Orchestrating high-throughput genomic analysis with Bioconductor
Wolfgang Huber,Vincent J. Carey,Robert Gentleman,Simon Anders,Marc R. J. Carlson,Benilton S. Carvalho,Héctor Corrada Bravo,Sean Davis,Laurent Gatto,Thomas Girke,Raphael Gottardo,Florian Hahne,Kasper D. Hansen,Rafael A. Irizarry,Michael S. Lawrence,Michael I. Love,James W. MacDonald,Valerie Obenchain,Andrzej K. Oleś,Hervé Pagès,Alejandro Reyes,Paul Shannon,Gordon K. Smyth,Dan Tenenbaum,Levi Waldron,Martin Morgan +25 more
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TLDR
An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.Abstract:
Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.read more
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A novel anti-HER2 anthracycline-based antibody-drug conjugate induces adaptive anti-tumor immunity and potentiates PD-1 blockade in breast cancer
Lucia D'Amico,Ulrike Menzel,Michael Prummer,Philipp Müller,Philipp Müller,Melanie Buchi,Abhishek S. Kashyap,Ulrike Haessler,Alexander Yermanos,Rémy Gebleux,Manfred Briendl,Tamara Hell,Fabian I. Wolter,Roger R. Beerli,Iva Truxova,Špíšek Radek,Tatjana Vlajnic,Ulf Grawunder,Sai T. Reddy,Alfred Zippelius +19 more
TL;DR: The therapeutic efficacy and immune-mediated mechanisms of a novel Her2-targeting ADC bearing a potent anthracycline derivate as payload (T-PNU) in a human HER2-expressing syngeneic breast cancer model resistant to trastuzumab and ado-trastuzuab emtansine are elucidated.
Journal ArticleDOI
Darkened Leaves Use Different Metabolic Strategies for Senescence and Survival.
Simon R. Law,Daria Chrobok,Marta Juvany,Nicolas Delhomme,Pernilla Lindén,Bastiaan Brouwer,Abdul Ahad,Thomas Moritz,Stefan Jansson,Per Gardeström,Olivier Keech +10 more
TL;DR: A model is proposed illustrating the specific metabolic strategies employed by leaves in response to these two darkening treatments, which support either rapid senescence or a strong capacity for survival.
Journal ArticleDOI
Aged murine hematopoietic stem cells drive aging-associated immune remodeling
Hanna Leins,Medhanie A. Mulaw,Karina Eiwen,Vadim Sakk,Ying Liang,Michael Denkinger,Michael Denkinger,Hartmut Geiger,Hartmut Geiger,Reinhold Schirmbeck +9 more
TL;DR: Young and aged HSCs reconstituted distinct T- and B-cell subsets in RAG1-/- hosts that mirrored young and aged immune systems that reestablished an immune system similar to that of young animals, and thus capable of mounting a strong immune response to vaccination.
Journal ArticleDOI
Genetic investigations of sudden unexpected deaths in infancy using next-generation sequencing of 100 genes associated with cardiac diseases.
Christin Loeth Hertz,Sofie Lindgren Christiansen,Maiken Kudahl Larsen,Morten Dahl,Laura Ferrero-Miliani,P.E Weeke,Oluf Pedersen,Torben Hansen,Torben Hansen,Niels Grarup,Gyda Lolk Ottesen,Rune Frank-Hansen,Jytte Banner,Niels Morling +13 more
TL;DR: Analysis of genes associated with cardiac diseases in SUDI victims is important in the forensic setting and a valuable supplement to the clinical investigation in all cases of sudden death.
Journal ArticleDOI
Pan-Cancer Metabolic Signature Predicts Co-Dependency on Glutaminase and De Novo Glutathione Synthesis Linked to a High-Mesenchymal Cell State
Anneleen Daemen,Bonnie Liu,Kyung Song,Mandy Kwong,Min Gao,Rebecca Hong,Michelle Nannini,David A. Peterson,Bianca M. Liederer,Cecile de la Cruz,Dewakar Sangaraju,Allan Jaochico,Xiaofeng Zhao,Wendy Sandoval,Thomas Hunsaker,Ron Firestein,Sheerin Latham,Deepak Sampath,Marie Evangelista,Georgia Hatzivassiliou +19 more
TL;DR: A pan-cancer metabolic signature predictive of GLS1/GCS co-dependency and validated in vivo using four lung patient-derived xenograft models revealed the additional requirement for expression of GAC above a threshold, suggesting that redox balance is a key function of G LS1 in tumors.
References
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Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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Bioconductor: open software development for computational biology and bioinformatics
Robert Gentleman,Vincent J. Carey,Douglas M. Bates,Benjamin M. Bolstad,Marcel Dettling,Sandrine Dudoit,Byron Ellis,Laurent Gautier,Yongchao Ge,Jeff Gentry,Kurt Hornik,Torsten Hothorn,Wolfgang Huber,Stefano Maria Iacus,Rafael A. Irizarry,Friedrich Leisch,Cheng Li,Martin Maechler,A. J. Rossini,Günther Sawitzki,Colin A. Smith,Gordon K. Smyth,Luke Tierney,Jean Yang,Jianhua Zhang +24 more
TL;DR: Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
Journal ArticleDOI
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
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