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Results: 101
Comparative Genomics
Duncan T Odom
Jan 31, 2020
Using a common analysis pipeline to compare data from three major lineages of complex eukaryotes reveals that transcription seems to evolve at a common rate.
The natverse, a versatile toolbox for combining and analysing neuroanatomical data.
Alexander Shakeel Bates, James D Manton, Sridhar R Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory SXE Jefferis
Jul 06, 2020
To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite...
Genome-wide Estrogen Receptor-α activation is sustained, not cyclical.
Estrogen Receptor-alpha (ER) drives 75% of breast cancers. Stimulation of the ER by estra-2-diol forms a transcriptionally-active chromatin-bound complex. Previous studies reported that ER binding follows a cyclical pattern....
Estrogen estrogen receptor MCF7 Breast Cancer Chromosomes Computational Biology endocrine Gene Expression human Systems Biology Base Sequence Binding Sites Estradiol Estrogen Receptor alpha Female Gene Expression Regulation Neoplastic Genome Human Genome-Wide Association Study Humans MCF-7 Cells Neoplasm Proteins Promoter Regions Genetic Protein Binding Receptors CXCR Signal Transduction Sorting Nexins Trefoil Factor-1
Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency.
Andreas Lackner, Robert Sehlke, Marius Garmhausen, Giuliano Giuseppe Stirparo, Michelle Huth, Fabian Titz-Teixeira, Petra van der Lelij, Julia Ramesmayer, Henry F Thomas, Meryem Ralser, Laura Santini, Elena Galimberti, Mihail Sarov, A Francis Stewart, Austin Smith, Andreas Beyer, Martin Leeb
Apr 15, 2021
In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in...
Identifying the immune interactions underlying HLA class I disease associations.
Bisrat J Debebe, Lies Boelen, James C Lee, IAVI Protocol C Investigators, Eduard J Sanders, Omu Anzala, Anatoli Kamali, Pontiano Kaleebu, Etienne Karita, William Kilembe, Mubiana Inambao, Shabir Lakhi, Susan Allen, Eric Hunter, Vinodh A Edward, Pat E Fast, Matt A Price, Jill Gilmour, Jianming Tang, Chloe L Thio, Jacquie Astemborski, Gregory Kirk, Salim I Khakoo, Sharyne M Donfield, James J Goedert, Becca Asquith
Jun 19, 2020
Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for...
Perturbation biology
Evan J Molinelli, Anil Korkut, Weiqing Wang, Martin L Miller, Nicholas P Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B Solit, Christine A Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander
Mar 23, 2018
We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The...
The Algal Revolution.
Juliet Brodie, Cheong Xin Chan, Olivier De Clerck, J Mark Cock, Susana M Coelho, Claire Gachon, Arthur R Grossman, Thomas Mock, John A Raven, Alison G Smith, Hwan Su Yoon, Debashish Bhattacharya
May 08, 2018
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and...
Mitochondrial metabolites
C Frezza
Mar 09, 2017
Model‐guided development of an evolutionarily stable yeast chassis
Filipa Pereira, Helder Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, Dimitrios Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R Patil
Jul 28, 2021
EMBO41 EMBO21 EMBO23 article ARTICLES adaptive laboratory evolution chassis cell Metabolic Engineering multi‐objective optimization Systems Biology
Published by: Molecular Systems Biology
HIF-2α is essential for carotid body development and function.
David Macias, Andrew S Cowburn, Hortensia Torres-Torrelo, Patricia Ortega-Sáenz, José López-Barneo, Randall S Johnson
Apr 25, 2018
Mammalian adaptation to oxygen flux occurs at many levels, from shifts in cellular metabolism to physiological adaptations facilitated by the sympathetic nervous system and carotid body (CB). Interactions between differing forms...
The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Emma Lundberg, Joakim Lundeberg, Partha Majumder, John C Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe'er, Anthony Phillipakis, Chris P Ponting, Stephen Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael JT Stubbington, Fabian J Theis, Matthias Uhlen, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, Human Cell Atlas Meeting Participants
Feb 16, 2018
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in...
