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Greg's Awesome Thesis
Analysis of alignment error and sitewise constraint in mammalian comparative genomics Gregory Jordan European Bioinformatics Institute University of Cambridge A dissertation submitted for the degree of Doctor of Philosophy November 30, 2011 To my parents, who kept us thinking and playing This dissertation is the result of my own work and includes nothing which is the out- come of work done in collaboration except where specifically indicated in the text and acknowledgements. This dissertation is not substantially the same as any I have submitted for a degree, diploma or other qualification at any other university, and no part has already been, or is currently being submitted for any degree, diploma or other qualification. This dissertation does not exceed the specified length limit of 60,000 words as defined by the Biology Degree Committee. November 30, 2011 Gregory Jordan ii Analysis of alignment error and sitewise constraint in mammalian comparative genomics Summary Gregory Jordan November 30, 2011 Darwin College Insight into the evolution of protein-coding genes can be gained from the use of phylogenetic codon models. Recently sequenced mammalian genomes and powerful analysis methods developed over the past decade provide the potential to globally measure the impact of natural selection on pro- tein sequences at a fine scale. The detection of positive selection in particular is of great interest, with relevance to the study of host-parasite conflicts, immune system evolution and adaptive dif- ferences between species. This thesis examines the performance of methods for detecting positive selection first with a series of simulation experiments, and then with two empirical studies in mammals and primates. -
AADACL4 (N-17): Sc-244849
SAN TA C RUZ BI OTEC HNOL OG Y, INC . AADACL4 (N-17): sc-244849 BACKGROUND CHROMOSOMAL LOCATION AADACL4 (arylacetamide deacetylase-like 4) is a 407 amino acid single-pass Genetic locus: AADACL4 (human) mapping to 1p36.21. type II membrane protein belonging to the “GDXG” lipolytic enzyme family. Integral to the cell membrane, AADACL4 participates in carboxylesterase SOURCE and hydrolase activities and is encoded by a gene that maps to human chro - AADACL4 (N-17) is an affinity purified goat polyclonal antibody raised mosome 1p36.21. Chromosome 1, the largest human chromosome, makes up against a peptide mapping near the N-terminus of AADACL4 of human origin. 8% of the human genome and contains about 260 million base pairs, which encode 3,000 genes. Chromosome 1 houses a large number of disease-asso - PRODUCT ciated genes, including those that are involved in familial adenomatous poly - posis, Stickler syndrome, Parkinson’s disease, Gaucher disease, schizophre - Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide nia and Usher syndrome. Aberrations in chromosome 1 are found in a variety and 0.1% gelatin. of cancers, including head and neck cancer, malignant melanoma and multi - Blocking peptide available for competition studies, sc-244849 P, (100 µg ple myeloma. peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). REFERENCES APPLICATIONS 1. Blackwood, D.H., Fordyce, A., Walker, M.T., St Clair, D.M., Porteous, D.J. AADACL4 (N-17) is recommended for detection of AADACL4 of human origin and Muir, W.J. -
Fátima Lopes Mscthesis VERSÃO FINAL IMPRESSÃO ANÓNIMO
Universidade de Aveiro Departamento de Química Ano 2011 Fátima Daniela Alterações de dosagem no genoma de doentes com Teixeira Lopes atraso mental Genomic imbalances in patients with intellectual disability Universidade de Aveiro Departamento de Química Ano 2011 Fátima Daniela Alterações de dosagem no genoma de doentes Teixeira Lopes com atraso mental Genomic imbalances in patients with intellectual disability Dissertação apresentada à Universidade de Aveiro para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Biotecnologia , realizada sob a orientação científica da Doutor a Patrícia Espinheira de Sá Maciel, Professora A uxiliar da Escola de Ciências da Saúde da Universidade do Minho, e da Doutora Odete Cruz e Silva, Professora A uxiliar do Departamento de Biologia da Universidade de Aveiro. Apoio financeiro da FCT (PIC/IC/83026/2007) no âmbito do III Quadro Comunitário de Apoio. “Sooner or later we will find the cause, and it will be in exactly the same way as we have found genes for other disorders - by lucky coincidence. (…)There isn't anything unique about not having discovered it yet." John Marius Opitz, 1997 Por este motivo, este pequeno contributo é dedicado aos pais das crianças envolvidas neste estudo. o júri presidente Professor Doutor Jorge Manuel Alexandre Saraiva Investigador Auxiliar do Departamento de Química da Universidade de Aveiro Professora Doutora Filipa Abreu Gomes de Carvalho Professora Associada com Agregação da Faculdade de Medicina da Universidade do Porto Professora Doutora Patrícia Espinheira de Sá Maciel Professora Auxiliar da Escola de Ciências da Saúde da Universidade do Minho Professora Doutora Odete Cruz e Silva Professora Auxiliar do Departamento de Biologia da Universidade de Aveiro. -
Transcriptional Co-Regulation of Micrornas and Protein-Coding Genes
