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Gabriella Sterne

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Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David F, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O’Brien LE, Dow JAT, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YCE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science 2022;375:eabk2432. [PMID: 35239393 PMCID: PMC8944923 DOI: 10.1126/science.abk2432] [Citation(s) in RCA: 202] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]

Affiliation(s)

Hongjie Li Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,Huffington Center on Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Jasper Janssens VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
Maxime De Waegeneer VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
Sai Saroja Kolluru Departments of Bioengineering and Applied Physics, Stanford University, Stanford CA USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
Kristofer Davie VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium
Vincent Gardeux Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
Wouter Saelens Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
Fabrice David Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
Maria Brbić Department of Computer Science, Stanford University, Stanford, CA 94305, USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
Katina Spanier VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
Jure Leskovec Department of Computer Science, Stanford University, Stanford, CA 94305, USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
Colleen N. McLaughlin Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
Qijing Xie Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
Robert C. Jones Departments of Bioengineering and Applied Physics, Stanford University, Stanford CA USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
Katja Brueckner Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
Jiwon Shim Department of Life Science, College of Natural Science, Hanyang University, Seoul, Republic of Korea 04763
Sudhir Gopal Tattikota Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115; Howard Hughes Medical Institute, Boston, MA, USA
Frank Schnorrer Aix-Marseille University, CNRS, IBDM (UMR 7288), Turing Centre for Living systems, 13009 Marseille, France
Katja Rust Institute of Physiology and Pathophysiology, Department of Molecular Cell Physiology, Philipps-University, Marburg, Germany,Department of Anatomy, University of California, San Francisco, CA 94143, USA
Todd G. Nystul Department of Anatomy, University of California, San Francisco, CA 94143, USA
Zita Carvalho-Santos Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
Carlos Ribeiro Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
Soumitra Pal National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
Sharvani Mahadevaraju Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Teresa M. Przytycka National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
Aaron M. Allen Centre for Neural Circuits & Behaviour, University of Oxford, Tinsley Building, Mansfield road, Oxford, OX1 3SR, UK
Stephen F. Goodwin Centre for Neural Circuits & Behaviour, University of Oxford, Tinsley Building, Mansfield road, Oxford, OX1 3SR, UK
Cameron W. Berry Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Margaret T. Fuller Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Helen White-Cooper Molecular Biosciences Division, Cardiff University, Cardiff, CF10 3AX UK
Erika L. Matunis Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Stephen DiNardo Perelman School of Medicine, The University of Pennsylvania, and The Penn Institute for Regenerative Medicine Philadelphia, PA 19104, USA
Anthony Galenza Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford CA 94305, USA
Lucy Erin O’Brien Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford CA 94305, USA
Julian A. T. Dow Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
FCA Consortium FCA Consortium: All authors listed before Acknowledgements, and all contributions and affiliations listed in the Supplementary Materials
Heinrich Jasper Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
Brian Oliver Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Norbert Perrimon Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115; Howard Hughes Medical Institute, Boston, MA, USA,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
Bart Deplancke Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
Stephen R. Quake Departments of Bioengineering and Applied Physics, Stanford University, Stanford CA USA, and Chan Zuckerberg Biohub, San Francisco CA, USA,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
Liqun Luo Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
Stein Aerts VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
Devika Agarwal MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
Yasir Ahmed-Braimah Department of Biology, Syracuse University, Syracuse, NY 13244 USA
Michelle Arbeitman Biomedical Sciences Department, Florida State University, Tallahassee, FL, USA
Majd M Ariss Department of Genetics, Harvard Medical School, Boston, MA, USA
Jordan Augsburger Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
Kumar Ayush Department of Computer Science, Stanford University, Stanford, CA 94305, USA
Catherine C Baker Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Torsten Banisch Skirball Institute and HHMI, New York University Langone Medical Center, New York City, NY 10016, USA
Katja Birker Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
Rolf Bodmer Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
Benjamin Bolival Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Susanna E Brantley Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Julie A Brill Cell Biology Program, The Hospital for Sick Children (SickKids), Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
Nora C Brown Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Norene A Buehner Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Xiaoyu Tracy Cai Immunology Discovery, Genentech, Inc., South San Francisco, CA 94080, USA
Rita Cardoso-Figueiredo Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
Fernando Casares CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
Amy Chang Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Thomas R Clandinin Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
Sheela Crasta Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco CA, USA
Claude Desplan Department of Biology, New York University, New York, New York 10003, USA
Angela M Detweiler Chan Zuckerberg Biohub, San Francisco CA, USA
Darshan B Dhakan Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
Erika Donà Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
Stefanie Engert Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Swann Floc'hlay VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven 3000, Belgium.,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
Nancy George European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Amanda J González-Segarra Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Andrew K Groves Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
Samantha Gumbin Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Yanmeng Guo Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Devon E Harris Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Yael Heifetz The Hebrew University of Jerusalem, Jerusalem, Israel
Stephen L Holtz Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
Felix Horns Department of Bioengineering and Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
Bruno Hudry Université Côte d'Azur, CNRS, INSERM, iBV, France
Ruei-Jiun Hung Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Yuh Nung Jan Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Jacob S Jaszczak Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Gregory S X E Jefferis Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
Jim Karkanias Chan Zuckerberg Biohub, San Francisco CA, USA
Timothy L Karr Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
Nadja Sandra Katheder Immunology Discovery, Genentech, Inc., South San Francisco, CA 94080, USA
James Kezos Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
Anna A Kim Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,University of California, Santa Barbara, CA 93106, USA.,Uppsala University, Sweden
Seung K Kim Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
Lutz Kockel Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Nikolaos Konstantinides Institut Jacques Monod, Centre National de la Recherche Scientifique-UMR 7592, Université Paris Diderot, Paris, France
Thomas B Kornberg Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
Henry M Krause Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
Andrew Thomas Labott Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Meghan Laturney Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Ruth Lehmann Skirball Institute, Department of Cell Biology and HHMI, New York University Langone Medical Center, New York City, NY 10016
Sarah Leinwand Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Jiefu Li Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
Joshua Shing Shun Li Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Kai Li Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Ke Li Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Liying Li Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Tun Li Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Maria Litovchenko Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
Han-Hsuan Liu Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Yifang Liu Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Tzu-Chiao Lu Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
Jonathan Manning European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Anjeli Mase Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
Mikaela Matera-Vatnick Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Neuza Reis Matias Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Caitlin E McDonough-Goldstein Department of Biology, Syracuse University, Syracuse, NY, USA.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
Aaron McGeever Chan Zuckerberg Biohub, San Francisco CA, USA
Alex D McLachlan Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
Paola Moreno-Roman Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Norma Neff Chan Zuckerberg Biohub, San Francisco CA, USA
Megan Neville Centre for Neural Circuits and Behaviour, University of Oxford, Oxford OX1 3SR, UK
Sang Ngo Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Tanja Nielsen Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
Caitlin E O'Brien Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
David Osumi-Sutherland European Bioinformatics Institute (EMBL/EBI), Wellcome Trust Genome Campus, Cambridge, UK
Mehmet Neset Özel Department of Biology, New York University, New York, NY 10003, USA
Irene Papatheodorou European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Maja Petkovic Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Clare Pilgrim Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
Angela Oliveira Pisco Chan Zuckerberg Biohub, San Francisco CA, USA
Carolina Reisenman Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Erin Nicole Sanders Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Gilberto Dos Santos The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Kristin Scott Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Aparna Sherlekar Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Philip Shiu Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
David Sims MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
Rene V Sit Chan Zuckerberg Biohub, San Francisco CA, USA
Maija Slaidina Skirball Institute, Faculty of Medicine, New York University, New York, NY 10016
Harold E Smith Genomics Core, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA
Gabriella Sterne Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Yu-Han Su Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Daniel Sutton Graduate Program in Genetics and Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
Marco Tamayo Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
Michelle Tan Chan Zuckerberg Biohub, San Francisco CA, USA
Ibrahim Tastekin Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
Christoph Treiber Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3TA, UK
David Vacek Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
Georg Vogler Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
Scott Waddell Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3TA, UK
Wanpeng Wang Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
Rachel I Wilson Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
Mariana F Wolfner Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Yiu-Cheung E Wong Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Anthony Xie Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
Jun Xu Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Shinya Yamamoto Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
Jia Yan Chan Zuckerberg Biohub, San Francisco CA, USA
Zepeng Yao Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Kazuki Yoda Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Ruijun Zhu Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
Robert P Zinzen Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany

