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Results: 163
Neuronatin deletion causes postnatal growth restriction and adult obesity in 129S2/Sv mice.
Steven J Millership, Simon J Tunster, Mathew Van de Pette, Agharul I Choudhury, Elaine E Irvine, Mark Christian, Amanda G Fisher, Rosalind M John, James Scott, Dominic J Withers
Nov 19, 2018
OBJECTIVE: Imprinted genes are crucial for the growth and development of fetal and juvenile mammals. Altered imprinted gene dosage causes a variety of human disorders, with growth and development during these crucial early...
Genotyping structural variants in pangenome graphs using the vg toolkit
Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, Benedict Paten
Jun 06, 2020
Abstract: Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an...
Integrating Unsupervised and Supervised ML Models for Analysis of Synthetic Data From VAE, GAN, and Clustering of Variables
Lakshmi Prayaga, Krishna Devulapalli, Chandra Prayaga, Aaron Wade, Gopi Reddy, Sri Pola
Jan 01, 2024
Clustering of variables is a specialized approach for dimensionality reduction. This strategy is evaluated for data reduction with a Kaggle diabetes dataset. Since the original dataset is small, Generative Adversarial Networks...
Published by: IGI Global Scientific Publishing
Genotyping structural variants in pangenome graphs using the vg toolkit.
Glenn Hickey, David Heller, Jean Monlong, Jonas A Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T Dawson, Erik Garrison, Adam M Novak, Benedict Paten
Feb 11, 2021
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means...
Genotyping structural variants in pangenome graphs using the vg toolkit.
Glenn Hickey, David Heller, Jean Monlong, Jonas A Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T Dawson, Erik Garrison, Adam M Novak, Benedict Paten
Mar 15, 2020
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means...
Published by: Genome biology
Inferring structural variant cancer cell fraction.
Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, Niall M Corcoran, Tony Papenfuss, Christopher M Hovens, Florian Markowetz, Geoff Macintyre
Mar 10, 2020
We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV...
Published by: Nature Communications
Inferring structural variant cancer cell fraction
Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, Niall M. Corcoran, Tony Papenfuss, Christopher M. Hovens, Florian Markowetz, Geoff Macintyre, David J. Adams, Pavana Anur, Rameen Beroukhim, Paul C. Boutros, David D. L. Bowtell, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Jonas Demeulemeester, Stefan C. Dentro, Amit G. Deshwar, Nilgun Donmez, Ruben M. Drews, Roland Eils, Yu Fan, Matthew W. Fittall, Dale W. Garsed, Moritz Gerstung, Gad Getz, Santiago Gonzalez, Gavin Ha, Kerstin Haase, Marcin Imielinski, Lara Jerman, Yuan Ji, Clemency Jolly, Kortine Kleinheinz, Juhee Lee, Henry Lee-Six, Ignaty Leshchiner, Dimitri Livitz, Salem Malikic, Iñigo Martincorena, Thomas J. Mitchell, Quaid D. Morris, Ville Mustonen, Layla Oesper, Martin Peifer, Myron Peto, Benjamin J. Raphael, Daniel Rosebrock, Yulia Rubanova, S. Cenk Sahinalp, Adriana Salcedo, Matthias Schlesner, Steven E. Schumacher, Subhajit Sengupta, Ruian Shi, Seung Jun Shin, Paul T. Spellman, Oliver Spiro, Lincoln D. Stein, Maxime Tarabichi, Peter Van Loo, Shankar Vembu, Ignacio Vázquez-García, Wenyi Wang, David C. Wedge, David A. Wheeler, Jeffrey A. Wintersinger, Tsun-Po Yang, Xiaotong Yao, Kaixian Yu, Hongtu Zhu
Feb 04, 2021
Abstract: We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies...
The first magnetic resonance imaging-detected case of bilateral seminal vesicle duplication
Given the increasing use of prostate magnetic resonance imaging (MRI) for imaging suspected cancer and male infertility, understanding imaging features of congenital anomalies of the seminal vesicles (SVs) is of clinical...
Validation of a Non-invasive Inverse Problem-Solving Method for Stroke Volume.
Vasiliki Bikia, Carmel M McEniery, Emma Marie Roussel, Georgios Rovas, Stamatia Pagoulatou, Ian B Wilkinson, Nikolaos Stergiopulos
Feb 09, 2022
Stroke volume (SV) is a major biomarker of cardiac function, reflecting ventricular-vascular coupling. Despite this, hemodynamic monitoring and management seldomly includes assessments of SV and remains predominantly guided by...