Model selection in systems biology depends on experimental design.
Experimental design attempts to maximise the information available for modelling tasks. An optimal experiment allows the inferred models or parameters to be chosen with the highest expected degree of confidence. If the true...
Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination.
BACKGROUND: Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis of...
Unsupervised data-driven stratification of mentalizing heterogeneity in autism.
Michael V Lombardo, Meng-Chuan Lai, Bonnie Auyeung, Rosemary J Holt, Carrie Allison, Paula Smith, Bhismadev Chakrabarti, Amber NV Ruigrok, John Suckling, Edward T Bullmore, MRC AIMS Consortium, Christine Ecker, Michael C Craig, Declan GM Murphy, Francesca Happé, Simon Baron-Cohen
Aug 16, 2017
Tumor diversity and the trade-off between universal cancer tasks.
Jean Hausser, Pablo Szekely, Noam Bar, Anat Zimmer, Hila Sheftel, Carlos Caldas, Uri Alon
Dec 04, 2019
Recent advances have enabled powerful methods to sort tumors into prognosis and treatment groups. We are still missing, however, a general theoretical framework to understand the vast diversity of tumor gene expression and...
Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging.
Janna Hastings, Abraham Mains, Bhupinder Virk, Nicolas Rodriguez, Sharlene Murdoch, Juliette Pearce, Sven Bergmann, Nicolas Le Novère, Olivia Casanueva
Jul 01, 2019
In this contribution, we describe a multi-omics systems biology study of the metabolic changes that occur during aging in Caenorhabditis elegans. Sampling several time points from young adulthood until early old age, our study...
Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis.
Alison L Kearney, Dougall M Norris, Milad Ghomlaghi, Martin Kin Lok Wong, Sean J Humphrey, Luke Carroll, Guang Yang, Kristen C Cooke, Pengyi Yang, Thomas A Geddes, Sungyoung Shin, Daniel J Fazakerley, Lan K Nguyen, David E James, James G Burchfield
Aug 13, 2021
The phosphoinositide 3-kinase (PI3K)-Akt network is tightly controlled by feedback mechanisms that regulate signal flow and ensure signal fidelity. A rapid overshoot in insulin-stimulated recruitment of Akt to the plasma...
human Insulin Cell Biology Phosphorylation Signal Transduction MOUSE plasma membrane Systems Biology Computational Biology PI3K Akt
Published by: eLife
Model-guided development of an evolutionarily stable yeast chassis.
Filipa Pereira, Helder Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, Dimitrios Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R Patil
Sep 20, 2021
First-principle metabolic modelling holds potential for designing microbial chassis that are resilient against phenotype reversal due to adaptive mutations. Yet, the theory of model-based chassis design has rarely been put to...
Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state.
Caterina Carraro, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Arik Horne, Marie Oestreich, Stefanie Warnat-Herresthal, Tim Helbing, Michele De Franco, Kristian Haendler, Sach Mukherjee, Thomas Ulas, Valentina Gandin, Richard Goettlich, Anna C Aschenbrenner, Joachim L Schultze, Barbara Gatto
Sep 30, 2022
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development...
The Immune Signatures data resource, a compendium of systems vaccinology datasets.
Joann Diray-Arce, Helen ER Miller, Evan Henrich, Bram Gerritsen, Matthew P Mulè, Slim Fourati, Jeremy Gygi, Thomas Hagan, Lewis Tomalin, Dmitry Rychkov, Dmitri Kazmin, Daniel G Chawla, Hailong Meng, Patrick Dunn, John Campbell, Human Immunology Project Consortium (HIPC), Minnie Sarwal, John S Tsang, Ofer Levy, Bali Pulendran, Rafick Sekaly, Aris Floratos, Raphael Gottardo, Steven H Kleinstein, Mayte Suárez-Fariñas
Nov 20, 2022
Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems...
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