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Sanders J, Singh A, Sterne G, Ye B, Zhou J. Learning-guided automatic three dimensional synapse quantification for drosophila neurons. BMC Bioinformatics 2015;16:177. [PMID: 26017624 PMCID: PMC4445279 DOI: 10.1186/s12859-015-0616-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/16/2015] [Indexed: 11/10/2022] Open

Soumian S, Al-Ani S, Sterne G. Randomized clinical trial on the effect of fibrin sealant on latissimus dorsi donor-site seroma formation after breast reconstruction (Br j surg 2012; 99: 1381-1388). Br J Surg 2013;100:1671. [PMID: 24264793 DOI: 10.1002/bjs.9313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]

Zhou J, Lamichhane S, Sterne G, Ye B, Peng H. BIOCAT: a pattern recognition platform for customizable biological image classification and annotation. BMC Bioinformatics 2013;14:291. [PMID: 24090164 PMCID: PMC3854450 DOI: 10.1186/1471-2105-14-291] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 09/11/2013] [Indexed: 11/29/2022] Open

Abstract

Background

Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effective and efficient image classification and annotation for the ever-increasing microscopic images, it is desirable to have tools that can combine and compare various algorithms, and build customizable solution for different biological problems. However, current tools often offer a limited solution in generating user-friendly and extensible tools for annotating higher dimensional images that correspond to multiple complicated categories.

