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Results: 24
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
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
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...
Persistence of haemostatic response following gene therapy with valoctocogene roxaparvovec in severe haemophilia A.
K John Pasi, Michael Laffan, Savita Rangarajan, Tara M Robinson, Nina Mitchell, Will Lester, Emily Symington, Bella Madan, Xinqun Yang, Benjamin Kim, Glenn F Pierce, Wing Yen Wong
Nov 08, 2021
INTRODUCTION: Valoctocogene roxaparvovec is an investigational AAV5-based factor VIII (FVIII) gene therapy that has demonstrated sustained clinical benefit in people with severe haemophilia A. AIM: To report safety...
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
Abstract: Background: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are...
Haplotype-aware graph indexes.
MOTIVATION: The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes. RESULTS...
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph.
BACKGROUND: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and...
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
Abstract: Background: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are...
Modification of a Constitutive to Glucose-Responsive Liver-Specific Promoter Resulted in Increased Efficacy of Adeno-Associated Virus Serotype 8-Insulin Gene Therapy of Diabetic Mice.
We have previously used a hepatotropic adeno-associated viral (AAV) vector with a modified human insulin gene to treat diabetic mice. The HLP (hybrid liver-specific promoter) used was constitutively active and non-responsive to...
adeno-associated virus serotype 8 (AAV8) albumin enhancer (3′iALB) diabetes gene therapy glucose responsive element (GlRE) liver-specific glucose-responsive promoter long-term basal insulin expression Animals Dependovirus Diabetes mellitus Experimental Disease Models Animal Gene Expression Genetic Therapy Genetic Vectors Glucose Hepatocytes Humans Insulin Mice Promoter Regions Genetic Transgenes
Notch inhibits Yorkie activity in Drosophila wing discs.
During development, tissues and organs must coordinate growth and patterning so they reach the right size and shape. During larval stages, a dramatic increase in size and cell number of Drosophila wing imaginal discs is...
Managing macropods without poisoning ecosystems
JO Hampton, JM Pay, TE Katzner, JM Arnemo, MA Pokras, E Buenz, N Kanstrup, VG Thomas, M Uhart, SA Lambertucci, O Krone, NJ Singh, V Naidoo, M Ishizuka, K Saito, B Helander, RE Green
Jun 07, 2022
Summary: A recent review of the management of hyperabundant macropods in Australia proposed that expanded professional shooting is likely to lead to better biodiversity and animal welfare outcomes. While the tenets of this...
A decade with vamdc
This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates...
D Albert, BK Antony, YA Ba, YL Babikov, P Bollard, V Boudon, F Delahaye, G Del Zanna, MS Dimitrijević, BJ Drouin, ML Dubernet, F Duensing, M Emoto, CP Endres, AZ Fazliev, JM Glorian, IE Gordon, P Gratier, C Hill, D Jevremović, C Joblin, DH Kwon, RV Kochanov, E Krishnakumar, G Leto, PA Loboda, AA Lukashevskaya, OM Lyulin, BP Marinković, A Markwick, T Marquart, NJ Mason, C Mendoza, TJ Millar, N Moreau, SV Morozov, T Möller, HSP Müller, G Mulas, I Murakami, Y Pakhomov, P Palmeri, J Penguen, VI Perevalov, N Piskunov, J Postler, AI Privezentsev, P Quinet, Y Ralchenko, YJ Rhee, C Richard, G Rixon, LS Rothman, E Roueff, T Ryabchikova, S Sahal-Bréchot, P Scheier, P Schilke, S Schlemmer, KW Smith, B Schmitt, IY Skobelev, VA Srecković, E Stempels, SA Tashkun, J Tennyson, VG Tyuterev, C Vastel, V Vujčić, V Wakelam, NA Walton, C Zeippen, CM Zwölf
Oct 22, 2020
Layered material platform for surface plasmon resonance biosensing.
