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Lynn M Schriml
 

Lynn M Schriml Ph.D.

Academic Title: Assistant Professor
Primary Appointment: Epidemiology & Public Health
Additional Title(s): Institute for Genome Sciences
lschriml@som.umaryland.edu
Location: BioPark II, 659
Phone: (410) 706-6776

Personal History:

Dr. Lynn M. Schriml is an Assistant Professor at the University of Maryland, School of Medicine in the Department of Epidemiology and Public Health and at the Institute of Genome Science (IGS) in Baltimore, Maryland. Dr. Schriml’s current research focuses on developing bioinformatic tools, metadata standards and ontologies to gain a broader understanding of the relationship between infectious pathogens, their genomic sequence and disease.

Dr. Schriml leads a number of ontology and metadata standard development and implementation projects. As PI of the Alfred P. Sloan Foundation funded Built Environment MIxS-BE Metadata project. Dr. Schriml leads efforts to provide tools to foster standard metadata collection and analysis across the Microbiology of the Built Environment program. As co-PI of the Disease Ontology, Dr. Schriml leads ontology community-based curation, expansion and utilization efforts. The Human Disease Ontology, a broadly adopted standard, is utilized across biomedical databases and resources for knowledge and data sharing through standardized annotation of biomedical data.

Dr. Schriml’s work involves extensive collaborative interactions with a diverse community of researchers and development of research projects involving consortiums, government and private sector collaborators. As a project leader, board member and developer in the Genomic Standards Consortium (GSC), Dr. Schriml is a promoter of metadata standards development and integration for genomic projects, including the HMP-DACC and NIAID GSCID projects hosted at the Institute for Genome Sciences, University of Maryland, Baltimore, into large scale genome databases (e.g. NCBI’s BioSample, NIAID BRC’s, JGI’s GOLD database). Dr. Schriml is the primary developer of a suite of OBO Foundry biomedical ontologies including the Disease Ontology, Symptom Ontology, Transmission Method Ontology, Influenza Ontology, Environmental (EnvO) ontology and geographic locations gazetteer (GAZ) vocabulary.

Following Dr. Schriml’s postdoctoral research at the National Cancer Institute - Frederick Cancer Research and Development Center conducting population studies and characterizing mouse ABC-transporters, Dr. Schriml transitioned to bioinformatics. Dr. Schriml development bioinformatics tools for model organism genome projects at the National Center for Biotechnology Information (NCBI) at NIH as a Staff Scientist prior to joining the Institute for Genome Research (TIGR) in 2005 to develop the microbial surveillance Gemina project.

Research Interests:

Human Disease, Infectious Diseases, Ontologies, Metadata Standards, Epidemiology, Bioinformatics, Data Mining, Statistics, Microbiome

Currently, I am interested in developing metadata standards and ontologies as bioinformatic tools to enhance our understanding of the relationship between microbial genomes and human health.

Ontologies represent a domain of knowledge in a semantic hierarchy. Collaborative, community-driven ontology development involves on-going coordinated efforts among clinicians, model organism databases and rare and common disease clinicians and researchers.

Structured sequence metadata describes the sample (collection date, location, sample source, body site, host age and gender) and sequence (sequence submitter, extraction and sequencing methods, publications) properties and is utilized by data providers to improve data management through more efficiently data descriptions and making sequence data more readily available and by researchers to discover, compare, and cite sequence records within and between data repositories based on relevant descriptors. Metadata standards are an important tool to achieve the needed structured metadata for genomic sequence records. Metadata annotations represent a novel dataset for researchers to utilize to identify critical associations between genomes, disease, and the environment.


Publications:

Dawn Field, Peter Sterk, Renzo Kottmann, J. Wim De Smet, Linda Amaral-Zettler, Guy Cochrane, James R. Cole, Neil Davies, Peter Dawyndt, George M. Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Hans-Peter Klenk, Rob Knight, Nikos Kyrpides, Folker Meyer, Ilene Karsch-Mizrachi, Norman Morrison, Robert Robbins, Inigo San Gil, Susanna Sansone, Lynn Schriml, Tatiana Tatusova, Dave Ussery, Pelin Yilmaz, Owen White, John Wooley, Gregory Caporaso. (2014) Genomic Standards Consortium Projects. Standards in Genomic Sciences. 9:3.

