Use of Figures in Literature Mining for Biomedical Digital Libraries
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University of Maryland Establishes Center for Health Related Informatics and Bioimaging
University of Maryland Establishes Center for Health Related Informatics and Bioimaging News & Events UNIVERSITY OF MARYLAND ESTABLISHES CENTER FOR HEALTH CONTACT RELATED INFORMATICS AND BIOIMAGING Monday, June 10, 2013 Karen Robinson, Media Relations New Center, Led By Distinguished Bioinformatics Scientist Owen White, (410) 706-7590 Ph.D., Unites Scientists Across Disciplines to Integrate Genomics and Personalized Medicine into Research and Clinical Care [email protected] University of Maryland, Baltimore campus President Jay A. Perman, M.D., and Media Relations Team University of Maryland School of Medicine Dean E. Albert Reece, M.D., Ph.D., M.B.A., wish to announce the establishment of a new center to unite research scientists and physicians across disciplines. The center will employ these SEARCH ARTICLES interdisciplinary connections to enhance the use of cutting edge medical science such as genomics and personalized medicine to accelerate research discoveries and improve health care outcomes. Participants in the new News Archives University of Maryland Center for Health-Related Informatics and Bioimaging (CHIB) will collaborate with computer scientists, engineers, life scientists and others at a similar center at the University of Maryland, College Park campus, CHIB Co-Director Owen White, Ph.D. together forming a joint center supported by the M-Power Maryland initiative. LEARN MORE University of Maryland School of Medicine Dean E. Albert Reece, M.D., Ph.D., M.B.A., with the concurrence of President Perman, has appointed as co-director of the new center Owen White, Ph.D., Professor of Epidemiology and Public Health and Director of Bioinformatics at the University of Maryland School of Medicine Institute for Genome Sciences. -
Supplementary Materials: Evaluation of Cytotoxicity and Α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids
Supplementary Materials: Evaluation of cytotoxicity and α-glucosidase inhibitory activity of amide and polyamino-derivatives of lupane triterpenoids Oxana B. Kazakova1*, Gul'nara V. Giniyatullina1, Akhat G. Mustafin1, Denis A. Babkov2, Elena V. Sokolova2, Alexander A. Spasov2* 1Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71, pr. Oktyabrya, 450054 Ufa, Russian Federation 2Scientific Center for Innovative Drugs, Volgograd State Medical University, Novorossiyskaya st. 39, Volgograd 400087, Russian Federation Correspondence Prof. Dr. Oxana B. Kazakova Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences 71 Prospeсt Oktyabrya Ufa, 450054 Russian Federation E-mail: [email protected] Prof. Dr. Alexander A. Spasov Scientific Center for Innovative Drugs of the Volgograd State Medical University 39 Novorossiyskaya st. Volgograd, 400087 Russian Federation E-mail: [email protected] Figure S1. 1H and 13C of compound 2. H NH N H O H O H 2 2 Figure S2. 1H and 13C of compound 4. NH2 O H O H CH3 O O H H3C O H 4 3 Figure S3. Anticancer screening data of compound 2 at single dose assay 4 Figure S4. Anticancer screening data of compound 7 at single dose assay 5 Figure S5. Anticancer screening data of compound 8 at single dose assay 6 Figure S6. Anticancer screening data of compound 9 at single dose assay 7 Figure S7. Anticancer screening data of compound 12 at single dose assay 8 Figure S8. Anticancer screening data of compound 13 at single dose assay 9 Figure S9. Anticancer screening data of compound 14 at single dose assay 10 Figure S10. -
Effects of Stressors on Differential Gene Expression And
EFFECTS OF STRESSORS ON DIFFERENTIAL GENE EXPRESSION AND SECONDARY METABOLITES BY AXINELLA CORRUGATA by Jennifer Grima A Thesis Submitted to the Faculty of Charles E. Schmidt College of Science in Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, Florida May 2013 ACKNOWLEDGEMENTS This thesis was made possible by the help and support of my mentors and friends. Without their guidance and expertise, I would not have been able to accomplish all that I have. Their belief and encouragement in my efforts have motivated and inspired me along through this journey and into a new era in my life. First and foremost, I am grateful to Dr. Shirley Pomponi for taking on the role as my advisor and giving me the opportunity to experience life as a researcher. Not only has she guided me in my scientific studies, she has become a wonderful, lifelong friend. Dr. Pomponi and Dr. Amy Wright have also provided financial support that enabled me to conduct the research and complete this thesis. I would also like to acknowledge Dr. Amy Wright for her willingness to tender advice on all things chemistry related as well as providing me with the space, equipment, and supplies to conduct the chemical analyses. I am grateful to Dr. Esther Guzman who not only served as a committee member, but has also been readily available to help me in any endeavor, whether it be research or personal related. She is truly one of kind with her breadth of knowledge in research and her loyal and caring character. -
