MAFin: Motif Detection in Multiple Alignment Files.

Autor: Patsakis M; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Provatas K; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece., Chantzi N; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Mouratidis I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece., Georgakopoulos-Soares I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA.

Publikováno v: ArXiv [ArXiv] 2024 Oct 14. Date of Electronic Publication: 2024 Oct 14.

kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.

Autor: Mouratidis I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA., Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece., Chantzi N; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Patsakis M; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Chan CSY; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Montgomery A; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Konnaris MA; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.; Department of Statistics, The Pennsylvania State University, University Park, PA, USA., Aplakidou E; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece.; Department of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece., Georgakopoulos GC; National Technical University of Athens, School of Electrical and Computer Engineering, Athens, Greece., Das A; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Chartoumpekis DV; Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Lausanne, Switzerland., Kovac J; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA., Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece.; Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece., Georgakopoulos-Soares I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.

Publikováno v: Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2024 Apr 21; Vol. 23, pp. 1919-1928. Date of Electronic Publication: 2024 Apr 21 (Print Publication: 2024).

MPRAbase: A Massively Parallel Reporter Assay Database.

Autor: Zhao J; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA., Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece., Konnaris MA; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Department of Statistics, Penn State University, State College, PA, USA., Mouratidis I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Department of Statistics, Penn State University, State College, PA, USA., Liu Z; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.; Department of Computer Science, City University of Hong Kong, Hong Kong, China., Sims J; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA., Agarwal V; mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA., Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, 16672, Greece., Georgakopoulos-Soares I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.; Department of Statistics, Penn State University, State College, PA, USA., Ahituv N; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Nov 22. Date of Electronic Publication: 2023 Nov 22.

Unraveling the functional dark matter through global metagenomics.

Autor: Pavlopoulos GA; Institute for Fundamental Biomedical Research, Biomedical Science Research Center Alexander Fleming, Vari, Greece. pavlopoulos@fleming.gr.; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. pavlopoulos@fleming.gr.; Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece. pavlopoulos@fleming.gr., Baltoumas FA; Institute for Fundamental Biomedical Research, Biomedical Science Research Center Alexander Fleming, Vari, Greece., Liu S; John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA., Selvitopi O; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Camargo AP; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Nayfach S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Azad A; Luddy School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, IN, USA., Roux S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Call L; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Ivanova NN; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Chen IM; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Paez-Espino D; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Karatzas E; Institute for Fundamental Biomedical Research, Biomedical Science Research Center Alexander Fleming, Vari, Greece., Iliopoulos I; Department of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece., Konstantinidis K; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA., Tiedje JM; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA., Pett-Ridge J; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Visel A; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Ouzounis CA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece.; Biological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, Greece., Ovchinnikov S; John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA., Buluç A; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA., Kyrpides NC; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. nckyrpides@lbl.gov.

Publikováno v: Nature [Nature] 2023 Oct; Vol. 622 (7983), pp. 594-602. Date of Electronic Publication: 2023 Oct 11.

Arena3D ^web : interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration.

Autor: Kokoli M; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari16672, Greece., Karatzas E; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari16672, Greece., Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari16672, Greece., Schneider R; University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, Esch-sur-Alzette, Luxembourg., Pafilis E; Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, Heraklion 71003, Greece., Paragkamian S; Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, Heraklion 71003, Greece.; Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013 Heraklion, Crete, Greece., Doncheva NT; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N DK-2200, Denmark., Jensen LJ; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N DK-2200, Denmark., Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari16672, Greece.; Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece.

Publikováno v: NAR genomics and bioinformatics [NAR Genom Bioinform] 2023 May 30; Vol. 5 (2), pp. lqad053. Date of Electronic Publication: 2023 May 30 (Print Publication: 2023).