F Wu, PA Thomas, VG Kravets, HO Arola, M Soikkeli, K Iljin, G Kim, M Kim, HS Shin, DV Andreeva, C Neumann, M Küllmer, A Turchanin, D De Fazio, O Balci, V Babenko, B Luo, I Goykhman, S Hofmann, AC Ferrari, KS Novoselov, AN Grigorenko
Feb 24, 2020
Plasmonic biosensing has emerged as the most sensitive label-free technique to detect various molecular species in solutions and has already proved crucial in drug discovery, food safety and studies of bio-reactions. This...
Fructose-driven glycolysis supports anoxia resistance in the naked mole-rat
TJ Park, J Reznick, BL Peterson, G Blass, D Omerbašić, NC Bennett, PHJL Kuich, C Zasada, BM Browe, W Hamann, DT Applegate, MH Radke, T Kosten, H Lutermann, V Gavaghan, O Eigenbrod, V Bégay, VG Amoroso, V Govind, RD Minshall, ESJ Smith, J Larson, M Gotthardt, S Kempa, GR Lewin
May 08, 2017
A new approach to define and diagnose cardiometabolic disorder in children.
Lars Bo Andersen, Jeppe Bo Lauersen, Jan Christian Brønd, Sigmund Alfred Anderssen, Luis B Sardinha, Jostein Steene-Johannessen, Robert G McMurray, Mauro VG Barros, Susi Kriemler, Niels Christian Møller, Anna Bugge, Peter Lund Kristensen, Mathias Ried-Larsen, Anders Grøntved, Ulf Ekelund
Aug 28, 2017
Are cost advantages from a modern Indian hospital transferable to the United States?
F Erhun, RS Kaplan, VG Narayanan, K Brayton, M Kalani, MC Mazza, C Nguyen, T Platchek, B Mistry, R Mann, D Kazi, C Pinnock, KA Schulman, J Xue, D Ballard, M Mack, B James, G Poulsen, J Punnen, D Shetty, A Milstein
May 18, 2020
Multiple modern Indian hospitals operate at very low cost while meeting US-equivalent quality accreditation standards. Though US hospitals face intensifying pressure to lower their cost, including proposals to extend Medicare...
Long-Term Sustained Effect of Liver-Targeted Adeno-Associated Virus Gene Therapy for Mitochondrial Neurogastrointestinal Encephalomyopathy.
Javier Torres-Torronteras, Raquel Cabrera-Pérez, Ferran Vila-Julià, Carlo Viscomi, Yolanda Cámara, Michio Hirano, Massimo Zeviani, Ramon Martí
Jul 04, 2018
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by mutations in TYMP, the gene encoding the enzyme thymidine phosphorylase (TP). TP dysfunction results in systemic accumulation of the noxious TP...
AAV MNGIE liver/metabolic Mitochondria thymidine phosphorylase Animals Carcinogenesis Deoxyuridine Dependovirus Female Gene Dosage Genetic Therapy Genetic Vectors Intestinal Pseudo-Obstruction Kaplan-Meier Estimate Liver Male Mice Mitochondria Liver Muscular Dystrophy Oculopharyngeal Ophthalmoplegia Thymidine Thymidine Phosphorylase Time Factors Transgenes
Factors affecting the electrocardiographic QT interval in malaria
Xin Hui S Chan, Yan Naung Win, Ilsa L Haeusler, Jireh Y Tan, Shanghavie Loganathan, Sompob Saralamba, Shu Kiat S Chan, Elizabeth A Ashley, Karen I Barnes, Rita Baiden, Peter U Bassi, Abdoulaye Djimde, Grant Dorsey, Stephan Duparc, Borimas Hanboonkunupakarn, Feiko O Ter Kuile, Marcus VG Lacerda, Amit Nasa, François H Nosten, Cyprian O Onyeji, Sasithon Pukrittayakamee, André M Siqueira, Joel Tarning, Walter RJ Taylor, Giovanni Valentini, Michèle van Vugt, David Wesche, Nicholas Pj Day, Christopher L-H Huang, Josep Brugada, Ric N Price, Nicholas J White
Apr 24, 2020
BACKGROUND: Electrocardiographic QT interval prolongation is the most widely used risk marker for ventricular arrhythmia potential and thus an important component of drug cardiotoxicity assessments. Several antimalarial...
