Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation.

Autor: Stahlberg EA; Cancer Data Science Initiatives, Frederick National Laboratory for Cancer Research, Frederick, MD, United States., Abdel-Rahman M; Department of Ophthalmology and Visual Sciences, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, United States., Aguilar B; Institute for Systems Biology, Seattle, WA, United States., Asadpoure A; Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, United States., Beckman RA; Innovation Center for Biomedical Informatics, Georgetown University, Washington DC, United States., Borkon LL; Cancer Data Science Initiatives, Frederick National Laboratory for Cancer Research, Frederick, MD, United States., Bryan JN; Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, United States., Cebulla CM; Department of Ophthalmology and Visual Sciences, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, United States., Chang YH; Department of Biomedical Engineering and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, United States., Chatterjee A; School of Statistics, University of Minnesota, Minneapolis, MN, United States., Deng J; Department of Therapeutic Radiology, Yale University School of Medicine, Yale University, New Haven, CT, United States., Dolatshahi S; Department of Biomedical Engineering, University of Virginia, Charlottesville VA, United States., Gevaert O; Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, United States., Greenspan EJ; Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States., Hao W; Department of Mathematics, The Pennsylvania State University, University Park, PA, United States., Hernandez-Boussard T; Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, United States., Jackson PR; Mathematical NeuroOncology Lab, Precision Neurotherapeutics Innovation Program, Mayo Clinic Arizona, Phoenix, AZ, United States., Kuijjer M; Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway University of Oslo, Oslo, Norway., Lee A; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States., Macklin P; Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, United States., Madhavan S; Innovation Center for Biomedical Informatics, Georgetown University, Washington DC, United States., McCoy MD; Innovation Center for Biomedical Informatics, Georgetown University, Washington DC, United States., Mohammad Mirzaei N; Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA, United States., Razzaghi T; School of Industrial and Systems Engineering, The University of Oklahoma, Norman, OK, United States., Rocha HL; Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, United States., Shahriyari L; Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA, United States., Shmulevich I; Institute for Systems Biology, Seattle, WA, United States., Stover DG; Division of Medical Oncology and Department of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States., Sun Y; Department of Mathematics, University of South Carolina, Columbia, SC, United States., Syeda-Mahmood T; Almaden Research Center, IBM Research, San Jose, CA, United States., Wang J; Institute for Health Informatics and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States., Wang Q; Department of Mathematics, University of South Carolina, Columbia, SC, United States., Zervantonakis I; Department of Bioengineering, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.

Publikováno v: Frontiers in digital health [Front Digit Health] 2022 Oct 06; Vol. 4, pp. 1007784. Date of Electronic Publication: 2022 Oct 06 (Print Publication: 2022).

Immune digital twins for complex human pathologies: applications, limitations, and challenges.

Autor: Niarakis, Anna^1,2 (AUTHOR) anna.niaraki@univ-tlse3.fr, Laubenbacher, Reinhard³ (AUTHOR), An, Gary⁴ (AUTHOR), Ilan, Yaron⁵ (AUTHOR), Fisher, Jasmin⁶ (AUTHOR), Flobak, Åsmund^7,8,9 (AUTHOR), Reiche, Kristin^10,11,12 (AUTHOR), Rodríguez Martínez, María¹³ (AUTHOR), Geris, Liesbet^14,15,16 (AUTHOR), Ladeira, Luiz¹⁶ (AUTHOR), Veschini, Lorenzo^17,18 (AUTHOR), Blinov, Michael L.¹⁹ (AUTHOR), Messina, Francesco²⁰ (AUTHOR), Fonseca, Luis L.³ (AUTHOR), Ferreira, Sandra²¹ (AUTHOR), Montagud, Arnau^22,23 (AUTHOR), Noël, Vincent^24,25,26 (AUTHOR), Marku, Malvina²⁷ (AUTHOR), Tsirvouli, Eirini^7,28 (AUTHOR), Torres, Marcella M.²⁹ (AUTHOR)

Publikováno v: NPJ Systems Biology & Applications. 11/30/2024, Vol. 10 Issue 1, p1-14. 14p.

The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry.

