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Ten simple rules for reproducible research in jupyter notebooks

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arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

Phosphor-IWS1-dependent U2AF2 splicing regulates trafficking of CAR-E-positive intronless gene mRNAs and sensitivity to viral infection

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Communications biology

Communications biology 2021年第1期4卷 1179页

作者： Georgios I Laliotis Adam D Kenney Evangelia Chavdoula Arturo Orlacchio Abdul Kaba Alessandro La Ferlita Vollter Anastas Christos Tsatsanis Joal D Beane Lalit Sehgal Vincenzo Coppola Jacob S Yount Philip N Tsichlis Department of Cancer Biology and Genetics The Ohio State University College of Medicine Columbus Columbus OH 43210 USA. glaliot1@jhmi.edu. The Ohio State University Comprehensive Cancer Center Columbus OH 43210 USA. glaliot1@jhmi.edu. University of Crete School of Medicine Heraklion Crete 71500 Greece. glaliot1@jhmi.edu. Sidney Kimmel Comprehensive Cancer Center and Department of Oncology Johns Hopkins School of Medicine Baltimore MD 21205 USA. glaliot1@jhmi.edu. The Ohio State University Comprehensive Cancer Center Columbus OH 43210 USA. Department of Microbial Infection and Immunity and Infectious Diseases Institute The Ohio State University Columbus OH 43210 USA. Department of Cancer Biology and Genetics The Ohio State University College of Medicine Columbus Columbus OH 43210 USA. Department of Clinical and Experimental Medicine Bioinformatics Unit University of Catania Catania 95131 Italy. Tufts Graduate School of Biomedical Sciences Program in Genetics Boston MA 02111 USA. University of Crete School of Medicine Heraklion Crete 71500 Greece. Institute of Molecular Biology and Biotechnology Heraklion Crete 70013 Greece. Department of Surgery Division of Surgical Oncology Columbus OH 43210 USA. Department of Medicine Division of Hematology The Ohio State University Columbus OH 43210 USA. Department of Cancer Biology and Genetics The Ohio State University College of Medicine Columbus Columbus OH 43210 USA. Philip.tsichlis@osumc.edu. The Ohio State University Comprehensive Cancer Center Columbus OH 43210 USA. Philip.tsichlis@osumc.edu. Tufts Graduate School of Biomedical Sciences Program in Genetics Boston MA 02111 USA. Philip.tsichlis@osumc.edu.

AKT-phosphorylated IWS1 promotes Histone H3K36 trimethylation and alternative RNA splicing of target genes, including the U2AF65 splicing factor-encoding U2AF2. The predominant U2AF2 transcript, upon IWS1 phosphorylation block, lacks the RS-domain-encoding exon 2, and encodes a protein which fails to bind Prp19. Here we show that although both U2AF65 isoforms bind intronless mRNAs containing cytoplasmic accumulation region elements (CAR-E), only the RS domain-containing U2AF65 recruits Prp19 and promotes their nuclear export. The loading of U2AF65 to CAR-Elements was RS domain-independent, but RNA PolII-dependent. Virus- or poly(I:C)-induced type I IFNs are encoded by genes targeted by the pathway. IWS1 phosphorylation-deficient cells therefore, express reduced levels of IFNα1/IFNβ1 proteins, and exhibit enhanced sensitivity to infection by multiple cytolytic viruses. Enhanced sensitivity of IWS1-deficient cells to Vesicular Stomatitis Virus and Reovirus resulted in enhanced apoptotic cell death via caspase activation. Inhibition of this pathway may therefore sensitize cancer cells to oncolytic viruses.

