Stereotyped B-Cell Receptor Immunoglobulins in B-Cell Lymphomas.

Autor: Agathangelidis A; Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece., Roussos A; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece., Kardamiliotis K; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece., Psomopoulos F; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece., Stamatopoulos K; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece. kostas.stamatopoulos@certh.gr.; Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden. kostas.stamatopoulos@certh.gr.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2865, pp. 125-143.

Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity.

Autor: Pechlivanis N; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece.; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece., Karakatsoulis G; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece., Kyritsis K; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece., Tsagiopoulou M; Centro Nacional de Analisis Genomico (CNAG), C/Baldiri Reixac 4, 08028, Barcelona, Spain., Sgardelis S; Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece., Kappas I; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece., Psomopoulos F; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece. fpsom@certh.gr.

Publikováno v: Scientific data [Sci Data] 2024 Jun 22; Vol. 11 (1), pp. 672. Date of Electronic Publication: 2024 Jun 22.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.

Autor: Sutcliffe SG; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada., Kraemer SA; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.; Environment and Climate Change Canada, Montreal, QC, Canada., Ellmen I; Department of Biology, University of Waterloo, Waterloo, ON, Canada., Knapp JJ; Department of Biology, University of Waterloo, Waterloo, ON, Canada., Overton AK; Department of Biology, University of Waterloo, Waterloo, ON, Canada., Nash D; Department of Biology, University of Waterloo, Waterloo, ON, Canada., Nissimov JI; Department of Biology, University of Waterloo, Waterloo, ON, Canada., Charles TC; Department of Biology, University of Waterloo, Waterloo, ON, Canada., Dreifuss D; Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland., Topolsky I; Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland., Baykal PI; Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland., Fuhrmann L; Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland., Jablonski KP; Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland., Beerenwinkel N; Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland., Levy JI; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Olabode AS; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada., Becker DG; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada., Gugan G; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada., Brintnell E; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada., Poon AFY; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada., Valieris R; Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil., Drummond RD; Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil., Defelicibus A; Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil., Dias-Neto E; Rutgers University, New Brunswick, NJ, USA., Rosales RA; Universidade de São Paulo, São Paulo, SP, Brazil., Tojal da Silva I; Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil., Orfanou A; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece., Psomopoulos F; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece., Pechlivanis N; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece., Pipes L; Department of Integrative Biology, University of California, Berkeley, CA, USA., Chen Z; School of Mathematical Sciences, Peking University, Beijing, BJ, PR China., Baaijens JA; Delft University of Technology, Delft, ZH, Netherlands.; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Baym M; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Shapiro BJ; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.

Publikováno v: Microbial genomics [Microb Genom] 2024 May; Vol. 10 (5).

DOME: recommendations for supervised machine learning validation in biology

Autor: Walsh, I., Fishman, D., Garcia-Gasulla, D., Titma, T., Pollastri, G., Capriotti, E., Casadio, R., Capella-Gutierrez, S., Cirillo, D., Del Conte, A., Dimopoulos, A. C., Del Angel, V. D., Dopazo, J., Fariselli, P., Fernandez, J. M., Huber, F., Kreshuk, A., Lenaerts, T., Martelli, P. L., Navarro, A., Broin, P. O., Pinero, J., Piovesan, D., Reczko, M., Ronzano, F., Satagopam, V., Savojardo, C., Spiwok, V., Tangaro, M. A., Tartari, G., Salgado, D., Valencia, A., Zambelli, F., Harrow, J., Psomopoulos, F. E., Tosatto, S. C. E.

Publikováno v: UPCommons. Portal del coneixement obert de la UPC
ORCID
arXiv.org e-Print Archive
Archivio istituzionale della ricerca-Alma Mater Studiorum Università di Bologna
Archivio Istituzionale della Ricerca dell'Università degli Studi di Milano
Universitat Politècnica de Catalunya (UPC)
Nature Methods

Supervised machine learning is widely used in biology and deserves more scrutiny. We present a set of community-wide recommendations (DOME) aiming to help establish standards of supervised machine learning validation in biology. Formulated as questio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e3820fb0b766649020b580b623bdf29
https://doi.org/10.1038/s41592-021-01205-4

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).

Autor: Kyritsis KA; Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece., Pechlivanis N; Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece., Psomopoulos F; Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.

Publikováno v: Frontiers in bioinformatics [Front Bioinform] 2023 Nov 07; Vol. 3, pp. 1275593. Date of Electronic Publication: 2023 Nov 07 (Print Publication: 2023).