Schriml L. et al. (2013) The 15th Genomic Standards Consortium meeting. Standards in Genomic Sciences. 8:124-164.

EM Glass, Y Dribinsky, P Yilmaz, H Levin, R Van Pelt, D Wendel, A Wilke, J A Eisen, S Huse, A Shipanova, M Sogin, J Stajich, R Knight, F Meyer and LM Schriml. (2013) MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2013 Oct 24.

Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012. 486:207-714.

Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Stand Genomic Sci. 2012 Oct 10;7(1):159-65.

Yilmaz P et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 29:415-420.

Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N. 2010. GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Res. 2010 Jan;38(Database issue):D754-64

Hirschman L, Clark C, Cohen K, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides Morrison N, Schriml LM, Field D and the Novo Project. 2008. Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata. OMICS A Journal of Integrative Biology. 12:2.

Field D, Garrity G, Sansone S, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner F, Kottmann R, Angiuoli S, White O, Dawyndt P, Thompson N, Gli I, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L, and the GSC. 2008. Meeting Report: The Fifth Genomic Standards Consortium (GSC) Workshop. OMICS A Journal of Integrative Biology. 12: 2.

Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner F, Cole J, Farris R, Schriml L, De Vos P, De Baets B, Field D, Dawyndt P & the GSC. 2008. Laying the Foundation for a Genomic Rosetta Stone (GRS): creating information hubs through the use of consensus identifiers. OMICS A Journal of Integrative Biology. 12: 2 2008.

Schriml LM, Gussman A, Phillippy K, Angiuoli S, Hari K, Goates A, Jain R, Davidsen T, Ganapathy A, Salzberg S, White O, Hall N. Gemina: a Web-Based epidemiology and genomic metadata system designed to identify infectious pathogens. D. Zeng et al. (Eds.): BioSurveillance 2007. LNCS 4506, pp. 228-229.

Hall, N and LM Schriml. Bioinformatics: Methods Express (Paul H. Dear, eds.) @Scion Publishing Limited, 2007. Chapter 1: Database resources for wet-bench scientists.

Klein SL, Gerhard DS, Wagner L, Richardson P, Schriml LM, Sater AK, Warren WC, McPherson JD. 2006. Resources for genetic and genomic studies of Xenopus. Methods in Molecular Biology. 322:1-16.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. 2006. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 34:D173-80.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. 2005. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33: D39-45.

Schriml, LM and Sprague J. Data Mining the Zebrafish Genome. 2004. Methods in Cell Biology 77: 415-437.

Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Suzek TO, Tatusova TA, Wagner L. Database resources of the National Center for Biotechnology Information: update. 2004. Nucleic Acids Res. 32: D35-40.

Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J. Development and evaluation of an automated annotation pipeline and cDNA annotation system. 2003. Genome Res. 13:1542-1551.

Baldarelli RM, Hill DP, Blake JA, Adachi J, Furuno M, Bradt D, Corbani LE, Cousins S, Frazer KS, Qi D, Yang L, Ramachandran S, Reed D, Zhu Y, Kasukawa T, Ringwald M, King BL, Maltais LJ, McKenzie LM, Schriml LM, Maglott D, Church DM, Pruitt K, Eppig JT, Richardson JE, Kadin JA, Bult CJ. Connecting sequence and biology in the laboratory mouse. 2003. Genome Res. 13: 1505-1519.

Schriml LM, Hill DP, Blake JA, Bono H, Wynshaw-Boris A, Pavan WJ, Ring BZ, Beisel K, Setou M, Okazaki Y; RIKEN GER Group; GSL Members.
Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set. 2003. Genome Res. 13: 1496-1500.

Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. Database resources of the National Center for Biotechnology. 2003. Nucleic Acids Res. 31: 28-33.

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. 2002. Nature 420: 563-573.

Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA.
Database resources of the National Center for Biotechnology Information: 2002 update. 2002. Nucleic Acids Res. 30:13-16.