Computational Analysis and Predictive Cheminformatics Modeling of Small Molecule Inhibitors of Epigenetic Modifiers
RESEARCH ARTICLE Computational Analysis and Predictive Cheminformatics Modeling of Small Molecule Inhibitors of Epigenetic Modifiers Salma Jamal1☯‡, Sonam Arora2☯‡, Vinod Scaria3* 1 CSIR Open Source Drug Discovery Unit (CSIR-OSDD), Anusandhan Bhawan, Delhi, India, 2 Delhi Technological University, Delhi, India, 3 GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India ☯ These authors contributed equally to this work. ‡ These authors are joint first authors on this work. * [email protected] a11111 Abstract Background The dynamic and differential regulation and expression of genes is majorly governed by the OPEN ACCESS complex interactions of a subset of biomolecules in the cell operating at multiple levels start- Citation: Jamal S, Arora S, Scaria V (2016) ing from genome organisation to protein post-translational regulation. The regulatory layer Computational Analysis and Predictive contributed by the epigenetic layer has been one of the favourite areas of interest recently. Cheminformatics Modeling of Small Molecule Inhibitors of Epigenetic Modifiers. PLoS ONE 11(9): This layer of regulation as we know today largely comprises of DNA modifications, histone e0083032. doi:10.1371/journal.pone.0083032 modifications and noncoding RNA regulation and the interplay between each of these major Editor: Wei Yan, University of Nevada School of components. Epigenetic regulation has been recently shown to be central to development Medicine, UNITED STATES of a number of disease processes. The availability of datasets of high-throughput screens Received: June 10, 2013 for molecules for biological properties offer a new opportunity to develop computational methodologies which would enable in-silico screening of large molecular libraries. -
DNA·RNA Triple Helix Formation Can Function As a Cis-Acting Regulatory
DNA·RNA triple helix formation can function as a cis-acting regulatory mechanism at the human β-globin locus Zhuo Zhoua, Keith E. Gilesa,b,c, and Gary Felsenfelda,1 aLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; bUniversity of Alabama at Birmingham Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294; and cDepartment of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294 Contributed by Gary Felsenfeld, February 4, 2019 (sent for review January 4, 2019; reviewed by James Douglas Engel and Sergei M. Mirkin) We have identified regulatory mechanisms in which an RNA tran- of the criteria necessary to establish the presence of a triplex script forms a DNA duplex·RNA triple helix with a gene or one of its structure, we first describe and characterize triplex formation at regulatory elements, suggesting potential auto-regulatory mecha- the FAU gene in human erythroid K562 cells. FAU encodes a nisms in vivo. We describe an interaction at the human β-globin protein that is a fusion containing fubi, a ubiquitin-like protein, locus, in which an RNA segment embedded in the second intron of and ribosomal protein S30. Although fubi function is unknown, the β-globin gene forms a DNA·RNA triplex with the HS2 sequence posttranslational processing produces S30, a component of the within the β-globin locus control region, a major regulator of glo- 40S ribosome. We used this system to refine methods necessary bin expression. We show in human K562 cells that the triplex is to detect triplex formation and to distinguish it from R-loop stable in vivo. -
Genome Informatics 2016 Davide Chicco1 and Michael M
