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Results: 380
f-scLVM
Florian Buettner, Naruemon Pratanwanich, Davis J McCarthy, John C Marioni, Oliver Stegle
Mar 26, 2018
Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing sources of variation...
Gene set annotations Single-cell RNA-seq Sparse factor analysis Animals Computer Simulation Databases as Topic Factor Analysis Statistical Gene Expression Regulation Mice Models Theoretical Mouse embryonic stem cells Neurons Reproducibility of Results Sequence Analysis RNA Single-Cell Analysis Software
Oxygen-Enhanced and Dynamic Contrast-Enhanced Optoacoustic Tomography Provide Surrogate Biomarkers of Tumor Vascular Function, Hypoxia, and Necrosis.
Michal R Tomaszewski, Marcel Gehrung, James Joseph, Isabel Quiros-Gonzalez, Jonathan A Disselhorst, Sarah E Bohndiek
Sep 29, 2018
Measuring the functional status of tumor vasculature, including blood flow fluctuations and changes in oxygenation, is important in cancer staging and therapy monitoring. Current clinically approved imaging modalities suffer...
PAGA
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis
Feb 18, 2019
A Decision Support System for Diagnostics and Treatment Planning in Traumatic Brain Injury.
Adil Umer, Jussi Mattila, Hilkka Liedes, Juha Koikkalainen, Jyrki Lotjonen, Ari Katila, Janek Frantzen, Virginia Newcombe, Olli Tenovuo, David Menon, Mark van Gils
Sep 20, 2018
Traumatic brain injury (TBI) occurs when an external force causes functional or structural alterations in the brain. Clinical characteristics of TBI vary greatly from patient to patient, and a large amount of data is gathered...
DeepSynergy
Kristina Preuer, Richard PI Lewis, Sepp Hochreiter, Andreas Bender, Krishna C Bulusu, Günter Klambauer
Nov 05, 2018
MOTIVATION: While drug combination therapies are a well-established concept in cancer treatment, identifying novel synergistic combinations is challenging due to the size of combinatorial space. However, computational approaches...
Freiburg RNA tools
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
Nov 06, 2018
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver...
FastSpar
SUMMARY: A common goal of microbiome studies is the elucidation of community composition and member interactions using counts of taxonomic units extracted from sequence data. Inference of interaction networks from sparse and...
PomBase 2018
Antonia Lock, Kim Rutherford, Midori A Harris, Jacqueline Hayles, Stephen G Oliver, Jürg Bähler, Valerie Wood
Nov 21, 2018
PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new...
Widespread inter-individual gene expression variability in Arabidopsis thaliana.
A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and...
Arabidopsis thaliana RNA‐seq inter‐individual heterogeneity noise in gene expression transcriptional variability Arabidopsis Arabidopsis Proteins Chromatin Circadian Rhythm Epigenesis Genetic Gene Expression Regulation Plant LIGHT Photoperiod Seedlings Sequence Analysis RNA Software Transcription Factors Transcriptome
An interactive genome browser of association results from the UK10K cohorts project.
Matthias Geihs, Ying Yan, Klaudia Walter, Jie Huang, Yasin Memari, Josine L Min, Daniel Mead, UK10K consortium, Tim J Hubbard, Nicholas J Timpson, Thomas A Down, Nicole Soranzo
Jun 25, 2018
UNLABELLED: High-throughput sequencing technologies survey genetic variation at genome scale and are increasingly used to study the contribution of rare and low-frequency genetic variants to human traits. As part of the Cohorts...
DynaMut
Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based...
TransRate
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly...
Detecting microRNA binding and siRNA off-target effects from expression data.
Sylamer is a method for detecting microRNA target and small interfering RNA off-target signals in 3' untranslated regions from a ranked gene list, sorted from upregulated to downregulated, after a microRNA perturbation or RNA...
A new R package and web application for detecting bilateral asymmetry in parasitic infections.
When parasites invade paired structures of their host non-randomly, the resulting asymmetry may have both pathological and ecological significance. To facilitate the detection and visualisation of asymmetric infections we have...
HGVA
Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
Aug 18, 2017
High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying...
Souporcell
Haynes Heaton, Arthur M Talman, Andrew Knights, Maria Imaz, Daniel J Gaffney, Richard Durbin, Martin Hemberg, Mara Kn Lawniczak
Apr 01, 2020
SimArray
Richard P Auburn, Roslin R Russell, Bettina Fischer, Lisa A Meadows, Santiago Sevillano Matilla, Steven Russell
Jun 13, 2011
Performing statistical analyses on quantitative data in Taverna workflows
Peter Li, Juan I Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R Pocock, Carole A Goble, Stephen G Oliver, Douglas B Kell
Jun 14, 2011
XGAP
Morris A Swertz, K Joeri van der Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Ritsert C Jansen
Jun 17, 2011
Copynumber
Gro Nilsen, Knut Liestøl, Peter Van Loo, Hans Kristian Moen Vollan, Marianne B Eide, Oscar M Rueda, Suet-Feung Chin, Roslin Russell, Lars O Baumbusch, Carlos Caldas, Anne-Lise Børresen-Dale, Ole Christian Lingjaerde
Feb 26, 2013
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