Hudson TJ, Church DM, Greenaway S, Nguyen H, Cook A, Steen RG, Van Etten WJ, Castle AB, Strivens MA, Trickett P, Heuston C, Davison C, Southwell A, Hardisty R, Varela-Carver A, Haynes AR, Rodriguez-Tome P, Doi H, Ko MS, Pontius J, Schriml L, Wagner L, Maglott D, Brown SD, Lander ES, Schuler G, Denny P. A radiation hybrid map of mouse genes. 2001. Nat Genet. 29: 201-205.

FANTOM Consortium: Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schonbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection. 2001. Nature 409: 685-690.

Broccardo C, Osorio J, Luciani MF, Schriml LM, Prades C, Shulenin S, Arnould I, Naudin L, Lafargue C, Rosier M, Jordan B, Mattei MG, Dean M, Denefle P, Chimini G. Comparative analysis of the promoter structure and genomic organization of the human and mouse ABCA7 gene encoding a novel ABCA transporter. 2001. Cytogenet Cell Genet 92: 264-270.

Mickley L, Jain P, Miyake K, Schriml LM, Rao K, Fojo T, Bates S, Dean M. An ATP-binding cassette gene (ABCG3) closely related to the multidrug transporter
ABCG2 (MXR/ABCP) has an unusual ATP-binding domain. 2001. Mamm Genome 12: 86-88.

Shulenin S, Schriml LM, Remaley AT, Fojo S, Brewer B, Allikmets R, Dean M. An ATP-binding cassette gene (ABCG5) from the ABCG (White) gene subfamily maps to human chromosome 2p21 in the region of the Sitosterolemia locus. 2001. Cytogenet Cell Genet 92: 204-208.

Schriml LM, Peterson RJ, Gerrard B, Dean M. Use of denaturing HPLC to map human and murine genes and to validate single-nucleotide polymorphisms. 2000. Biotechniques 28: 740-745.

Schriml LM, Dean M. Identification of 18 mouse ABC genes and characterization of the ABC superfamily in Mus musculus. 2000. Genomics 64: 24-31.

Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA. Database resources of the National Center for Biotechnology Information. 2001. Nucleic Acids Res. 29: 11-16.

Ali IU, Schriml LM, Dean M. Mutational spectra of PTEN/MMAC1 gene: a tumor suppressor with lipid phosphatase activity. 1999. J Natl Cancer Inst. 91: 1922-1932.

Schriml LM, Padilla-Nash HM, Coleman A, Moen P, Nash WG, Menninger J, Jones G, Ried T, Dean M. Tyramide signal amplification (TSA)-FISH applied to mapping PCR-labeled probes less than 1 kb in size. 1999. Biotechniques 27: 608-613.

Saxena A, Schriml LM, Dean M, Ali IU. Comparative molecular genetic profiles of anaplastic astrocytomas/glioblastomas multiforme and their subsequent recurrences. 1999. Oncogene 18: 1385-1390.

Allikmets R, Schriml LM, Hutchinson A, Romano-Spica V, Dean M. A human placenta-specific ATP-binding cassette gene (ABCP) on chromosome 4q22 that is involved in multidrug resistance. 1998. Cancer Research 58: 5337-5339.

Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, Gerrard B, Malasky M, Ramos MD, Morlot S, Tzetis M, Oddoux C, di Giovine FS, Nasioulas G, Chandler D, Aseev M, Hanson M, Kalaydjieva L, Glavac D, Gasparini P, Kanavakis E, Claustres M, Kambouris M, Ostrer H, Duff G, Baranov V, Sibul H, Metspalu A, Goldman D, Martin N, Duffy D, Schmidtke J, Estivill X, O'Brien SJ, and Dean M.
Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. 1998. Am J Hum Genet. 62: 1507-1515.

Parent S and Schriml LM. A model for the determination of fish species at risk based upon life-history traits and ecological data. 1995. Can. J. Fish. Aqu. Sci. 52: 1768-1781.

Picman J and Schriml LM. A camera study of temporal patterns of nest predation in different habitats. 1994. Wilson Bulletin 106: 456-465.