neoplasms - genetics | Genome | Neoplasms - pathology | Humans | Medical research | Breast cancer | Mutation | Genomics | Tumors | Index Medicus | Genetik | Medicinsk genetik | Medical Genetics | Genetics
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10. Full Text A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
by Wagner, Alex H and Walsh, Brian and Mayfield, Georgia and Tamborero, David and Sonkin, Dmitriy and Krysiak, Kilannin and Deu-Pons, Jordi and Duren, Ryan P and Gao, Jianjiong and McMurry, Julie and Patterson, Sara and del Vecchio Fitz, Catherine and Pitel, Beth A and Sezerman, Ozman U and Ellrott, Kyle and Warner, Jeremy L and Rieke, Damian T and Aittokallio, Tero and Cerami, Ethan and Ritter, Deborah I and Schriml, Lynn M and Freimuth, Robert R and Haendel, Melissa and Raca, Gordana and Madhavan, Subha and Baudis, Michael and Beckmann, Jacques S and Dienstmann, Rodrigo and Chakravarty, Debyani and Li, Xuan Shirley and Mockus, Susan and Elemento, Olivier and Schultz, Nikolaus and Lopez-Bigas, Nuria and Lawler, Mark and Goecks, Jeremy and Griffith, Malachi and Griffith, Obi L and Margolin, Adam A and Variant Interpretation For Canc Co and Variant Interpretation for Cancer Consortium
Nature genetics, ISSN 1061-4036, 04/2020, Volume 52, Issue 4, pp. 448 - 457
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Diploidy | Knowledge Bases | Neoplasms - genetics | Humans | Databases, Genetic | Genetic Variation - genetics | Genomics - methods | Precision Medicine - methods | Knowledge bases (artificial intelligence) | Ontology | Genomics | Biomarkers | Oncology | Kinases | Cancer | Index Medicus | Analysis | Genetics research | Medicin och hälsovetenskap
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11. Full Text Germline contamination and leakage in whole genome somatic single nucleotide variant detection
by Sendorek, Dorota H and Caloian, Cristian and Ellrott, Kyle and Bare, J.Christopher and Yamaguchi, Takafumi N and Ewing, Adam D and Houlahan, Kathleen E and Norman, Thea C and Margolin, Adam A and Stuart, Joshua M and Boutros, Paul C
BMC bioinformatics, ISSN 1471-2105, 01/2018, Volume 19, Issue 1, pp. 28 - 28
Germline leakage | Patient identifiability | Next-generation sequencing | Germline contamination | SNV | Mutation calling | Cancer genomics | Single nucleotide variant | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | Mathematical & Computational Biology | Medical research | Analysis | Medicine, Experimental | Genetic aspects | Nucleotides | Research | Nucleotide sequencing | Single nucleotide polymorphisms | DNA sequencing | Cancer | Index Medicus
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