NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.

Autor: Simoneau CR; Gladstone Institute of Virology, San Francisco, CA, USA.; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA., Chen PY; Gladstone Institute of Virology, San Francisco, CA, USA., Xing GK; Chan-Zuckerberg Biohub, San Francisco, CA, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Hayashi JM; Gladstone Institute of Virology, San Francisco, CA, USA., Chen IP; Gladstone Institute of Virology, San Francisco, CA, USA.; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA., Khalid MM; Gladstone Institute of Virology, San Francisco, CA, USA., Meyers NL; Gladstone Institute of Virology, San Francisco, CA, USA., Taha TY; Gladstone Institute of Virology, San Francisco, CA, USA., Leon KE; Gladstone Institute of Virology, San Francisco, CA, USA.; Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA., Suryawanshi RK; Gladstone Institute of Virology, San Francisco, CA, USA., McCavitt-Malvido M; Gladstone Institute of Virology, San Francisco, CA, USA., Ashuach T; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Fontaine KA; Gladstone Institute of Virology, San Francisco, CA, USA., Rodriguez L; ImmunoX CoLabs, University of California San Francisco, San Francisco, CA, USA., Joehnk B; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Walcott K; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Vasudevan S; Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA., Fang X; Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA., Maishan M; Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA., Schultz S; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Roose JP; Department of Anatomy, University of California San Francisco, San Francisco, CA, USA., Matthay MA; Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA., Sil A; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Arjomandi M; Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA.; Division of Pulmonary and Critical Care, Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Yosef N; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. nir.yosef@weizmann.ac.il.; Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel. nir.yosef@weizmann.ac.il., Ott M; Gladstone Institute of Virology, San Francisco, CA, USA. melanie.ott@gladstone.ucsf.edu.; Chan-Zuckerberg Biohub, San Francisco, CA, USA. melanie.ott@gladstone.ucsf.edu.; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. melanie.ott@gladstone.ucsf.edu.

Publikováno v: Scientific reports [Sci Rep] 2024 Jul 04; Vol. 14 (1), pp. 15351. Date of Electronic Publication: 2024 Jul 04.

Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.

Autor: Liu J; Graduate Program in Cell & Developmental Biology, Rutgers, The State University of New Jersey, 604 Allison Rd, Piscataway, NJ 08854, USA.; Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA.; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, Piscataway, NJ 08854, USA., Ashuach T; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, 387 Soda Hall, Berkeley, CA 94720, USA., Inoue F; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Faculty of Medicine Building B, Yoshidatachibanacho, Sakyo Ward, Kyoto 606-8303, Japan., Ahituv N; Department of Bioengineering and Therapeutic Sciences, University of California, 1700 4th Street, San Francisco, CA 94158, USA.; Institute for Human Genetics, University of California, 513 Parnassus Ave, San Francisco, CA 94143, USA., Yosef N; Department of Systems Immunology, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel.; Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.; Department of Systems Immunology, Ragon Institute of MGH, MIT, and Harvard Institute of Science, 400 Technology Square, Cambridge, MA 02139, USA., Kreimer A; Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA.; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, Piscataway, NJ 08854, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2024 Feb 28; Vol. 52 (4), pp. 1613-1627.

Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.

Autor: Kreimer A; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA. kreimer@cabm.rutgers.edu.; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA. kreimer@cabm.rutgers.edu.; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA. kreimer@cabm.rutgers.edu.; Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA. kreimer@cabm.rutgers.edu., Ashuach T; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA., Inoue F; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan., Khodaverdian A; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA., Deng C; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA., Yosef N; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA. niryosef@berkeley.edu.; Chan-Zuckerberg Biohub, San Francisco, CA, 94158, USA. niryosef@berkeley.edu.; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA. niryosef@berkeley.edu., Ahituv N; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA. nadav.ahituv@ucsf.edu.; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA. nadav.ahituv@ucsf.edu.

Publikováno v: Nature communications [Nat Commun] 2022 Mar 21; Vol. 13 (1), pp. 1504. Date of Electronic Publication: 2022 Mar 21.

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.

Autor: Simoneau CR; Gladstone Institute of Virology, San Francisco, CA, USA.; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA., Chen PY; Gladstone Institute of Virology, San Francisco, CA, USA., Xing GK; Chan-Zuckerberg Biohub, San Francisco, CA, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA., Khalid MM; Gladstone Institute of Virology, San Francisco, CA, USA., Meyers NL; Gladstone Institute of Virology, San Francisco, CA, USA., Hayashi JM; Gladstone Institute of Virology, San Francisco, CA, USA., Taha TY; Gladstone Institute of Virology, San Francisco, CA, USA., Leon KE; Gladstone Institute of Virology, San Francisco, CA, USA.; Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA., Ashuach T; Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA., Fontaine KA; Gladstone Institute of Virology, San Francisco, CA, USA., Rodriguez L; ImmunoX CoLabs, University of California San Francisco, San Francisco, CA, USA., Joehnk B; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Walcott K; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Vasudevan S; Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA., Fang X; Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA., Maishan M; Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA., Schultz S; Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA., Roose J; Department of Anatomy, University of California San Francisco, San Francisco, CA, USA., Matthay MA; Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA., Sil A; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Arjomandi M; Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA.; Division of Pulmonary and Critical Care, Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Yosef N; Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA.; Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel., Ott M; Gladstone Institute of Virology, San Francisco, CA, USA.; Chan-Zuckerberg Biohub, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2022 Aug 02. Date of Electronic Publication: 2022 Aug 02.

A Python library for probabilistic analysis of single-cell omics data.

Autor: Gayoso A; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Lopez R; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA., Xing G; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Chan Zuckerberg Biohub, San Francisco, CA, USA., Boyeau P; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.; École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France., Valiollah Pour Amiri V; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA., Hong J; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA., Wu K; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA., Jayasuriya M; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA., Mehlman E; École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France.; Centre de Mathématiques Appliquées, École polytechnique, Palaiseau, France., Langevin M; Centre de Mathématiques Appliquées, École polytechnique, Palaiseau, France.; Pasteur, Department of Chemistry, École Normale Supérieure, PSL University, Paris, France.; Molecular Design Sciences - Integrated Drug Discovery, Sanofi R&D, Vitry-sur-Seine, France., Liu Y; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.; Department of Computer Science, Columbia University, New York, NY, USA., Samaran J; Mines Paristech, PSL University, Paris, France., Misrachi G; Centre de Mathématiques Appliquées, École polytechnique, Palaiseau, France.; Gleamer, Paris, France., Nazaret A; Centre de Mathématiques Appliquées, École polytechnique, Palaiseau, France.; Department of Computer Science, Columbia University, New York, NY, USA., Clivio O; École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France.; Department of Statistics, University of Oxford, Oxford, UK., Xu C; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Ashuach T; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA., Gabitto M; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA., Lotfollahi M; Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.; School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany., Svensson V; Serqet Therapeutics, Cambridge, MA, USA., da Veiga Beltrame E; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA., Kleshchevnikov V; Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Talavera-López C; Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.; EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK., Pachter L; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA., Theis FJ; Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.; School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany., Streets A; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Chan Zuckerberg Biohub, San Francisco, CA, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA., Jordan MI; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.; Department of Statistics, University of California, Berkeley, Berkeley, CA, USA., Regier J; Department of Statistics, University of Michigan, Ann Arbor, MI, USA., Yosef N; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu.; Chan Zuckerberg Biohub, San Francisco, CA, USA. niryosef@berkeley.edu.; Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA, USA. niryosef@berkeley.edu.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2022 Feb; Vol. 40 (2), pp. 163-166.