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Mark Adams

Research Profile

Concepts & Ideas

Procedures

Chemicals & Drugs

Genes & Molecular Sequences

Physiology

Gene Expression

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Publications

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Rom S Leidner; Anirban Maitra; Sanford D Markowitz; Lakshmeswari Ravi; Mirte Streppel; Joseph Willis; JEAN WANG; Mark D Adams; Jill S Barnholtz-Sloan; Beth Bednarchik; Marcia Canto; Amitabh Chak; Yanwen Chen; Patrick Leahy; Kishore Guda
The microRNAs, MiR-31 and MiR-375, as candidate markers in Barrett's esophageal carcinogenesis.
Allison R Baker; Jill S Barnholtz-Sloan; W Henry Boom; Willem A Hanekom; Thomas R Hawn; David J Horne; Gilla Kaplan; Harriet Mayanja-Kizza; Feiyou Qiu; April Kaur Randhawa; Muki Shey; Catherine M Stein; Mark D Adams
Genetic variation in TLR genes in Ugandan and South African populations and comparison with HapMap data.
Xiaoqing Yu; Martina Veigl; Zhenghe Wang; Joseph Willis; Mark D Adams; Kishore Guda; Sanford Markowitz; Shuying Sun
How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

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All Publications

2012: Rom S Leidner; Anirban Maitra; Sanford D Markowitz; Lakshmeswari Ravi; Mirte Streppel; Joseph Willis; JEAN WANG; Mark D Adams; Jill S Barnholtz-Sloan; Beth Bednarchik; Marcia Canto; Amitabh Chak; Yanwen Chen; Patrick Leahy; Kishore Guda
The microRNAs, MiR-31 and MiR-375, as candidate markers in Barrett's esophageal carcinogenesis.
Genes, chromosomes & cancer 2012;51(5):473-9.
2012: Allison R Baker; Jill S Barnholtz-Sloan; W Henry Boom; Willem A Hanekom; Thomas R Hawn; David J Horne; Gilla Kaplan; Harriet Mayanja-Kizza; Feiyou Qiu; April Kaur Randhawa; Muki Shey; Catherine M Stein; Mark D Adams
Genetic variation in TLR genes in Ugandan and South African populations and comparison with HapMap data.
PloS one 2012;7(10):e47597.
2012: Xiaoqing Yu; Martina Veigl; Zhenghe Wang; Joseph Willis; Mark D Adams; Kishore Guda; Sanford Markowitz; Shuying Sun
How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?
BioData mining 2012;5(1):6.
2012: Gabrielle C Nickel; Andrew E Sloan; Sarah McMahon; Mark D Adams; Jill S Barnholtz-Sloan; Andrea Cohen; Mark Cohen; Meetha P Gould; Kishore Guda; Thomas LaFramboise
Characterizing mutational heterogeneity in a glioblastoma patient with double recurrence.
PloS one 2012;7(4):e35262.
2011: Debarshi Mustafi; Kiichiro Okano; Alejandro J Roman; Alexander Sumaroka; Mark D Adams; Artur V Cideciyan; Andreas Engel; Christel Genoud; Samuel G Jacobson; Brian M Kevany; Krzysztof Palczewski
Defective photoreceptor phagocytosis in a mouse model of enhanced S-cone syndrome causes progressive retinal degeneration.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2011;25(9):3157-76.
2011: Gabriel E Zentner; Mark D Adams; Pavel Manaenkov; Alina Saiakhova; Peter C Scacheri
Integrative genomic analysis of human ribosomal DNA.
Nucleic acids research 2011;39(12):4949-60.
2011: Allison R Baker; Sarah Zalwango; LaShaunda L Malone; Robert P Igo; Feiyou Qiu; Mary Nsereko; Mark D Adams; Pamela Supelak; Harriet Mayanja-Kizza; W Henry Boom; Catherine M Stein
Genetic susceptibility to tuberculosis associated with cathepsin Z haplotype in a Ugandan household contact study.
Human immunology 2011;72(5):426-30.
2011: Federico Perez; Rafael Ponce-Terashima; Mark D Adams; Robert A Bonomo
Are we closing in on an "elusive enemy"? The current status of our battle with Acinetobacter baumannii.
Virulence 2011;2(2):86-90.
2010: Emma K Larkin; Sanjay R Patel; Robert J Goodloe; Yali Li; Xiaofeng Zhu; Courtney Gray-McGuire; Mark D Adams; Susan Redline