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A structural variation reference for medical and population genetics (vol 581, pg 444, 2020)

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NATURE 2021年第7846期590卷 E55-E55页

作者： Collins, Ryan L. Brand, Harrison Karczewski, Konrad J. Zhao, Xuefang Alfoldi, Jessica Francioli, Laurent C. Khera, Amit V. Lowther, Chelsea Gauthier, Laura D. Wang, Harold Watts, Nicholas A. Solomonson, Matthew O'Donnell-Luria, Anne Baumann, Alexander Munshi, Ruchi Walker, Mark Whelan, Christopher W. Huang, Yongqing Brookings, Ted Sharpe, Ted Stone, Matthew R. Valkanas, Elise Fu, Jack Tiao, Grace Laricchia, Kristen M. Ruano-Rubio, Valentin Stevens, Christine Gupta, Namrata Cusick, Caroline Margolin, Lauren Taylor, Kent D. Lin, Henry J. Rich, Stephen S. Post, Wendy S. Chen, Yii-Der Ida Rotter, Jerome I. Nusbaum, Chad Philippakis, Anthony Lander, Eric Gabriel, Stacey Neale, Benjamin M. Kathiresan, Sekar Daly, Mark J. Banks, Eric MacArthur, Daniel G. Talkowski, Michael E. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Division of Medical Sciences Harvard Medical School Boston MA USA Department of Neurology Massachusetts General Hospital and Harvard Medical School Boston MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Department of Medicine Harvard Medical School Boston MA USA Data Science Platform Broad Institute of MIT and Harvard Cambridge MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Cardiac Arrhythmia Service Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Division of Cardiology Massachusetts General Hospital Boston MA USA Cardiovascular Disease Initiative Broad Institute of MIT and Harvard Cambridge MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland Department of Public Health Faculty of Medicine University

Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates

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arXiv 2017年

作者： George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Short Abstract: Is it better to be left- or right-handed? The answer depends on whether the goal is making a handshake or winning a boxing match. The need for coordination favors the handedness of the majority, but being different could also provide an advantage. The same rules could apply to microbial colonies and cancer tumors. Like humans, cells often have handedness (chirality) that reflects the lack of mirror symmetry in their shapes or movement patterns. We find that cells gain a substantial fitness advantage by either increasing the magnitude of their chirality or switching to the opposite handedness. Selection for specific chirality is mediated by the formation of bulges along the colony edge in regions where cells with different chiralities meet. Long Abstract: Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers' equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in

关键词： Chirality

The importance of transparency and reproducibility in artificial intelligence research

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arXiv 2020年

作者： Haibe-Kains, Benjamin Adam, George Alexandru Hosny, Ahmed Khodakarami, Farnoosh Waldron, Levi Wang, Bo McIntosh, Chris Kundaje, Anshul Greene, Casey S. Hoffman, Michael M. Leek, Jeffrey T. Huber, Wolfgang Brazma, Alvis Pineau, Joelle Tibshirani, Robert Hastie, Trevor Ioannidis, John P.A. Quackenbush, John Aerts, Hugo J.W.L. Princess Margaret Cancer Centre University Health Network TorontoON Canada Department of Medical Biophysics University of Toronto TorontoON Canada Department of Computer Science University of Toronto TorontoON Canada Ontario Institute for Cancer Research TorontoON Canada Vector Institute for Artificial Intelligence TorontoON Canada Program Brigham and Women's Hospital Harvard Medical School BostonMA United States Radiation Oncology and Radiology Dana-Farber Cancer Institute Brigham and Women's Department of Epidemiology and Biostatistics Institute for Implementation Science in Population Health CUNY Graduate School of Public Health and Health Policy New YorkNY United States Peter Munk Cardiac Centre University Health Network TorontoON Canada Hospital Harvard Medical School BostonMA United States Department of Genetics Stanford University School of Medicine StanfordCA United States Dept. of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Childhood Cancer Data Lab Alex's Lemonade Stand Foundation PhiladelphiaPA United States Department of Biostatistics Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany European Molecular Biology Laboratory European Bioinformatics Institute EMBL-EBI Hinxton United Kingdom McGill University MontrealQC Canada Montreal Institute for Learning Algorithms QC Canada StanfordCA United States Department of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Departments of Medicine of Health Research and Policy and of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Department of Statistics Stanford University School of Humanities and Sciences StanfordCA United States Department of Biostatistics Harvard T.H Chan School of Public Health BostonMA Un

In their study, McKinney et al. showed the high potential of artificial intelligence for breast cancer screening. However, the lack of detailed methods and computer code undermines its scientific value. We identify obstacles hindering transparent and reproducible AI research as faced by McKinney et al and provide solutions with implications for the broader field. Copyright © 2020, The Authors. All rights reserved.

