An atlas of healthy and injured cell states and niches in the human kidney.

Autor: Lake BB; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.; San Diego Institute of Science, Altos Labs, San Diego, CA, USA., Menon R; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Winfree S; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA., Hu Q; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Melo Ferreira R; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA., Kalhor K; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Barwinska D; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA., Otto EA; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA., Ferkowicz M; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA., Diep D; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.; San Diego Institute of Science, Altos Labs, San Diego, CA, USA., Plongthongkum N; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Knoten A; Department of Medicine, Washington University School of Medicine, St Louis, MO, USA., Urata S; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Mariani LH; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA., Naik AS; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA., Eddy S; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA., Zhang B; Department of Medicine, Washington University School of Medicine, St Louis, MO, USA., Wu Y; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.; San Diego Institute of Science, Altos Labs, San Diego, CA, USA., Salamon D; Department of Medicine, Washington University School of Medicine, St Louis, MO, USA., Williams JC; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA., Wang X; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Balderrama KS; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Hoover PJ; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Murray E; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Marshall JL; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Noel T; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Vijayan A; Department of Medicine, Washington University School of Medicine, St Louis, MO, USA., Hartman A; New York Genome Center, New York, NY, USA., Chen F; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Waikar SS; Section of Nephrology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA., Rosas SE; Kidney and Hypertension Unit, Joslin Diabetes Center, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Wilson FP; Department of Medicine, Yale University School of Medicine, New Haven, CT, USA., Palevsky PM; Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA., Kiryluk K; Department of Medicine, Columbia University, New York, NY, USA., Sedor JR; Lerner Research and Glickman Urology and Kidney Institutes, Cleveland Clinic, Cleveland, OH, USA., Toto RD; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA., Parikh CR; Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, MD, USA., Kim EH; Department of Surgery, Washington University School of Medicine, St Louis, MO, USA., Satija R; New York Genome Center, New York, NY, USA., Greka A; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Macosko EZ; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Kharchenko PV; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.; San Diego Institute of Science, Altos Labs, San Diego, CA, USA., Gaut JP; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA., Hodgin JB; Department of Pathology, University of Michigan, Ann Arbor, MI, USA., Eadon MT; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. meadon@iupui.edu., Dagher PC; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. pdaghe2@iu.edu., El-Achkar TM; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. telachka@iu.edu., Zhang K; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. kzhang@bioeng.ucsd.edu.; San Diego Institute of Science, Altos Labs, San Diego, CA, USA. kzhang@bioeng.ucsd.edu., Kretzler M; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA. kretzler@med.umich.edu., Jain S; Department of Medicine, Washington University School of Medicine, St Louis, MO, USA. sanjayjain@wustl.edu.; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. sanjayjain@wustl.edu.

Publikováno v: Nature [Nature] 2023 Jul; Vol. 619 (7970), pp. 585-594. Date of Electronic Publication: 2023 Jul 19.

Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation.

Autor: Ford K; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA., Munson BP; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.; Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Fong SH; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.; Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Panwala R; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA., Chu WK; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA., Rainaldi J; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.; Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA., Plongthongkum N; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA., Arunachalam V; Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA., Kostrowicki J; Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA., Meluzzi D; Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Kreisberg JF; Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Jensen-Pergakes K; Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA., VanArsdale T; Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA., Paul T; Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA., Tamayo P; Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA., Zhang K; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA., Bienkowska J; Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA. Jadwiga.R.Bienkowska@pfizer.com., Mali P; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA. pmali@ucsd.edu., Ideker T; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA. tideker@health.ucsd.edu.; Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA. tideker@health.ucsd.edu.

Publikováno v: Scientific reports [Sci Rep] 2023 May 11; Vol. 13 (1), pp. 7678. Date of Electronic Publication: 2023 May 11.

Comparative cellular analysis of motor cortex in human, marmoset and mouse.