A candidate gene study of obstructive sleep apnea in European Americans and African Americans.
American journal of respiratory and critical care medicine 2010;182(7):947-53.
2010: Dubert M Guerrero; Federico Perez; Nicholas G Conger; Joseph S Solomkin; Mark D Adams; Philip N Rather; Robert A Bonomo
Acinetobacter baumannii-associated skin and soft tissue infections: recognizing a broadening spectrum of disease.
Surgical infections 2010;11(1):49-57.
2009: Mark D Adams; Gabrielle C Nickel; Saralee Bajaksouzian; Heather Lavender; A Rekha Murthy; Michael R Jacobs; Robert A Bonomo
Resistance to colistin in Acinetobacter baumannii associated with mutations in the PmrAB two-component system.
Antimicrobial agents and chemotherapy 2009;53(9):3628-34.
2009: Kristine M Hujer; Andrea Hujer; Andrea Endimiani; Jodi M Thomson; Mark D Adams; Karrie Goglin; Philip N Rather; Thuy-Trang D Pennella; Christian Massire; Mark W Eshoo; Rangarajan Sampath; Lawrence B Blyn; David J Ecker; Robert A Bonomo
Rapid determination of quinolone resistance in Acinetobacter spp.
Journal of clinical microbiology 2009;47(5):1436-42.
2009: E Ricky Chan; Heather Lavender; Geqiang Li; Peter Haviernik; Kevin D Bunting; Mark D Adams
An ENU-induced recessive mutation in Mpl leads to thrombocytopenia with overdominance.
Experimental hematology 2009;37(2):276-84.
2008: Mark D Adams; Karrie Goglin; Neil Molyneaux; Kristine M Hujer; Heather Lavender; Jennifer J Jamison; Ian J MacDonald; Kristienna M Martin; Thomas Russo; Anthony A Campagnari; Andrea Hujer; Robert A Bonomo; Steven R Gill
Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii.
Journal of bacteriology 2008;190(24):8053-64.
2008: Gabrielle C Nickel; David L Tefft; Karrie Goglin; Mark D Adams
An empirical test for branch-specific positive selection.
Genetics 2008;179(4):2183-93.
2008: Gabrielle C Nickel; David Tefft; Mark D Adams
Human PAML browser: a database of positive selection on human genes using phylogenetic methods.
Nucleic acids research 2008;36(Database issue):D800-8.
2005: Jeffrey M Kidd; Karrie C Trevarthen; David L Tefft; Ze Cheng; Michaele Mooney; Mark D Adams
A catalog of nonsynonymous polymorphism on mouse chromosome 16.
Mammalian genome : official journal of the International Mammalian Genome Society 2005;16(12):925-33.
2005: Mark D Adams
Conserved sequences and the evolution of gene regulatory signals.
Current opinion in genetics & development 2005;15(6):628-33.
2004: Elodie Ghedin; Frédéric Bringaud; Jeremy Peterson; Peter J Myler; Matthew Berriman; Alasdair Ivens; Björn Andersson; Esteban Bontempi; Jonathan Eisen; Samuel V Angiuoli; David Wanless; Anna Von Arx; Lee Murphy; Nicola Lennard; Steven L Salzberg; Mark D Adams; Owen R White; Neil Hall; Kenneth Stuart; Claire M Fraser-Liggett; Najib M El-Sayed
Gene synteny and evolution of genome architecture in trypanosomatids.
Molecular and biochemical parasitology 2004;134(2):183-91.
2003: Elizabeth Waters; Michael J Hohn; Ivan Ahel; David E Graham; Mark D Adams; Mary Barnstead; Karen Y Beeson; Lisa Bibbs; Randall Bolanos; Martin Keller; Keith A Kretz; Xiaoying Lin; Eric J Mathur; Jingwei Ni; Mircea Podar; Toby Richardson; Granger Sutton; Melvin Simon; Dieter Soll; Karl O Stetter; Jay Short; Michiel Noordewier
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(22):12984-8.
2003: Timothy Wiltshire; Mathew Pletcher; Serge Batalov; S Whitney Barnes; Lisa Tarantino; Michael P Cooke; Hua Wu; Kevin Smylie; Andrey Santrosyan; Neal G Copeland; Nancy A Jenkins; Francis Kalush; Richard J Mural; Richard J Glynne; Steve A Kay; Mark D Adams; Colin F Fletcher
Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(6):3380-5.
2003: Antonio Carvalho; Maria Dulcetti Vibranovski; Joseph W Carlson; Susan E Celniker; Roger A Hoskins; Gerald M Rubin; Granger Sutton; Mark D Adams; Eugene W Myers; andrew clark
Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?
Genetica 2003;117(2-3):227-37.
2002: Jeffrey A Bailey; Zhiping Gu; Royden A Clark; Knut Reinert; Rhea Vallente; Stuart Schwartz; Mark D Adams; Eugene W Myers; Peter W Li; Evan E Eichler
Recent segmental duplications in the human genome.
Science (New York, N.Y.) 2002;297(5583):1003-7.
2002: Eugene W Myers; Granger Sutton; Hamilton O Smith; Mark D Adams; J Craig Venter
On the sequencing and assembly of the human genome.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4145-6.
2001: G. SUBRAMANIAN; Mark D Adams; J Craig Venter; Samuel Broder
Implications of the human genome for understanding human biology and medicine.
JAMA : the journal of the American Medical Association 2001;286(18):2296-307.
2001: A B Sparks; Scott N Peterson; C Bell; B J Loftus; L Hocking; D P Cahill; Frank J Frassica; Elizabeth A Streeten; Michael A. Levine; Claire M Fraser-Liggett; Mark D Adams; Samuel Broder; J Craig Venter; Kenneth W Kinzler; Bert Vogelstein; S H Ralston
Mutation screening of the TNFRSF11A gene encoding receptor activator of NF kappa B (RANK) in familial and sporadic Paget's disease of bone and osteosarcoma.
Calcified tissue international 2001;68(3):151-5.
2000: Eugene W Myers; Granger Sutton; Arthur L Delcher; I M Dew; D P Fasulo; M J Flanigan; Saul A Kravitz; Clark Mobarry; Knut Reinert; Karin Remington; E L Anson; R A Bolanos; H H Chou; C M Jordan; Aaron L Halpern; Stefano Lonardi; E M Beasley; R C Brandon; L Chen; P J Dunn; Z Lai; Y Liang; D R Nusskern; M Zhan; Qing Zhang; X Zheng; Gerald M Rubin; Mark D Adams; J Craig Venter
A whole-genome assembly of Drosophila.
Science (New York, N.Y.) 2000;287(5461):2196-204.
2000: Shaying Zhao; JA Malek; Greg Mahairas; L Fu; William C Nierman; J Craig Venter; Mark D Adams
Human BAC ends quality assessment and sequence analyses.
Genomics 2000;63(3):321-32.
2000: L Cai; Berthold Struk; Mark D Adams; W Ji; T Haaf; HL Kang; S H Dho; X Xu; F Ringpfeil; J Nancarrow; S Zäch; L Schaen; M Stumm; T Niu; J Chung; K Lunze; B Verrecchia; lowell goldsmith; D Viljoen; Luis Figuera; W Fuchs; Mark Lebwohl; Jouni Uitto; R Richards; Daniel Hohl; Raj Kumar S Ramesar
A 500-kb region on chromosome 16p13.1 contains the pseudoxanthoma elasticum locus: high-resolution mapping and genomic structure.
Journal of molecular medicine (Berlin, Germany) 2000;78(1):36-46.
2000: Julie E Horvath; Luigi Viggiano; B J Loftus; Mark D Adams; Nicoletta Archidiacono; Mariano Rocchi; Evan E Eichler
Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11.
Human molecular genetics 2000;9(1):113-23.
1999: B J Loftus; UJ Kim; V P Sneddon; Francis Kalush; R Brandon; J Fuhrmann; T Mason; M L Crosby; M Barnstead; L Cronin; A Deslattes Mays; Y Cao; R X Xu; HL Kang; S Mitchell; Evan E Eichler; P C Harris; J Craig Venter; Mark D Adams
Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q.
Genomics 1999;60(3):295-308.
1999: Y Cao; HL Kang; X Xu; M Wang; S H Dho; Jun R Huh; B J Lee; Francis Kalush; D Bocskai; Y Ding; JG Tesmer; J Lee; E Moon; V Jurecic; Antonio Baldini; Heinz-Ulrich G Weier; Norman A Doggett; MI Simon; Mark D Adams; UJ Kim
A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2.
Genome research 1999;9(8):763-74.
1999: J M Kelley; C E Field; M B Craven; D Bocskai; UJ Kim; S D Rounsley; Mark D Adams
High throughput direct end sequencing of BAC clones.
Nucleic acids research 1999;27(6):1539-46.
1998: Malcolm J Gardner; Hervé Tettelin; Daniel J Carucci; LM Cummings; L Aravind; E V Koonin; S Shallom; T Mason; K Yu; C Fujii; J Pederson; K Shen; J Jing; C Aston; Z Lai; David C Schwartz; Mihaela Pertea; Steven L Salzberg; L Zhou; Granger Sutton; R Clayton; Owen R White; Hamilton O Smith; Claire M Fraser-Liggett; Mark D Adams; J Craig Venter; Stephen L Hoffman