Transcriptional co-regulation of microRNAs and protein-coding genes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2013 By Aaron Webber Table of Contents Abstract ......................................................................................................................................... 8 Declaration .................................................................................................................................... 9 Copyright statement ................................................................................................................... 10 Acknowledgements ..................................................................................................................... 11 Preface ........................................................................................................................................ 12 Chapter 1: Introduction .............................................................................................................. 13 1.1 The protein-coding gene expression pathway ............................................................ 13 1.2 Regulation of transcription ......................................................................................... 17 1.2.1 Transcription factors ........................................................................................... 19 1.2.2 Transcriptional regulatory regions ...................................................................... 22 -
Comprehensive Structural Variation Genome Map of Individuals Carrying Complex Chromosomal Rearrangements
RESEARCH ARTICLE Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements 1,2☯ 1,3☯ 4 1,5 Jesper Eisfeldt , Maria PetterssonID , Francesco VezziID , Josephine Wincent , 6 7 1,2,3,5 1,3,5 Max KaÈllerID , Joel Gruselius , Daniel NilssonID , Elisabeth Syk Lundberg , Claudia 8 1,3,5 M. B. CarvalhoID , Anna LindstrandID * 1 Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden, 2 Science for a1111111111 Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden, 3 Center for Molecular Medicine, a1111111111 Karolinska Institutet, Stockholm, Sweden, 4 Science for Life Laboratory, Department of Biochemistry and a1111111111 Biophysics, Stockholm University, Stockholm, Sweden, 5 Department of Clinical Genetics, Karolinska a1111111111 University Hospital, Stockholm, Sweden, 6 Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden, 7 Science for a1111111111 Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden, 8 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Eisfeldt J, Pettersson M, Vezzi F, Wincent J, KaÈller M, Gruselius J, et al. (2019) Comprehensive structural variation genome map of Abstract individuals carrying complex chromosomal rearrangements. PLoS Genet -
Genetic Imbalance in Patients with Cervical Artery Dissection
206 Send Orders for Reprints to [email protected] Current Genomics, 2017, 18, 206-213 RESEARCH ARTICLE ISSN: 1389-2029 eISSN: 1875-5488 Impact Factor: 2.43 Genetic Imbalance in Patients with Cervical Artery Dissection BENTHAM SCIENCE Caspar Grond-Ginsbach1,*, Bowang Chen2, Michael Krawczak3, Rastislav Pjontek4, Philip Ginsbach5, Yanxiang Jiang6, Shérine Abboud7, Marie-Luise Arnold1, Anna Bersano8, Tobias Brandt9, Valeria Caso10, Stéphanie Debette11, Martin Dichgans12,13, Andreas Geschwendtner12, Giacomo Giacalone14, Juan-José Martin15, Antti J. Metso16, Tiina M. Metso16, Armin J. Grau17, Manja Kloss1, Christoph Lichy18, Alessandro Pezzini19, Christopher Traenka20, Stefan Schreiber21, Vincent Thijs22, Emmanuel Touzé23,24, Elisabetta Del Zotto25, Turgut Tatlisumak16,26,27, Didier Leys28, Philippe A. Lyrer20, Stefan T. Engelter20,29 for the CADISP group. 1Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany; 2Department of Biology, South University of Science and Technology of China, Shenzhen, China; 3Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Kiel, Germany; 4Department of Neuroradiology, University of Aachen, Aachen, Germany; 5School of Informatics, University of Edinburgh, United Kingdom; 6Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany; 7Laboratory of Experimental Neurology, Université Libre de Bruxelles, Brussels, Belgium; 8Cerebrovascular Unit IRCCS Founda- tion C.Besta Neurological Institute, via Celoria 11, Milan, Italy; -
From Linkage to GWAS: a Multifaceted Exploration of the Genetic Risk for Alcohol Dependence
Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2012 From Linkage to GWAS: A Multifaceted Exploration of the Genetic Risk for Alcohol Dependence Amy Adkins Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Medical Genetics Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2920 This Dissertation is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Amy E. Adkins, December 2012 All Rights Reserved From Linkage to GWAS: A Multifaceted Exploration of the Genetic Risk for Alcohol Dependence A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. by Amy Elizabeth Adkins, B.S. Department of Human and Molecular Genetics Virginia Commonwealth University Director: Brien P. Riley, Ph.D. Associate Professor, Departments Psychiatry and Human and Molecular Genetics Virginia Commonwealth University Richmond, Virginia December, 2012 ACKNOWLEDGMENT I have been lucky enough to be surrounded by wonderful friends, family and colleagues that have supported me professionally and personally during my tenure in graduate school. My advisor, Brien Riley, has been exceedingly kind and generous with his time. He has taught me what it means to be a great teacher and kindled a desire in me to pursue the same. Danielle Dick, Jill Bettinger and Mike Grotewiel have been incredibly supportive committee members who helped me develop as a scientist and as an individual. -