Autor: Lischka H; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA., Shepard R; Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA., Müller T; Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich 52428, Germany., Szalay PG; ELTE Eötvös Loránd University, Institute of Chemistry, Budapest, Hungary., Pitzer RM; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA., Aquino AJA; School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, People's Republic of China., Araújo do Nascimento MM; Universidade Federal da Paraíba, 58059-900 João Pessoa, PB, Brazil., Barbatti M; Aix Marseille University, CNRS, ICR, Marseille, France., Belcher LT; Laser and Optics Research Center, Department of Physics, US Air Force Academy, Colorado 80840, USA., Blaudeau JP; PRKK, LLC, 1424 NW Coconut LN, Stuart, Florida 34994, USA., Borges I Jr; Departamento de Química, Instituto Militar de Engenharia, Rio de Janeiro, RJ 22290-270, Brazil., Brozell SR; Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA., Carter EA; Office of the Chancellor and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Box 951405, Los Angeles, California 90095-1405, USA., Das A; Indian Institute of Engineering Science and Technology, Shibpur, Howrah, India., Gidofalvi G; Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA., González L; Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria., Hase WL; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA., Kedziora G; Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA., Kertesz M; Department of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, DC 20057-1227, USA., Kossoski F; Aix Marseille University, CNRS, ICR, Marseille, France., Machado FBC; Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil., Matsika S; Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia, Pennsylvania 19122, USA., do Monte SA; Universidade Federal da Paraíba, 58059-900 João Pessoa, PB, Brazil., Nachtigallová D; Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 160610 Prague 6, Czech Republic., Nieman R; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA., Oppel M; Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria., Parish CA; Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, USA., Plasser F; Department of Chemistry, Loughborough University, Loughborough LE11 3TU, United Kingdom., Spada RFK; Departamento de Física, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil., Stahlberg EA; Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA., Ventura E; Universidade Federal da Paraíba, 58059-900 João Pessoa, PB, Brazil., Yarkony DR; Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA., Zhang Z; Stanford Research Computing Center, Stanford University, 255 Panama Street, Stanford, California 94305, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2020 Apr 07; Vol. 152 (13), pp. 134110.

Predicting tumor cell line response to drug pairs with deep learning.

Autor: Xia F; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL, USA. fangfang@anl.gov.; Computation Institute, The University of Chicago, Chicago, IL, USA. fangfang@anl.gov., Shukla M; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL, USA., Brettin T; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL, USA., Garcia-Cardona C; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA., Cohn J; Computer Science, Los Alamos National Laboratory, Los Alamos, NM, USA., Allen JE; Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA., Maslov S; Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Holbeck SL; Developmental Therapeutics Branch, National Cancer Institute, Frederick, MD, USA., Doroshow JH; Developmental Therapeutics Branch, National Cancer Institute, Frederick, MD, USA., Evrard YA; Developmental Therapeutics Branch, National Cancer Institute, Frederick, MD, USA., Stahlberg EA; Data Science and Information Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Stevens RL; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL, USA.; Computation Institute, The University of Chicago, Chicago, IL, USA.

Publikováno v: BMC bioinformatics [BMC Bioinformatics] 2018 Dec 21; Vol. 19 (Suppl 18), pp. 486. Date of Electronic Publication: 2018 Dec 21.

CCDC58 is a potential biomarker for diagnosis, prognosis, immunity, and genomic heterogeneity in pan-cancer.

Autor: Yang, Kai¹ (AUTHOR), Ma, Yan² (AUTHOR), Chen, Weigang¹ (AUTHOR), Liu, Lu³ (AUTHOR), Yang, Zelong¹ (AUTHOR), He, Chaokui⁴ (AUTHOR), Zheng, Nanbei⁵ (AUTHOR), Liu, Xinyu¹ (AUTHOR), Cheng, Xin¹ (AUTHOR), Song, Junbo¹ (AUTHOR), Chen, Yong¹ (AUTHOR) gdwkcy@163.com, Qiao, Hongyu⁶ (AUTHOR) qiaohongyu.1990@163.com, Zhang, Ruohan¹ (AUTHOR) zhangrh1990@outlook.com

Publikováno v: Scientific Reports. 4/12/2024, Vol. 14 Issue 1, p1-19. 19p.