Results

We develop the BIOimage Classification and Annotation Tool (BIOCAT). It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and annotation. We also propose a 3D anisotropic wavelet feature extractor for extracting textural features from 3D images with xy-z resolution disparity. The extractor is one of the about 20 built-in algorithms of feature extractors, selectors and classifiers in BIOCAT. The algorithms are modularized so that they can be “chained” in a customizable way to form adaptive solution for various problems, and the plugin-based extensibility gives the tool an open architecture to incorporate future algorithms. We have applied BIOCAT to classification and annotation of images and ROIs of different properties with applications in cell biology and neuroscience.

Conclusions

BIOCAT provides a user-friendly, portable platform for pattern recognition based biological image classification of two- and three- dimensional images and ROIs. We show, via diverse case studies, that different algorithms and their combinations have different suitability for various problems. The customizability of BIOCAT is thus expected to be useful for providing effective and efficient solutions for a variety of biological problems involving image classification and annotation. We also demonstrate the effectiveness of 3D anisotropic wavelet in classifying both 3D image sets and ROIs.

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Sircar T, Choudhry A, Katerinaki E, Sterne G. O-1 Breast skin envelope necrosis after skin sparing mastectomy and immediate breast reconstruction – How common is it? EJC Suppl 2010. [DOI: 10.1016/j.ejcsup.2010.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open

Dalal M, Sterne G, Murray DS. Streptococcal myositis: a lesson. Br J Plast Surg 2002;55:682-4. [PMID: 12550125 DOI: 10.1054/bjps.2002.3953] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]

Sterne G, Shields LE, Dubinsky TJ. Abnormal fetal cerebral and umbilical Doppler measurements in fetuses with intrauterine growth restriction predicts the severity of perinatal morbidity. J Clin Ultrasound 2001;29:146-151. [PMID: 11329157 DOI: 10.1002/1097-0096(200103/04)29:3<146::aid-jcu1014>3.0.co;2-i] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]

Abstract

PURPOSE

This prospective study was performed to determine if the ratio of the middle cerebral artery (MCA) S/D ratio (ratio of peak systolic blood flow velocity to diastolic velocity) to the umbilical artery (UA) S/D ratio (MCA/UA S/D ratio) predicts the degree of neonatal morbidity in fetuses suspected of having intrauterine growth restriction (IUGR).

METHODS

Sixty-one fetuses were identified prospectively by sonography as having an estimated fetal weight below the 10th percentile for gestational age. The 61 fetuses underwent Doppler sonography in the third trimester and then were stratified into 3 groups based on the MCA/UA S/D ratio: group A, MCA/UA S/D ratio > 1.0 (controls; n = 37); group B, MCA/UA S/D ratio < or = 1.0 (intracerebral blood flow redistribution; n = 16); and group C, reversed or absent UA diastolic flow (n = 8). Outcome variables assessed included gestational age at delivery, birth weight, UA pH, mode of delivery, respiratory distress syndrome requiring intubation, and intracranial hemorrhage.

RESULTS

The mean MCA/UA S/D ratios in groups A and B were 1.69 + /- 0.61 and 0.59 + /- 0.24, respectively (p < 0.01). The mean gestational ages at delivery for groups A, B, and C were 34.7, 33.2, and 29.0 weeks, respectively. The mean birth weights were below the fifth percentile for age for groups B and C and significantly related to the severity of abnormal Doppler findings (p < 0.01) after correction for age. Mean UA pHs were 7.25 + /- 0.01, 7.19 + /- 0.01, and 7.14 + /- 0.13 for groups A, B, and C, respectively, with significant differences between groups A and B (p < 0.05) and groups A and C (p < 0.05). Respiratory distress syndrome and intracranial hemorrhage were not associated with abnormal Doppler findings after correction for gestational age. The interval between the abnormal Doppler examination and delivery (p < 0.001) and the occurrence of fetal distress requiring cesarean section (p < 0.001) were significantly related to the severity of Doppler findings.

CONCLUSIONS

In fetuses with suspected IUGR, abnormal MCA/UA S/D ratios are strongly associated with low gestational age at delivery, low birth weight, and low UA pH. Abnormal MCA/UA S/D ratios are also significantly associated with shorter interval to delivery and the need for emergent delivery.

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Sterne G. TV making children obese and cognitively compromised. Can Crit Care Nurs J 1991;8:10. [PMID: 1954555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]