Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.

Autor: Lerma-Martin C; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany., Badia-I-Mompel P; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany.; GSK, Cellzome, Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Ramirez Flores RO; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Sekol P; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany., Schäfer PSL; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Riedl CJ; Department of Neurology, Division of Neuropathology and Neurochemistry, Medical University of Vienna, Vienna, Austria.; Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria., Hofmann A; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany., Thäwel T; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany., Wünnemann F; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany., Ibarra-Arellano MA; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany., Trobisch T; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany., Eisele P; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.; Mannheim Center for Translational Neuroscience, Medical Faculty, Mannheim Heidelberg University, Mannheim, Germany., Schapiro D; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany.; Institute of Pathology, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany.; Translational Spatial Profiling Center (TSPC), Heidelberg, Germany., Haeussler M; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA., Hametner S; Department of Neurology, Division of Neuropathology and Neurochemistry, Medical University of Vienna, Vienna, Austria.; Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria., Saez-Rodriguez J; Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany. pub.saez@uni-heidelberg.de.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK. pub.saez@uni-heidelberg.de., Schirmer L; Department of Neurology, Division of Neuroimmunology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. lucas.schirmer@medma.uni-heidelberg.de.; Mannheim Center for Translational Neuroscience, Medical Faculty, Mannheim Heidelberg University, Mannheim, Germany. lucas.schirmer@medma.uni-heidelberg.de.; Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany. lucas.schirmer@medma.uni-heidelberg.de.

Publikováno v: Nature neuroscience [Nat Neurosci] 2024 Dec; Vol. 27 (12), pp. 2354-2365. Date of Electronic Publication: 2024 Nov 05.

Dissecting the treatment-naive ecosystem of human melanoma brain metastasis.

Autor: Biermann J; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA., Melms JC; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA., Amin AD; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA., Wang Y; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA., Caprio LA; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA., Karz A; Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA., Tagore S; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA., Barrera I; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Ibarra-Arellano MA; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany., Andreatta M; Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Fullerton BT; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Gretarsson KH; Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA., Sahu V; Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA., Mangipudy VS; Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA., Nguyen TTT; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA., Nair A; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Rogava M; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA., Ho P; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA., Koch PD; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Banu M; Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA., Humala N; Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA., Mahajan A; Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA., Walsh ZH; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Shah SB; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Vaccaro DH; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Caldwell B; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Mu M; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Wünnemann F; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany., Chazotte M; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany., Berhe S; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Luoma AM; Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA., Driver J; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Ingham M; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Khan SA; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Rapisuwon S; Division of Hematology/Oncology, Medstar Washington Cancer Institute, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA., Slingluff CL Jr; Department of Surgery, University of Virginia, Charlottesville, VA, USA., Eigentler T; Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venereology and Allergology, 10117, Berlin, Germany., Röcken M; Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany., Carvajal R; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Atkins MB; Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA., Davies MA; Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA., Agustinus A; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School, New York, NY 10065, USA., Bakhoum SF; Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA., Azizi E; Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA., Siegelin M; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA., Lu C; Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA., Carmona SJ; Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Hibshoosh H; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA., Ribas A; Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90024, USA., Canoll P; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA., Bruce JN; Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA., Bi WL; Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Agrawal P; Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA., Schapiro D; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany., Hernando E; Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA., Macosko EZ; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA., Chen F; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA., Schwartz GK; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Izar B; Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address: bi2175@cumc.columbia.edu.

Publikováno v: Cell [Cell] 2022 Jul 07; Vol. 185 (14), pp. 2591-2608.e30.

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

Autor: Ibarra-Arellano MA; Group of Regulatory Systems Biology, Evolutionary Genomics Program, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México., Campos-González AI; Group of Regulatory Systems Biology, Evolutionary Genomics Program, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México., Treviño-Quintanilla LG; Departamento De Tecnología Ambiental, Universidad Politécnica Del Estado De Morelos, Blvd. Cuauhnáhuac 566, Col. Lomas Del Texcal, Jiutepec, Morelos 62550, México., Tauch A; Centrum Für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, Bielefeld, 33615, Germany., Freyre-González JA; Group of Regulatory Systems Biology, Evolutionary Genomics Program, Universidad Nacional Autónoma De México, Av. Universidad S/N, Col. Chamilpa, Cuernavaca, Morelos 62210, México jfreyre@ccg.unam.mx.

Publikováno v: Database : the journal of biological databases and curation [Database (Oxford)] 2016 May 30; Vol. 2016. Date of Electronic Publication: 2016 May 30 (Print Publication: 2016).

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation.

Autor: Ibraim, Izabela Coimbra¹ (AUTHOR), Parise, Mariana Teixeira Dornelles¹ (AUTHOR), Parise, Doglas¹ (AUTHOR), Sfeir, Michelle Zibetti Tadra² (AUTHOR), de Paula Castro, Thiago Luiz³ (AUTHOR), Wattam, Alice Rebecca⁴ (AUTHOR), Ghosh, Preetam⁵ (AUTHOR), Barh, Debmalya¹ (AUTHOR), Souza, Emannuel Maltempi² (AUTHOR), Góes-Neto, Aristóteles⁶ (AUTHOR), Gomide, Anne Cybelle Pinto¹ (AUTHOR), Azevedo, Vasco¹ (AUTHOR) vasco@icb.ufmg.br

Publikováno v: BMC Genomics. 8/20/2019, Vol. 20 Issue 1, pN.PAG-N.PAG. 1p. 2 Diagrams, 2 Charts, 4 Graphs.

Machine Learning and Systems Biology in Genomics and Health

Autor: Shailza Singh

This book discusses the application of machine learning in genomics. Machine Learning offers ample opportunities for Big Data to be assimilated and comprehended effectively using different frameworks. Stratification, diagnosis, classification and sur