TY - JOUR T1 - Reporting guidelines for human microbiome research: the STORMS checklist. JF - Nat Med Y1 - 2021 A1 - Mirzayi, Chloe A1 - Renson, Audrey A1 - Zohra, Fatima A1 - Elsafoury, Shaimaa A1 - Geistlinger, Ludwig A1 - Kasselman, Lora J A1 - Eckenrode, Kelly A1 - van de Wijgert, Janneke A1 - Loughman, Amy A1 - Marques, Francine Z A1 - MacIntyre, David A A1 - Arumugam, Manimozhiyan A1 - Azhar, Rimsha A1 - Beghini, Francesco A1 - Bergstrom, Kirk A1 - Bhatt, Ami A1 - Bisanz, Jordan E A1 - Braun, Jonathan A1 - Bravo, Hector Corrada A1 - Buck, Gregory A A1 - Bushman, Frederic A1 - Casero, David A1 - Clarke, Gerard A1 - Collado, Maria Carmen A1 - Cotter, Paul D A1 - Cryan, John F A1 - Demmer, Ryan T A1 - Devkota, Suzanne A1 - Elinav, Eran A1 - Escobar, Juan S A1 - Fettweis, Jennifer A1 - Finn, Robert D A1 - Fodor, Anthony A A1 - Forslund, Sofia A1 - Franke, Andre A1 - Furlanello, Cesare A1 - Gilbert, Jack A1 - Grice, Elizabeth A1 - Haibe-Kains, Benjamin A1 - Handley, Scott A1 - Herd, Pamela A1 - Holmes, Susan A1 - Jacobs, Jonathan P A1 - Karstens, Lisa A1 - Knight, Rob A1 - Knights, Dan A1 - Koren, Omry A1 - Kwon, Douglas S A1 - Langille, Morgan A1 - Lindsay, Brianna A1 - McGovern, Dermot A1 - McHardy, Alice C A1 - McWeeney, Shannon A1 - Mueller, Noel T A1 - Nezi, Luigi A1 - Olm, Matthew A1 - Palm, Noah A1 - Pasolli, Edoardo A1 - Raes, Jeroen A1 - Redinbo, Matthew R A1 - Rühlemann, Malte A1 - Balfour Sartor, R A1 - Schloss, Patrick D A1 - Schriml, Lynn A1 - Segal, Eran A1 - Shardell, Michelle A1 - Sharpton, Thomas A1 - Smirnova, Ekaterina A1 - Sokol, Harry A1 - Sonnenburg, Justin L A1 - Srinivasan, Sujatha A1 - Thingholm, Louise B A1 - Turnbaugh, Peter J A1 - Upadhyay, Vaibhav A1 - Walls, Ramona L A1 - Wilmes, Paul A1 - Yamada, Takuji A1 - Zeller, Georg A1 - Zhang, Mingyu A1 - Zhao, Ni A1 - Zhao, Liping A1 - Bao, Wenjun A1 - Culhane, Aedin A1 - Devanarayan, Viswanath A1 - Dopazo, Joaquin A1 - Fan, Xiaohui A1 - Fischer, Matthias A1 - Jones, Wendell A1 - Kusko, Rebecca A1 - Mason, Christopher E A1 - Mercer, Tim R A1 - Sansone, Susanna-Assunta A1 - Scherer, Andreas A1 - Shi, Leming A1 - Thakkar, Shraddha A1 - Tong, Weida A1 - Wolfinger, Russ A1 - Hunter, Christopher A1 - Segata, Nicola A1 - Huttenhower, Curtis A1 - Dowd, Jennifer B A1 - Jones, Heidi E A1 - Waldron, Levi KW - Computational Biology KW - Dysbiosis KW - Humans KW - Microbiota KW - Observational Studies as Topic KW - Research Design KW - Translational Science, Biomedical AB -

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

VL - 27 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34789871?dopt=Abstract ER - TY - JOUR T1 - Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. JF - Nat Commun Y1 - 2019 A1 - Menden, Michael P A1 - Wang, Dennis A1 - Mason, Mike J A1 - Szalai, Bence A1 - Bulusu, Krishna C A1 - Guan, Yuanfang A1 - Yu, Thomas A1 - Kang, Jaewoo A1 - Jeon, Minji A1 - Wolfinger, Russ A1 - Nguyen, Tin A1 - Zaslavskiy, Mikhail A1 - Jang, In Sock A1 - Ghazoui, Zara A1 - Ahsen, Mehmet Eren A1 - Vogel, Robert A1 - Neto, Elias Chaibub A1 - Norman, Thea A1 - Tang, Eric K Y A1 - Garnett, Mathew J A1 - Veroli, Giovanni Y Di A1 - Fawell, Stephen A1 - Stolovitzky, Gustavo A1 - Guinney, Justin A1 - Dry, Jonathan R A1 - Saez-Rodriguez, Julio KW - ADAM17 Protein KW - Antineoplastic Combined Chemotherapy Protocols KW - Benchmarking KW - Biomarkers, Tumor KW - Cell Line, Tumor KW - Computational Biology KW - Datasets as Topic KW - Drug Antagonism KW - Drug Resistance, Neoplasm KW - Drug Synergism KW - Genomics KW - Humans KW - Molecular Targeted Therapy KW - mutation KW - Neoplasms KW - pharmacogenetics KW - Phosphatidylinositol 3-Kinases KW - Phosphoinositide-3 Kinase Inhibitors KW - Treatment Outcome AB -

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.

VL - 10 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/31209238?dopt=Abstract ER -