OpenPBTA: The Open Pediatric Brain Tumor Atlas.

Autor: Shapiro JA; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA., Gaonkar KS; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Spielman SJ; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.; Rowan University, Glassboro, NJ 08028, USA., Savonen CL; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA., Bethell CJ; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA., Jin R; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Rathi KS; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Zhu Y; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Egolf LE; Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Farrow BK; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Miller DP; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Yang Y; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA., Koganti T; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Noureen N; Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA., Koptyra MP; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Duong N; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Santi M; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA., Kim J; Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA., Robins S; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Storm PB; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Mack SC; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA., Lilly JV; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Xie HM; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Jain P; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Raman P; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Rood BR; Children's National Research Institute, Washington, DC 20012, USA.; George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA., Lulla RR; Division of Hematology/Oncology, Hasbro Children's Hospital, Providence, RI 02903, USA.; Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA., Nazarian J; Children's National Research Institute, Washington, DC 20012, USA.; George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA.; Department of Pediatrics, University of Zurich, Zurich, Switzerland., Kraya AA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Vaksman Z; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Heath AP; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Kline C; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Scolaro L; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Viaene AN; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA., Huang X; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Way GP; Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA., Foltz SM; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA., Zhang B; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Poetsch AR; Biotechnology Center, Technical University Dresden, Dresden, Germany.; National Center for Tumor Diseases, Dresden, Germany., Mueller S; Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA., Ennis BM; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Prados M; University of California, San Francisco, San Francisco, CA 94115, USA., Diskin SJ; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA., Zheng S; Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA., Guo Y; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Kannan S; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Waanders AJ; Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA., Margol AS; Division of Hematology and Oncology, Children's Hospital of Los Angeles, Los Angeles, CA 90027, USA.; Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA., Kim MC; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Hanson D; Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA.; Hackensack University Medical Center, Hackensack, NJ 07601, USA., Van Kuren N; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Wong J; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Kaufman RS; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Coleman N; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Blackden C; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Cole KA; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA.; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA., Mason JL; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Madsen PJ; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Koschmann CJ; Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA.; Pediatric Hematology Oncology, Mott Children's Hospital, Ann Arbor, MI 48109, USA., Stewart DR; Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA., Wafula E; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Brown MA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Resnick AC; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Greene CS; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.; Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA.; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA., Rokita JL; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA., Taroni JN; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.

Publikováno v: Cell genomics [Cell Genom] 2023 May 31; Vol. 3 (7), pp. 100340. Date of Electronic Publication: 2023 May 31 (Print Publication: 2023).

The expanding network of mineral chemistry throughout earth history reveals global shifts in crustal chemistry during the Proterozoic.

Autor: Moore EK; Department of Environmental Science, School of Earth and the Environment, Rowan University, Glassboro, NJ, USA. mooreek@rowan.edu., Golden JJ; Department of Geosciences, University of Arizona, Tucson, AZ, USA., Morrison SM; Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC, USA., Hao J; CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China.; CAS Center for Excellence in Comparative Planetology, USTC, Hefei, 230026, Anhui, China.; Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA., Spielman SJ; Department of Biological Sciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, USA.

Publikováno v: Scientific reports [Sci Rep] 2022 Mar 23; Vol. 12 (1), pp. 4956. Date of Electronic Publication: 2022 Mar 23.

Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.

Autor: Spielman SJ; Department of Biological Sciences, Rowan University, Glassboro, NJ.

Publikováno v: Molecular biology and evolution [Mol Biol Evol] 2020 Jul 01; Vol. 37 (7), pp. 2110-2123.

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.

Autor: Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Poon AFY; Pathology and Laboratory Medicine, Western University, London, ON, Canada., Velazquez R; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Weaver S; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Hepler NL; 10× Genomics, Pleasanton, CA., Murrell B; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden., Shank SD; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Magalis BR; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA., Bouvier D; Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA., Nekrutenko A; Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA., Wisotsky S; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.; Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC., Spielman SJ; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.; Rowan University, Glassboro, NJ., Frost SDW; Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.; The Alan Turing Institute, London, United Kingdom., Muse SV; Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC.

Publikováno v: Molecular biology and evolution [Mol Biol Evol] 2020 Jan 01; Vol. 37 (1), pp. 295-299.

Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.

Autor: Maddamsetti R; Department of Biological Sciences, Old Dominion University, Norfolk, Virginia., Johnson DT; Division of Biological Sciences, University of California San Diego, La Jolla, California., Spielman SJ; Department of Biological Sciences, Rowan University, Glassboro, New Jersey., Petrie KL; Division of Biological Sciences, University of California San Diego, La Jolla, California.; Earth-Life Science Institute, Tokyo Institute of Technology, Japan., Marks DS; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts., Meyer JR; Division of Biological Sciences, University of California San Diego, La Jolla, California.

Publikováno v: Evolution; international journal of organic evolution [Evolution] 2018 Oct; Vol. 72 (10), pp. 2234-2243. Date of Electronic Publication: 2018 Sep 11.