关键词： Artificial intelligence

Interactions between species introduce spurious associations in microbiome studies

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arXiv 2017年

作者： Menon, Rajita Ramanan, Vivek Korolev, Kirill S. Department of Physics Boston University BostonMA United States BRITE Bioinformatics REU Program Boston University BostonMA United States Graduate Program in Bioinformatics Boston University BostonMA United States Department of Biology and Computer Science Swarthmore College SwarthmorePA United States

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease. Copyright © 2017, The Authors. All rights reserved.

关键词： Association reactions

Void distributions reveal structural link between jammed packings and protein cores

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arXiv 2018年

作者： Treado, John D. Mei, Zhe Regan, Lynne O'Hern, Corey S. Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Integrated Graduate Program in Physical & Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction φ ≈ 0.56, which is the same as dense, random packing of amino acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. By measuring the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation, we show that void percolation in packings of amino acid-shaped particles and protein cores belong to the same universality class, which is different from that for void percolation in jammed sphere packings. We propose that the connected void regions of proteins are a defining feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations. Copyright © 2018, The Authors. All rights reserved.

关键词： Amino acids

Author Correction: African-centric TP53 variant increases iron accumulation and bacterial pathogenesis but improves response to malaria toxin

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Nature communications 2020年第1期11卷 1541页

作者： Kumar Sachin Singh Julia I-Ju Leu Thibaut Barnoud Prashanthi Vonteddu Keerthana Gnanapradeepan Cindy Lin Qin Liu James C Barton Andrew V Kossenkov Donna L George Maureen E Murphy Farokh Dotiwala Vaccine and Immunotherapy Center The Wistar Institute Philadelphia PA 19104 USA. Department of Genetics The Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA. Program in Molecular and Cellular Oncogenesis The Wistar Institute Philadelphia PA 19104 USA. Graduate Group in Biochemistry and Molecular Biophysics The Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA. Program in Immunology Microenvironment and Metastasis The Wistar Institute Philadelphia PA 19104 USA. Southern Iron Disorders Center Birmingham AL 35209 USA and Department of Medicine University of Alabama at Birmingham Birmingham AL 35294 USA. Bioinformatics Facility The Wistar Institute Philadelphia PA 19104 USA. Department of Genetics The Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania Philadelphia PA 19104 USA. georged@pennmedicine.upenn.edu. Program in Molecular and Cellular Oncogenesis The Wistar Institute Philadelphia PA 19104 USA. mmurphy@***. Vaccine and Immunotherapy Center The Wistar Institute Philadelphia PA 19104 USA. fdotiwala@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants

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Nature communications 2020年第1期11卷 4426页

作者： Margaret K R Donovan Agnieszka D'Antonio-Chronowska Matteo D'Antonio Kelly A Frazer Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA 92093 USA. Department of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA. Department of Pediatrics and Rady Children's Hospital University of California San Diego La Jolla CA 92093 USA. Department of Pediatrics and Rady Children's Hospital University of California San Diego La Jolla CA 92093 USA. madantonio@health.ucsd.edu. Department of Pediatrics and Rady Children's Hospital University of California San Diego La Jolla CA 92093 USA. kafrazer@health.ucsd.edu. Institute for Genomic Medicine University of California San Diego La Jolla CA 92093 USA. kafrazer@health.ucsd.edu.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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