Action Potentials Adolescent Adult Aged Aged 80 and over Antimalarials Arrhythmias Cardiac Body Temperature Regulation Cardiotoxicity Child Child Preschool Electrocardiography Female Heart Conduction System Heart Rate Humans Infant Malaria Male Middle Aged Predictive Value of Tests Risk Assessment Risk Factors Severity of Illness Index Treatment Outcome Young Adult
A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.
Hidayat Trimarsanto, Roberto Amato, Richard D Pearson, Edwin Sutanto, Rintis Noviyanti, Leily Trianty, Jutta Marfurt, Zuleima Pava, Diego F Echeverry, Tatiana M Lopera-Mesa, Lidia M Montenegro, Alberto Tobón-Castaño, Matthew J Grigg, Bridget Barber, Timothy William, Nicholas M Anstey, Sisay Getachew, Beyene Petros, Abraham Aseffa, Ashenafi Assefa, Awab G Rahim, Nguyen H Chau, Tran T Hien, Mohammad S Alam, Wasif A Khan, Benedikt Ley, Kamala Thriemer, Sonam Wangchuck, Yaghoob Hamedi, Ishag Adam, Yaobao Liu, Qi Gao, Kanlaya Sriprawat, Marcelo U Ferreira, Moses Laman, Alyssa Barry, Ivo Mueller, Marcus VG Lacerda, Alejandro Llanos-Cuentas, Srivicha Krudsood, Chanthap Lon, Rezika Mohammed, Daniel Yilma, Dhelio B Pereira, Fe EJ Espino, Cindy S Chu, Iván D Vélez, Chayadol Namaik-Larp, Maria F Villegas, Justin A Green, Gavin Koh, Julian C Rayner, Eleanor Drury, Sónia Gonçalves, Victoria Simpson, Olivo Miotto, Alistair Miles, Nicholas J White, Francois Nosten, Dominic P Kwiatkowski, Ric N Price, Sarah Auburn
Dec 23, 2022
A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.
Hidayat Trimarsanto, Roberto Amato, Richard D Pearson, Edwin Sutanto, Rintis Noviyanti, Leily Trianty, Jutta Marfurt, Zuleima Pava, Diego F Echeverry, Tatiana M Lopera-Mesa, Lidia M Montenegro, Alberto Tobón-Castaño, Matthew J Grigg, Bridget Barber, Timothy William, Nicholas M Anstey, Sisay Getachew, Beyene Petros, Abraham Aseffa, Ashenafi Assefa, Awab G Rahim, Nguyen H Chau, Tran T Hien, Mohammad S Alam, Wasif A Khan, Benedikt Ley, Kamala Thriemer, Sonam Wangchuck, Yaghoob Hamedi, Ishag Adam, Yaobao Liu, Qi Gao, Kanlaya Sriprawat, Marcelo U Ferreira, Moses Laman, Alyssa Barry, Ivo Mueller, Marcus VG Lacerda, Alejandro Llanos-Cuentas, Srivicha Krudsood, Chanthap Lon, Rezika Mohammed, Daniel Yilma, Dhelio B Pereira, Fe EJ Espino, Cindy S Chu, Iván D Vélez, Chayadol Namaik-Larp, Maria F Villegas, Justin A Green, Gavin Koh, Julian C Rayner, Eleanor Drury, Sónia Gonçalves, Victoria Simpson, Olivo Miotto, Alistair Miles, Nicholas J White, Francois Nosten, Dominic P Kwiatkowski, Ric N Price, Sarah Auburn
Jan 27, 2023
Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method...