Autor: Bakken TE; Allen Institute for Brain Science, Seattle, WA, USA. trygveb@alleninstitute.org., Jorstad NL; Allen Institute for Brain Science, Seattle, WA, USA., Hu Q; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Lake BB; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Tian W; The Salk Institute for Biological Studies, La Jolla, CA, USA., Kalmbach BE; Allen Institute for Brain Science, Seattle, WA, USA.; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA., Crow M; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Hodge RD; Allen Institute for Brain Science, Seattle, WA, USA., Krienen FM; Department of Genetics, Harvard Medical School, Boston, MA, USA., Sorensen SA; Allen Institute for Brain Science, Seattle, WA, USA., Eggermont J; LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands., Yao Z; Allen Institute for Brain Science, Seattle, WA, USA., Aevermann BD; J. Craig Venter Institute, La Jolla, CA, USA., Aldridge AI; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA., Bartlett A; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA., Bertagnolli D; Allen Institute for Brain Science, Seattle, WA, USA., Casper T; Allen Institute for Brain Science, Seattle, WA, USA., Castanon RG; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA., Crichton K; Allen Institute for Brain Science, Seattle, WA, USA., Daigle TL; Allen Institute for Brain Science, Seattle, WA, USA., Dalley R; Allen Institute for Brain Science, Seattle, WA, USA., Dee N; Allen Institute for Brain Science, Seattle, WA, USA., Dembrow N; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.; Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA., Diep D; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Ding SL; Allen Institute for Brain Science, Seattle, WA, USA., Dong W; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Fang R; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA., Fischer S; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Goldman M; Department of Genetics, Harvard Medical School, Boston, MA, USA., Goldy J; Allen Institute for Brain Science, Seattle, WA, USA., Graybuck LT; Allen Institute for Brain Science, Seattle, WA, USA., Herb BR; Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Hou X; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA., Kancherla J; Department of Computer Science, University of Maryland College Park, College Park, MD, USA., Kroll M; Allen Institute for Brain Science, Seattle, WA, USA., Lathia K; Allen Institute for Brain Science, Seattle, WA, USA., van Lew B; LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands., Li YE; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.; Ludwig Institute for Cancer Research, La Jolla, CA, USA., Liu CS; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.; Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA., Liu H; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA., Lucero JD; The Salk Institute for Biological Studies, La Jolla, CA, USA., Mahurkar A; Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., McMillen D; Allen Institute for Brain Science, Seattle, WA, USA., Miller JA; Allen Institute for Brain Science, Seattle, WA, USA., Moussa M; University of Connecticut, Storrs, CT, USA., Nery JR; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA., Nicovich PR; Allen Institute for Brain Science, Seattle, WA, USA., Niu SY; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.; Computer Science and Engineering Program, University of California, San Diego, La Jolla, CA, USA., Orvis J; Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Osteen JK; The Salk Institute for Biological Studies, La Jolla, CA, USA., Owen S; Allen Institute for Brain Science, Seattle, WA, USA., Palmer CR; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.; Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA., Pham T; Allen Institute for Brain Science, Seattle, WA, USA., Plongthongkum N; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Poirion O; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA., Reed NM; Department of Genetics, Harvard Medical School, Boston, MA, USA., Rimorin C; Allen Institute for Brain Science, Seattle, WA, USA., Rivkin A; The Salk Institute for Biological Studies, La Jolla, CA, USA., Romanow WJ; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA., Sedeño-Cortés AE; Allen Institute for Brain Science, Seattle, WA, USA., Siletti K; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden., Somasundaram S; Allen Institute for Brain Science, Seattle, WA, USA., Sulc J; Allen Institute for Brain Science, Seattle, WA, USA., Tieu M; Allen Institute for Brain Science, Seattle, WA, USA., Torkelson A; Allen Institute for Brain Science, Seattle, WA, USA., Tung H; Allen Institute for Brain Science, Seattle, WA, USA., Wang X; McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA., Xie F; Department of Physics, University of California, San Diego, La Jolla, CA, USA., Yanny AM; Allen Institute for Brain Science, Seattle, WA, USA., Zhang R; J. Craig Venter Institute, La Jolla, CA, USA., Ament SA; Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Behrens MM; The Salk Institute for Biological Studies, La Jolla, CA, USA., Bravo HC; Department of Computer Science, University of Maryland College Park, College Park, MD, USA., Chun J; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA., Dobin A; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Gillis J; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Hertzano R; Departments of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA., Hof PR; Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Höllt T; Computer Graphics and Visualization Group, Delt University of Technology, Delft, The Netherlands., Horwitz GD; Department of Physiology and Biophysics, Washington National Primate Research Center, University of Washington, Seattle, WA, USA., Keene CD; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Kharchenko PV; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Ko AL; Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA.; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA., Lelieveldt BP; LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.; Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, The Netherlands., Luo C; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA., Mukamel EA; Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA., Pinto-Duarte A; The Salk Institute for Biological Studies, La Jolla, CA, USA., Preissl S; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA., Regev A; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Ren B; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.; Ludwig Institute for Cancer Research, La Jolla, CA, USA., Scheuermann RH; J. Craig Venter Institute, La Jolla, CA, USA.; Department of Pathology, University of California, San Diego, CA, USA.; Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA., Smith K; Allen Institute for Brain Science, Seattle, WA, USA., Spain WJ; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.; Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA., White OR; Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Koch C; Allen Institute for Brain Science, Seattle, WA, USA., Hawrylycz M; Allen Institute for Brain Science, Seattle, WA, USA., Tasic B; Allen Institute for Brain Science, Seattle, WA, USA., Macosko EZ; Broad Institute of MIT and Harvard, Cambridge, MA, USA., McCarroll SA; Department of Genetics, Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Ting JT; Allen Institute for Brain Science, Seattle, WA, USA.; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA., Zeng H; Allen Institute for Brain Science, Seattle, WA, USA., Zhang K; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Feng G; McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Ecker JR; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA., Linnarsson S; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden., Lein ES; Allen Institute for Brain Science, Seattle, WA, USA. edl@alleninstitute.org.

Publikováno v: Nature [Nature] 2021 Oct; Vol. 598 (7879), pp. 111-119. Date of Electronic Publication: 2021 Oct 06.

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2).

Autor: Plongthongkum N; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.; Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand., Diep D; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Chen S; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Lake BB; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Zhang K; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. kzhang@bioeng.ucsd.edu.

Publikováno v: Nature protocols [Nat Protoc] 2021 Nov; Vol. 16 (11), pp. 4992-5029. Date of Electronic Publication: 2021 Oct 14.

Methylation patterns at the adjacent CpG sites within enhancers are a part of cell identity.

Autor: Taryma-Leśniak, Olga¹ (AUTHOR), Bińkowski, Jan¹ (AUTHOR), Przybylowicz, Patrycja Kamila¹ (AUTHOR), Sokolowska, Katarzyna Ewa¹ (AUTHOR), Borowski, Konrad¹ (AUTHOR), Wojdacz, Tomasz Kazimierz¹ (AUTHOR) tomasz.wojdacz@pum.edu.pl

Publikováno v: Epigenetics & Chromatin. 10/10/2024, Vol. 17 Issue 1, p1-14. 14p.