Chicco and Hoffman Genome Biology (2017) 18:5 DOI 10.1186/s13059-016-1135-5 MEETINGREPORT Open Access Genome Informatics 2016 Davide Chicco1 and Michael M. Hoffman1,2,3* Abstract of sequence variants. Konrad Karczewski (Massachusetts General Hospital, USA) presented the Loss Of Func- A report on the Genome Informatics conference, held tion Transcript Effect Estimator (LOFTEE, https://github. at the Wellcome Genome Campus Conference Centre, com/konradjk/loftee). LOFTEE uses a support vector Hinxton, United Kingdom, 19–22 September 2016. machine to identify sequence variants that significantly disrupt a gene and potentially affect biological processes. We report a sampling of the advances in computational Martin Kircher (University of Washington, USA) dis- genomics presented at the most recent Genome Informat- cussed a massively parallel reporter assay (MPRA) that ics conference. As in Genome Informatics 2014 [1], speak- uses a lentivirus for genomic integration, called lentiM- ers presented research on personal and medical genomics, PRA [3]. He used lentiMPRA to predict enhancer activity, transcriptomics, epigenomics, and metagenomics, new and to more generally measure the functional effect of sequencing techniques, and new computational algo- non-coding variants. William McLaren (European Bioin- rithms to crunch ever-larger genomic datasets. Two formatics Institute, UK) presented Haplosaurus, a variant changes were notable. First, there was a marked increase effect predictor that uses haplotype-phased data (https:// in the number of projects involving single-cell analy- github.com/willmclaren/ensembl-vep). ses, especially single-cell RNA-seq (scRNA-seq). Second, Two presenters discussed genome informatics while participants continued the practice of present- approaches to the analysis of cancer immunotherapy ing unpublished results, a large number of the presen- response. -
Teaching Bioinformatics and Neuroinformatics Using Free Web-Based Tools
UCLA Behavioral Neuroscience Title Teaching Bioinformatics and Neuroinformatics Using Free Web-based Tools Permalink https://escholarship.org/uc/item/2689x2hk Author Grisham, William Publication Date 2009 Supplemental Material https://escholarship.org/uc/item/2689x2hk#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California – SUBMITTED – [Article; 34,852 Characters] Teaching Bioinformatics and Neuroinformatics Using Free Web-based Tools William Grisham 1, Natalie A. Schottler 1, Joanne Valli-Marill 2, Lisa Beck 3, Jackson Beatty 1 1Department of Psychology, UCLA; 2 Office of Instructional Development, UCLA; 3Department of Psychology, Bryn Mawr College Keywords: quantitative trait locus, digital teaching tools, web-based learning, genetic analysis, in silico tools DRAFT: Copyright William Grisham, 2009 Address correspondence to: William Grisham Department of Psychology, UCLA PO Box 951563 Los Angeles, CA 90095-1563 [email protected] Grisham Teaching Bioinformatics Using Web-Based Tools ABSTRACT This completely computer-based module’s purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. This module integrates information gathered from websites dealing with anatomy (Mouse Brain Library), Quantitative Trait Locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, NCBI Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). This module provides for teaching genetics from the phenotypic level to the molecular level, some neuroanatomy, some aspects of histology, statistics, Quantitaive Trait Locus analysis, molecular biology including in situ hybridization and microarray analysis in addition to introducing bioinformatic resources. -
Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. -
Gene Selection Using Gene Expression Data in a Virtual Environment
276 Genome Informatics 13: 276-277 (2002) Gene Selection Using Gene Expression Data in a Virtual Environment Kunihiro Nishimura1 Shumpei Ishikawa2 [email protected] [email protected] Shuichi Tsutsumi2 Hiroyuki Aburatani2 [email protected] [email protected] Koichi Hirota2 Michitaka Hirose2 [email protected] [email protected] 1 Graduate School of Information Science and Technology , The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 2 Reseach Center for Advanced Science and Technology , The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan Keywords: gene selection, gene expression, virtual reality, visualization 1 Gene Selection for Drug Discovery The gene expression data of many normal and diseased tissues enables the selection of genes that satisfy the conditions for finding a new drug. In the process of selecting genes is required to determine many filtering parameters. The system of the selection of genes from all genes is required to have the following features: 1) visualization of the data to provide the users to grasp both holistic and detail views of the data, 2) interactivity to determine many filtering parameters, 3) provides spatial cue to understand intuitively because there are many filtering parameters. In order to visualize various information of large number of genes, the system also needs a wide field of view. Virtual reality technology satisfies these requirements above. 2 Virtual Reality Virtual reality technology can help improve genome data analysis by enabling interactive visualization and providing a three-dimensional virtual environment. -