Inferring structural variant cancer cell fraction.
Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, PCAWG Evolution and Heterogeneity Working Group, Niall M Corcoran, Tony Papenfuss, Christopher M Hovens, Florian Markowetz, Geoff Macintyre, PCAWG Consortium
Dec 18, 2019
We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV...
Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.
Alvin Wei Tian Ng, Gianmarco Contino, Sarah Killcoyne, Ginny Devonshire, Ray Hsu, Sujath Abbas, Jing Su, Aisling M Redmond, Jamie MJ Weaver, Matthew Eldridge, Simon Tavaré, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Paul AW Edwards, Rebecca Fitzgerald
Apr 08, 2022
Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed...
Protein phase separation hotspots at the presynapse.
Janin Lautenschläger
Mar 13, 2022
Fundamental discoveries have shaped our molecular understanding of presynaptic processes, such as neurotransmitter release, active zone organization and mechanisms of synaptic vesicle (SV) recycling. However, certain regulatory...
Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.
Alvin Wei Tian Ng, Gianmarco Contino, Sarah Killcoyne, Ginny Devonshire, Ray Hsu, Sujath Abbas, Jing Su, Aisling M Redmond, Jamie MJ Weaver, Matthew D Eldridge, Simon Tavaré, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Paul AW Edwards, Rebecca C Fitzgerald
May 09, 2022
Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed...
Protein phase separation hotspots at the presynapse
Janin Lautenschläger
Mar 04, 2022
Fundamental discoveries have shaped our molecular understanding of presynaptic processes, such as neurotransmitter release, active zone organization and mechanisms of synaptic vesicle (SV) recycling. However, certain regulatory...
Interactive nanocluster compaction of the ELKS scaffold and Cacophony Ca2+ channels drives sustained active zone potentiation.
Tina Ghelani, Marc Escher, Ulrich Thomas, Klara Esch, Janine Lützkendorf, Harald Depner, Marta Maglione, Pierre Parutto, Scott Gratz, Tanja Matkovic-Rachid, Stefanie Ryglewski, Alexander M Walter, David Holcman, Kate O'Connor Giles, Martin Heine, Stephan J Sigrist
Mar 20, 2023
At presynaptic active zones (AZs), conserved scaffold protein architectures control synaptic vesicle (SV) release by defining the nanoscale distribution and density of voltage-gated Ca2+ channels (VGCCs). While AZs can...
Protein phase separation hotspots at the presynapse.
Janin Lautenschläger
Feb 09, 2022
Fundamental discoveries have shaped our molecular understanding of presynaptic processes, such as neurotransmitter release, active zone organization and mechanisms of synaptic vesicle (SV) recycling. However, certain regulatory...
The impact of community health workers on antenatal and infant health in India
BACKGROUND: Community health workers (CHWs) are central to India's strategy for reaching the Sustainable Development Goals around maternal and child health. Despite India's significant investment in these programs, few studies...
Engineering chemistry for the future of organic synthesis
SV Ley
Aug 29, 2018
Societal and commercial pressures are impacting more than ever on the methods and techniques by which we assemble today's functional molecules. A holistic appreciation of this complex eco-system necessitates the invention of new...
Maternal traditional dietary pattern and antiretroviral treatment exposure are associated with neonatal size and adiposity in urban, black South Africans
© 2018 The Authors. This study examines the associations between maternal Traditional dietary pattern adherence and HIV/treatment with neonatal size and adiposity in urban, black South Africans, as well as how specific maternal...
ADP air displacement plethysmography ART antiretroviral treatment DXA dual-energy X-ray absorptiometry FMI fat mass index GWG gestational weight gain QFFQ quantitative FFQ WLR weight:length ratio antiretroviral treatment Neonatal adiposity Pregnancy South Africa Traditional dietary patterns Adiposity Adult Anti-Retroviral Agents Birth Weight Black People Body composition Body Height culture Diet Female HIV Infections Humans Infant Newborn Male Maternal Nutritional Physiological Phenomena Mothers obesity Preconception Care Pregnancy Pregnancy Complications Infectious Prenatal Care South Africa Urban Population Weight Gain
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