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.
Science (New York, N.Y.) 1998;282(5391):1126-32.
1998: Daniel J Carucci; Malcolm J Gardner; Hervé Tettelin; LM Cummings; Hamilton O Smith; Mark D Adams; J Craig Venter; Stephen L Hoffman
Sequencing the genome of Plasmodium falciparum.
Current opinion in infectious diseases 1998;11(5):531-4.
1998: JA Kramer; Mark D Adams; GB Singh; Norman A Doggett; Stephen A Krawetz
Extended analysis of the region encompassing the PRM1-->PRM2-->TNP2 domain: genomic organization, evolution and gene identification.
The Journal of experimental zoology 1998;282(1-2):245-53.
1998: J Craig Venter; Mark D Adams; Granger Sutton; AR Kerlavage; Hamilton O Smith; M Hunkapiller
Shotgun sequencing of the human genome.
Science (New York, N.Y.) 1998;280(5369):1540-2.
1998: Daniel J Carucci; Malcolm J Gardner; Hervé Tettelin; LM Cummings; Hamilton O Smith; Mark D Adams; Stephen L Hoffman; J Craig Venter
The malaria genome sequencing project.
Expert reviews in molecular medicine 1998;1998():1-9.
1998: JA Kramer; Mark D Adams; GB Singh; Norman A Doggett; Stephen A Krawetz
A matrix associated region localizes the human SOCS-1 gene to chromosome 16p13.13.
Somatic cell and molecular genetics 1998;24(2):131-3.
1997: X Huang; Mark D Adams; H Zhou; AR Kerlavage
A tool for analyzing and annotating genomic sequences.
Genomics 1997;46(1):37-45.
1996: S D Rounsley; A Glodek; G Sutton; Mark D Adams; chris somerville; J Craig Venter; A R Kerlavage
The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.
Plant physiology 1996;112(3):1177-83.
1996: Mark D Adams; J Craig Venter
Should non-peer-reviewed raw DNA sequence data release be forced on the scientific community?
Science (New York, N.Y.) 1996;274(5287):534-6.
1996: Gerold Schuler; Mark S Boguski; E A Stewart; L D Stein; Gabor Gyapay; K Rice; R E White; P Rodriguez-Tomé; A Aggarwal; E Bajorek; S Bentolila; B B Birren; A Butler; A B Castle; N Chiannilkulchai; A Chu; C Clee; S Cowles; Philip Day; T Dibling; N Drouot; Carl Bruder; S Duprat; C East; C Edwards; Jian-Bing Fan; N Fang; C Fizames; C Garrett; L Green; D Hadley; M Harris; P Harrison; S Brady; A Hicks; E Holloway; L Hui; S Hussain; C Louis-Dit-Sully; J Ma; A MacGilvery; C Mader; A Maratukulam; TC Matise; K B McKusick; J Morissette; Andrew Mungall; D Muselet; H C Nusbaum; David C Page; A Peck; S Perkins; M Piercy; F Qin; John Quackenbush; S Ranby; T Reif; Steve Rozen; C Sanders; X She; J Silva; DK Slonim; CA Soderlund; W L Sun; P Tabar; T Thangarajah; N Vega-Czarny; D Vollrath; S Voyticky; T Wilmer; X Wu; Mark D Adams; Charles Auffray; Nicole Walter; R Brandon; AM Dehejia; PN Goodfellow; R Houlgatte; J R Hudson; S E Ide; K R Iorio; W Y Lee; N Seki; T Nagase; K Ishikawa; N Nomura; C Phillips; Mihael H Polymeropoulos; M Sandusky; K Schmitt; R Berry; K Swanson; R Torres; J Craig Venter; James M Sikela; Jacques Beckmann; Jean Weissenbach; Richard Myers; D R Cox; M R James; D Bentley; Panos Deloukas; Eric S Lander; Thomas J Hudson
A gene map of the human genome.
Science (New York, N.Y.) 1996;274(5287):540-6.
1996: Carol Bult; Owen R White; Gary J Olsen; L Zhou; Robert D Fleischmann; Granger Sutton; J A Blake; L M FitzGerald; R A Clayton; J D Gocayne; A R Kerlavage; B A Dougherty; J F Tomb; Mark D Adams; C I Reich; Ross Overbeek; Ewen F Kirkness; K G Weinstock; J M Merrick; A Glodek; J L Scott; N S Geoghagen; J Craig Venter
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii.
Science (New York, N.Y.) 1996;273(5278):1058-73.
