Mark Adams
Associate Professor
Ph.D. Training Faculty
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Department of Genetics
School of Medicine
Case Western Reserve University
Biomedical Research Building 624
2109 Adelbert Road
Cleveland, Ohio 44106-4955
Tel: (216) 368-2791
Fax: (216) 368-3432
E-mail: mark.d.adams@case.edu
http://mendel.gene.cwru.edu/adamslab/
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About Mark Adams
Mark Adams received a B.A. in Chemistry from Warren Wilson College in Swannanoa, NC in 1984. He received his Ph.D. in Biological Chemistry from the University of Michigan in 1990. His dissertation work involved characterization of the genes involved in branched-chain amino acid transport in Escherichia coli. As a postdoctoral fellow in the laboratory of Dr. J. Craig Venter at the National Institute of Neurological Disorders and Stroke at the NIH, Dr. Adams developed the expressed sequence tag (EST) methodology for rapid characterization of the expressed set of genes in a tissue. As one of the founding scientists at The Institute for Genomic Research, Dr. Adams established and managed the large-scale DNA sequencing facility. The initial work focused on developing a large collection of ESTs from several hundred cDNA libraries. He also contributed extensively to determining the first genome sequence of a free-living organism, Haemophilus influenzae, as well as to several additional microbial genomes.In 1998, Dr. Adams co-founded Celera Genomics, where he was responsible for the DNA sequencing and genome annotation groups. In this role he directed the Drosophila, human, and mouse genome sequencing projects and the effort to re-sequence exons and regulatory regions of all human genes to identify novel functional SNPs. Dr. Adams joined the faculty of Case Western Reserve University in 2003 as an Associate Professor.
Research
His research interests focus around the evolution, mechanism, and detection of antimicrobial resistance in Gram-negative pathogens, particularly Acinetobacter baumannii. A. baumannii is a nosocomial pathogen that primarily causes pneumonia in immunocompromised individuals. Multidrug resistance in A. baumannii has increased dramatically in the last 10 years, with fewer viable therapeutic options available for physicians. Comparative genome analysis revealed a set of more than 400 genes that are shared among clinical isolates of A. baumannii but are absent from the related non-pathogen Acinetobacter baylyi ADP1 and that may contribute to A. baumannii's role as a human pathogen. Analysis of resistance determinants showed that resistance genes are often clustered into genomic islands of quite variable composition that are defined by continuing ongoing lateral gene transfer. Rapid detection of resistance genes in clinical isolates should facilitate more effective selection of antimicrobial therapy. Dr. Adams group also works on the genetic and biochemical basis for resistance to the 'last line' antimicrobial colistin.
Selected Publications
| Adams MD, Nickel GC, Bajaksouzian S, Lavender H, Murthy AR, Jacobs MR, Bonomo RA (2009) | | Resistance to colistin in Acinetobacter baumannii associated with mutations in the PmrAB two-component system. | | Antimicrob Agents Chemother;: | | See PubMed abstract |
| Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG (2009) | | Darwinian and demographic forces affecting human protein coding genes. | | Genome Res;19(5):838-49 | | See PubMed abstract |