Accepted Version
Article A catalog of genetic loci associated with kidney function from analyses of a million individuals WUTTKE, Matthias, et al. Abstract Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through trans-ancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n?=?1,046,070), we identified 264 associated loci (166 new). Of these, 147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n?=?416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority [...] Reference WUTTKE, Matthias, et al. A catalog of genetic loci associated with kidney function from analyses of a million individuals. Nature Genetics, 2019, vol. 51, no. 6, p. 957-972 DOI : 10.1038/s41588-019-0407-x PMID : 31152163 Available at: http://archive-ouverte.unige.ch/unige:147447 Disclaimer: layout of this document may differ from the published version. 1 / 1 HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Genet Manuscript Author . Author manuscript; Manuscript Author available in PMC 2019 August 19. -
UNDERGRADUATE RESEARCH SYMPOSIUM 03.31.17 March 31St, 2017
Sev ent h Annu a l UNDERGRADUATE RESEARCH SYMPOSIUM 03.31.17 March 31st, 2017 Live Oak Pavilion and Grand Palm Room Boca Raton Campus WELCOME Welcome to the 7th Annual Undergraduate Research Sym- posium, which showcases undergraduate students at FAU who are engaged in research, scholarship and creative ac- tivities. Students present their findings through poster or visual and oral or performing arts presentations, and rep- resent all disciplines, all colleges, and all campuses of FAU. Few activities are as rewarding intellectually as research and inquiry. In addition to the acquisition of invaluable re- search skills, students learn how knowledge is created and how that knowledge can be overturned with new evidence or new perspectives. Such scholarly activities engage stu- dents in working independently, overcoming obstacles, and learning the importance of ethics and personal conduct in the research process. The Office of Undergraduate Research and Inquiry (OURI) serves as a centralized support office of both faculty and students who are engaged in undergraduate research and inquiry. We offer and support university wide programs such as undergraduate research grants, annual undergraduate research symposia, and undergraduate research journals, to name a few. We also support all departments and all col- leges across all campuses in their undergraduate research and inquiry initiatives. The Undergraduate Research Symposium is part of our University’s Quality Enhancement Plan (QEP) efforts aimed at expanding a culture of undergraduate research -
Cheminformatics Education
Cheminformatics Education Introduction Despite some skepticism at the turn of the century1,2 the terms “cheminformatics” and “chemoinformatics” are now in common parlance. The term “chemical informatics” is used less. The premier journal in the field, the Journal of Chemical Information and Modeling, does not use any of these terms and its cheminformatics papers are scattered across multiple sections including “chemical Information”. Unfortunately it is not just the name of the discipline that is undefined: opinions also vary on the scope. Paris supplied the following definition1 (shortened here): “Chem(o)informatics is a generic term that encompasses the design, creation, organization, storage, management, retrieval, analysis, dissemination, visualization and use of chemical information, not only in its own right, but as a surrogate or index for other data, information and knowledge”. Brown3 says the discipline is “mixing of information resources to transform data into information, and information into knowledge, for the intended purpose of making better decisions faster in the arena of drug lead identification and optimization”. Gasteiger4 says that cheminformatics is the application of informatics methods to solve chemical problems and Bajorath5 agrees that a broad definition such as that is needed to cover all the different scientific activities that have evolved, or have been assimilated, under the cheminformatics umbrella. Varnek’s definition6,7 is rather different. He considers that cheminformatics is a part of theoretical chemistry based on its own molecular model; unlike quantum chemistry in which molecules are represented as ensemble of electrons and nuclei, or force fields molecular modeling dealing with classical “atoms” and “bonds”, cheminformatics considers molecules as objects (graphs and vectors) in multidimensional chemical space.