1995: Claire M Fraser-Liggett; J D Gocayne; Owen R White; Mark D Adams; R A Clayton; Robert D Fleischmann; Carol Bult; A R Kerlavage; G Sutton; J M Kelley; R D Fritchman; J F Weidman; K V Small; M Sandusky; J Fuhrmann; D Nguyen; T R Utterback; D M Saudek; C A Phillips; J M Merrick; J F Tomb; B A Dougherty; Kenneth Bott; P C Hu; T S Lucier; S N Peterson; Hamilton O Smith; Clyde A Hutchison; J Craig Venter
The minimal gene complement of Mycoplasma genitalium.
Science (New York, N.Y.) 1995;270(5235):397-403.
1995: Mark D Adams; A R Kerlavage; Robert D Fleischmann; R A Fuldner; Carol Bult; N H Lee; Ewen F Kirkness; K G Weinstock; J D Gocayne; Owen R White
Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.
Nature 1995;377(6547 Suppl):3-174.
1995: L A McDonald; J M Kelley; R C Brandon; Mark D Adams
Optimization of Applied Biosystems 373 sequencer stretch modification.
BioTechniques 1995;19(3):464-71.
1995: N H Lee; K G Weinstock; Ewen F Kirkness; J A Earle-Hughes; R A Fuldner; S Marmaros; A Glodek; J D Gocayne; Mark D Adams; A R Kerlavage
Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(18):8303-7.
1995: Robert D Fleischmann; Mark D Adams; Owen R White; R A Clayton; Ewen F Kirkness; A R Kerlavage; Carol Bult; J F Tomb; B A Dougherty; J M Merrick
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Science (New York, N.Y.) 1995;269(5223):496-512.
1995: Glória Regina Franco; Mark D Adams; M B Soares; Andrew J G Simpson; J C Venter; Sergio Pena
Identification of new Schistosoma mansoni genes by the EST strategy using a directional cDNA library.
Gene 1995;152(2):141-7.
1994: C Fields; Mark D Adams; Owen R White; J Craig Venter
How many genes in the human genome?
Nature genetics 1994;7(3):345-6.
1994: Mark D Adams; A R Kerlavage; J M Kelley; J D Gocayne; C Fields; Claire M Fraser-Liggett; J Craig Venter
A model for high-throughput automated DNA sequencing and analysis core facilities.
Nature 1994;368(6470):474-5.
1994: Nickolas Papadopoulos; N C Nicolaides; YF Wei; S M Ruben; KC Carter; C A Rosen; W A Haseltine; R D Fleischmann; Claire M Fraser-Liggett; Mark D Adams
Mutation of a mutL homolog in hereditary colon cancer.
Science (New York, N.Y.) 1994;263(5153):1625-9.
1994: C Fields; Mark D Adams
Expressed sequence tags identify a human isolog of the suil translation initiation factor.
Biochemical and biophysical research communications 1994;198(1):288-91.
1993: Mark D Adams; M B Soares; A R Kerlavage; C Fields; J Craig Venter
Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library.
Nature genetics 1993;4(4):373-80.
1993: Mark D Adams; A R Kerlavage; C Fields; J Craig Venter
3,400 new expressed sequence tags identify diversity of transcripts in human brain.
Nature genetics 1993;4(3):256-67.
1992: W R McCombie; Mark D Adams; J M Kelley; M G FitzGerald; T R Utterback; M Khan; M Dubnick; A R Kerlavage; J Craig Venter; C Fields
Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues.
Nature genetics 1992;1(2):124-31.
1992: Mihael H Polymeropoulos; H Xiao; A Glodek; M Gorski; Mark D Adams; R F Moreno; M G Fitzgerald; J Craig Venter; C R Merril
Chromosomal assignment of 46 brain cDNAs.
Genomics 1992;12(3):492-6.
1992: Mark D Adams; M Dubnick; A R Kerlavage; R Moreno; J M Kelley; T R Utterback; James W Nagle; C Fields; J Craig Venter
Sequence identification of 2,375 human brain genes.
Nature 1992;355(6361):632-4.
1992: J Craig Venter; Mark D Adams; A Martin-Gallardo; W R McCombie; C Fields
Genome sequence analysis: scientific objectives and practical strategies.
Trends in biotechnology 1992;10(1-2):8-11.
1991: Mark D Adams; J M Kelley; J D Gocayne; M Dubnick; Mihael H Polymeropoulos; H Xiao; C R Merril; A Wu; B Olde; R F Moreno
Complementary DNA sequencing: expressed sequence tags and human genome project.
Science (New York, N.Y.) 1991;252(5013):1651-6.