Genetic Imbalance in Patients with Cervical Artery Dissection
Send Orders for Reprints to [email protected] Current Genomics, 2017, 18, 000-000 1 RESEARCH ARTICLE Genetic Imbalance in Patients with Cervical Artery Dissection Caspar Grond-Ginsbach1,*, Bowang Chen2, Michael Krawczak3, Rastislav Pjontek4, Philip Ginsbach5, Yanxiang Jiang6, Shérine Abboud7, Marie-Luise Arnold1, Anna Bersano8, Tobias Brandt9, Valeria Caso10, Stéphanie Debette11, Martin Dichgans12,13, Andreas Geschwendtner12, Giacomo Giacalone14, Juan-José Martin15, Antti J. Metso16, Tiina M. Metso16, Armin J. Grau17, Manja Kloss1, Christoph Lichy18, Alessandro Pezzini19, Christopher Traenka20, Stefan Schreiber21, Vincent Thijs22, Emmanuel Touzé23,24, Elisabetta Del Zotto25, Turgut Tatlisumak16,26,27, Didier Leys28, Philippe A. Lyrer20, Stefan T. Engelter20,29 for the CADISP group. 1Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany; 2Department of Biology, South University of Science and Technology of China, Shenzhen, China; 3Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Kiel, Germany; 4Department of Neuroradiology, University of Aachen, Aachen, Germany; 5School of Informatics, University of Edinburgh, United Kingdom; 6Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany; 7Laboratory of Experimental Neurology, Université Libre de Bruxelles, Brussels, Belgium; 8Cerebrovascular Unit IRCCS Founda- tion C.Besta Neurological Institute, via Celoria 11, Milan, Italy; 9Clinics for Neurologic Rehabilitation, Kliniken Schmieder, Heidel- -
Molecular and Cellular Pathways Associated with Chromosome 1P Deletions During Colon Carcinogenesis
Clinical and Experimental Gastroenterology Dovepress open access to scientific and medical research Open Access Full Text Article REVIEW Molecular and cellular pathways associated with chromosome 1p deletions during colon carcinogenesis Claire M Payne Abstract: Chromosomal instability is a major pathway of sporadic colon carcinogenesis. Cheray Crowley-Skillicorn Chromosome arm 1p appears to be one of the “hot spots” in the non-neoplastic mucosa that, Carol Bernstein when deleted, is associated with the initiation of carcinogenesis. Chromosome arm 1p contains Hana Holubec genes associated with DNA repair, spindle checkpoint function, apoptosis, multiple microRNAs, Harris Bernstein the Wnt signaling pathway, tumor suppression, antioxidant activities, and defense against environmental toxins. Loss of 1p is dangerous since it would likely contribute to genomic Department of Cell Biology instability leading to tumorigenesis. The 1p deletion-associated colon carcinogenesis pathways and Anatomy, College of Medicine, University of Arizona Tucson, AZ, USA are reviewed at the molecular and cellular levels. Sporadic colon cancer is strongly linked to a high-fat/low-vegetable/low-micronutrient, Western-style diet. We also consider how selected For personal use only. dietary-related compounds (eg, excess hydrophobic bile acids, and low levels of folic acid, niacin, plant-derived antioxidants, and other modulatory compounds) might affect processes leading to chromosomal deletions, and to the molecular and cellular pathways specifically altered by chromosome -
(12) Patent Application Publication (10) Pub. No.: US 2012/0053062 A1 BROOKS (43) Pub
US 20120053062A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0053062 A1 BROOKS (43) Pub. Date: Mar. 1, 2012 (54) DEFINING DAGNOSTIC AND Publication Classification THERAPEUTIC TARGETS OF CONSERVED FREE FLOATING FETAL DNA IN MATERNAL (51) Int. Cl. CIRCULATING BLOOD C40B 20/00 (2006.01) G06F 7/30 (2006.01) (75) Inventor: Andrew BROOKS, New York, NY C40B 40/06 (2006.01) (US) (73) Assignee: Bio Dx, Inc., San Diego, CA (US) (52) U.S. Cl. ......... 506/2:506/16; 707/758; 707/E17.014 (21) Appl. No.: 13/216,992 (22) Filed: Aug. 24, 2011 (57) ABSTRACT Related U.S. Application Data The present invention provides methods and materials useful (60) Provisional application No. 61/376,637, filed on Aug. for detecting cell free fetal DNA as well as markers for fetal 24, 2010. conditions by using biological samples of a maternal host. US 2012/0053062 A1 Mar. 1, 2012 DEFINING DAGNOSTIC AND 0009. In one embodiment, the conserved genomic seg THERAPEUTIC TARGETS OF CONSERVED ment is a genomic segment provided in Table 1. In one FREE FLOATING FETAL DNA IN MATERNAL embodiment, the conserved genomic segment includes any CIRCULATING BLOOD probe identified in Table 1. In another embodiment, the con served genomic segment includes any geneidentified in Table CROSS REFERENCE TO RELATED 1. In yet another embodiment, the conserved genomic seg APPLICATIONS ment is a fragment of a gene identified in Table 1, e.g., a fragment associated with any genotype marker of a gene 0001. This application claims priority to U.S. Provisional identified in Table 1.