| Hujer KM, Hujer AM, Endimiani A, Thomson JM, Adams MD, Goglin K, Rather PN, Pennella TT, Massire C, Eshoo MW, Sampath R, Blyn LB, Ecker DJ, Bonomo RA (2009) | | Rapid determination of quinolone resistance in Acinetobacter spp. | | J Clin Microbiol;47(5):1436-42 | | See PubMed abstract |
| Endimiani A, Hujer AM, Perez F, Bethel CR, Hujer KM, Kroeger J, Oethinger M, Paterson DL, Adams MD, Jacobs MR, Diekema DJ, Hall GS, Jenkins SG, Rice LB, Tenover FC, Bonomo RA (2009) | | Characterization of blaKPC-containing Klebsiella pneumoniae isolates detected in different institutions in the Eastern USA. | | J Antimicrob Chemother;63(3):427-37 | | See PubMed abstract |
| Chan ER, Lavender H, Li G, Haviernik P, Bunting KD, Adams MD (2009) | | An ENU-induced recessive mutation in Mpl leads to thrombocytopenia with overdominance. | | Exp Hematol;37(2):276-84 | | See PubMed abstract |
| Neilson DE, Adams MD, Orr CM, Schelling DK, Eiben RM, Kerr DS, Anderson J, Bassuk AG, Bye AM, Childs AM, Clarke A, Crow YJ, Di Rocco M, Dohna-Schwake C, Dueckers G, Fasano AE, Gika AD, Gionnis D, Gorman MP, Grattan-Smith PJ, Hackenberg A, Kuster A, Lentschig MG, Lopez-Laso E, Marco EJ, Mastroyianni S, Perrier J, Schmitt-Mechelke T, Servidei S, Skardoutsou A, Uldall P, van der Knaap MS, Goglin KC, Tefft DL, Aubin C, de Jager P, Hafler D, Warman ML (2009) | | Infection-triggered familial or recurrent cases of acute necrotizing encephalopathy caused by mutations in a component of the nuclear pore, RANBP2. | | Am J Hum Genet;84(1):44-51 | | See PubMed abstract |
| Adams MD, Goglin K, Molyneaux N, Hujer KM, Lavender H, Jamison JJ, MacDonald IJ, Martin KM, Russo T, Campagnari AA, Hujer AM, Bonomo RA, Gill SR (2008) | | Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii. | | J Bacteriol;190(24):8053-64 | | See PubMed abstract |
| Nickel GC, Tefft DL, Goglin K, Adams MD (2008) | | An empirical test for branch-specific positive selection. | | Genetics;179(4):2183-93 | | See PubMed abstract |
| Nickel GC, Tefft D, Adams MD (2008) | | Human PAML browser: a database of positive selection on human genes using phylogenetic methods. | | Nucleic Acids Res;36(Database issue):D | | See PubMed abstract |
| Adams MD (2005) | | Conserved sequences and the evolution of gene regulatory signals. | | Curr Opin Genet Dev;15(6):628-33 | | See PubMed abstract |
| Kidd, J.M., Trevarthen, K.C., Tefft, D.L., Cheng, G., Mooney, M., and Adams, M.D. (2005) | | A catalog of non-synonymous polymorphism on mouse chromosome 16 | | Mamm. Genome;16:925-933 | | See PubMed abstract |
| Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, Hannenhalli S, Turner R, Yooseph S, Lu F, Nusskern DR, Shue BC, Zheng XH, Zhong F, Delcher AL, Huson DH, Kravitz SA, Mouchard L, Reinert K, Remington KA, Clark AG, Waterman MS, Eichler EE, Adams MD, Hunkapiller MW, Myers EW, Venter JC (2004) | | Whole-genome shotgun assembly and comparison of human genome assemblies | | Proc Natl Acad Sci U S A;101(7):1916-21 | | See PubMed abstract |
| Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M (2003) | | Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios | | Science;302(5652):1876-7 | | See PubMed abstract |
| Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M (2003) | | The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism | | Proc Natl Acad Sci U S A;100(22):12984-8 | | See PubMed abstract |
| El-Sayed NM, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S, Tweedie A, Biteau N, Khalak HG, Lin X, Mason T, Hannick L, Caler E, Blandin G, Bartholomeu D, Simpson AJ, Kaul S, Zhao H, Pai G, Van Aken S, Utterback T, Haas B, Koo HL, Umayam L, Suh B, Gerrard C, Leech V, Qi R, Zhou S, Schwartz D, Feldblyum T, Salzberg S, Tait A, Turner CM, Ullu E, White O, Melville S, Adams MD, Fraser CM, Donelson JE (2003) | | The sequence and analysis of Trypanosoma brucei chromosome II | | Nucleic Acids Res;31(16):4856-63 | | See PubMed abstract |
| Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HH, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GA, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJ, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Dohner H, Dohner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC (2003) | | Human chromosome 7: DNA sequence and biology | | Science;300:767-772 | | See PubMed abstract |
| Wiltshire T, Pletcher MT, Batalov S, Barnes SW, Tarantino LM, Cooke MP, Wu H, Smylie K, Santrosyan A, Copeland NG, Jenkins NA, Kalush F, Mural RJ, Glynne RJ, Kay SA, Adams MD, Fletcher CF (2003) | | Genome-wide SNP analysis defines haplotype patterns | | Proc. Natl. Acad. Sci. USA;100:3380-3385 | | See PubMed abstract |
| Carvalho AB, Vibranovski MD, Carlson JW, Celniker SE, Hoskins RA, Rubin GM, Sutton GG, Adams MD, Myers EW, Clark AG (2003) | | Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go? | | Genetica;117(2-3):227-37 | | See PubMed abstract |
| Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL (2002) | | The genome sequence of the malaria mosquito Anopheles gambiae | | Science;298:129-149 | | See PubMed abstract |
| Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, Deng Z, Evangelista CC, Gan W, Heiman TJ, Li J, Li Z, Merkulov GV, Milshina NV, Naik AK, Qi R, Shue BC, Wang A, Wang J, Wang X, Yan X, Ye J, Yooseph S, Zhao Q, Zheng L, Zhu SC, Biddick K, Bolanos R, Delcher AL, Dew IM, Fasulo D, Flanigan MJ, Huson DH, Kravitz SA, Miller JR, Mobarry CM, Reinert K, Remington KA, Zhang Q, Zheng XH, Nusskern DR, Lai Z, Lei Y, Zhong W, Yao A, Guan P, Ji RR, Gu Z, Wang ZY, Zhong F, Xiao C, Chiang CC, Yandell M, Wortman JR, Amanatides PG, Hladun SL, Pratts EC, Johnson JE, Dodson KL, Woodford KJ, Evans CA, Gropman B, Rusch DB, Venter E, Wang M, Smith TJ, Houck JT, Tompkins DE, Haynes C, Jacob D, Chin SH, Allen DR, Dahlke CE, Sanders R, Li K, Liu X, Levitsky AA, Majoros WH, Chen Q, Xia AC, Lopez JR, Donnelly MT, Newman MH, Glodek A, Kraft CL, Nodell M, Ali F, An HJ, Baldwin-Pitts D, Beeson KY, Cai S, Carnes M, Carver A, Caulk PM, Center A, Chen YH, Cheng ML, Coyne MD, Crowder M, Danaher S, Davenport LB, Desilets R, Dietz SM, Doup L, Dullaghan P, Ferriera S, Fosler CR, Gire HC, Gluecksmann A, Gocayne JD, Gray J, Hart B, Haynes J, Hoover J, Howland T, Ibegwam C, Jalali M, Johns D, Kline L, Ma DS, MacCawley S, Magoon A, Mann F, May D, McIntosh TC, Mehta S, Moy L, Moy MC, Murphy BJ, Murphy SD, Nelson KA, Nuri Z, Parker KA, Prudhomme AC, Puri VN, Qureshi H, Raley JC, Reardon MS, Regier MA, Rogers YH, Romblad DL, Schutz J, Scott JL, Scott R, Sitter CD, Smallwood M, Sprague AC, Stewart E, Strong RV, Suh E, Sylvester K, Thomas R, Tint NN, Tsonis C, Wang G, Wang G, Williams MS, Williams SM, Windsor SM, Wolfe K, Wu MM, Zaveri J, Chaturvedi K, Gabrielian AE, Ke Z, Sun J, Subramanian G, Venter JC, Pfannkoch CM, Barnstead M, Stephenson LD (2002) | | A comparison of whole genome shotgun-derived mouse chromosome 16 and the human genome. | | Science;296:1661-1671 | | See PubMed abstract |
| Venter, J.C., Adams, M.D., Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) | | The sequence of the human genome | | Science;291, 1304-1351 | | See PubMed abstract |
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