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Patrick Chain

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Michael S Fitzsimons; Cheryl D Gleasner; Wei Gu; Patrick S G Chain; Olga Chertkov; Ashlynn R Daughton; Karen W Davenport; John C Detter; Armand E K Dichosa; Jian He; Shannon L Johnson; Roger S Lasken; Chien-Chi Lo; Kim McMurry; Mark Novotny; Beverly Parson-Quintana; Krista G Reitenga; Jeremy P Snook; Patti L Wills; Joyclyn L Yee-Greenbaum; Cliff S Han
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Parveen K Sharma; Richard Sparling; Xiangli Zhang; Patrick S G Chain; Karen Davenport; Brian W Fristensky; Jilagamazhi Fu; David B Levin
Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46.
Jeremy A Dodsworth; Paul C Blainey; Patrick S G Chain; Chien-Chi Lo; Senthil K Murugapiran; Stephen R Quake; Jason Raymond; Christian A Ross; Matthew B Scholz; Wesley D Swingley; Susannah Green Tringe; Brian P Hedlund
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.

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All Publications

2013: Michael S Fitzsimons; Cheryl D Gleasner; Wei Gu; Patrick S G Chain; Olga Chertkov; Ashlynn R Daughton; Karen W Davenport; John C Detter; Armand E K Dichosa; Jian He; Shannon L Johnson; Roger S Lasken; Chien-Chi Lo; Kim McMurry; Mark Novotny; Beverly Parson-Quintana; Krista G Reitenga; Jeremy P Snook; Patti L Wills; Joyclyn L Yee-Greenbaum; Cliff S Han
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Genome research 2013;23(5):878-88.
2013: Parveen K Sharma; Richard Sparling; Xiangli Zhang; Patrick S G Chain; Karen Davenport; Brian W Fristensky; Jilagamazhi Fu; David B Levin
Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46.
Genome announcements 2013;1(2):e0015113.
2013: Jeremy A Dodsworth; Paul C Blainey; Patrick S G Chain; Chien-Chi Lo; Senthil K Murugapiran; Stephen R Quake; Jason Raymond; Christian A Ross; Matthew B Scholz; Wesley D Swingley; Susannah Green Tringe; Brian P Hedlund
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
Nature communications 2013;4():1854.
2013: Birgit Mitter; Jerzy Nowak; Alexandra Petric; Barbara Reinhold-Hurek; Patrick S G Chain; Lena Hauberg-Lotte; Maria W Shin; Angela Sessitsch
Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants.
Frontiers in plant science 2013;4():120.
2013: Gary Xie; Robert A Bonomo; Karen Davenport; Andrea Endimiani; Kristine M Hujer; Shannon Johnson; Po-E Li; Chien-Chi Lo; Steven H Marshall; Maria S Ramirez; Marcelo E Tolmasky; Patrick S G Chain
Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360).
Genome announcements 2013;1(2):.
2013: Shun'ichi Ishii; Kenneth H Nealson; Trina M Norden-Krichmar; Matthew B Scholz; Shino Suzuki; Aaron Tenney; Patrick S G Chain; Orianna Bretschger
A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer.
Nature communications 2013;4():1601.
2012: Olivia U Mason; Edward M Rubin; Lauren M Tom; Susannah Green Tringe; Tanja Woyke; Jizhong Zhou; Regina Lamendella; Rachel Mackelprang; Stephanie Malfatti; Sharon Borglin; Patrick S G Chain; Eric A Dubinsky; Julian L Fortney; James Han; Terry C Hazen; Hoi-Ying N Holman; Jenni Hultman; Janet K Jansson
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
The ISME journal 2012;6(9):1715-27.
2012: Ahmet Zeytun; Emilio Garcia; Stephanie Malfatti; Maria Shin; Lisa M Vergez; Patrick S G Chain
Complete genome sequence of Francisella philomiragia ATCC 25017.
Journal of bacteriology 2012;194(12):3266.
2012: Jeffrey B Kaplan; Chienchi Lo; Gary Xie; Patrick S G Chain; Robert Donnelly; Shannon L Johnson; Scott Charles Kachlany; Nataliya V Balashova
Genome sequence of Kingella kingae septic arthritis isolate PYKK081.
Journal of bacteriology 2012;194(11):3017.
2012: Matthew B Scholz; Chien-Chi Lo; Patrick S G Chain
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.
Current opinion in biotechnology 2012;23(1):9-15.
2012: Armand E K Dichosa; Michael S Fitzsimons; Lance D Green; Wei Gu; Chien-Chi Lo; Kim McMurry; Lara G Preteska; Jeremy P Snook; Lea L Weston; Xiaojing Zhang; Patrick S G Chain; J Chris Detter; Cliff S Han
Artificial polyploidy improves bacterial single cell genome recovery.
PloS one 2012;7(5):e37387.
2012: Nicholas Beckloff; Tracey Freitas; Shawn R Starkenburg; Patrick S G Chain
Bacterial genome annotation.
Methods in molecular biology (Clifton, N.J.) 2012;881():471-503.
2012: Manuel Martinez-Garcia; Dashiell E D Masland; Nicole J Poulton; Krista G Reitenga; Brandon K Swan; Brian Thompson; Gary Xie; Kai Ziervogel; Monica Lluesma Gomez; Sanaa Ahmed; Carol Arnosti; Wendy K Bellows; David M Brazel; Patrick S G Chain; Chris J Detter; Cheryl D Gleasner; Chien-Chi Lo; Ramunas Stepanauskas
Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia.
PloS one 2012;7(4):e35314.
2011: Shawn R Starkenburg; Krista G Reitenga; Patrick S G Chain; Tracey Freitas; Ferran Garcia-Pichel; Shannon Johnson; Cheryl R Kuske
Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide.
Journal of bacteriology 2011;193(17):4569-70.
2011: Patrick S G Chain; Diego COMERCI; Emilio Garcia; Dorothy M Lang; Stephanie A Malfatti; Maria Shin; Rodolfo A Ugalde; Lisa M Vergez; Marcelo E Tolmasky
Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts.
Journal of bacteriology 2011;193(16):4274-5.
2011: Alexandra Weilharter; Maria V Shin; Patrick S G Chain; Birgit Mitter; Jerzy Nowak; Angela Sessitsch
Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN.
Journal of bacteriology 2011;193(13):3383-4.
2011: Mark A Campbell; Patrick S G Chain; Hongyue Dang; Amal F El-Sheikh; Jeanette M Norton; Naomi L Ward; Bess B Ward; Martin Klotz
Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'.
FEMS microbiology ecology 2011;76(1):39-48.
2011: Patrick S G Chain; Gary Xie; Shawn R Starkenburg; Matthew B Scholz; Nicholas Beckloff; Chien-Chi Lo; Karen W Davenport; Krista G Reitenga; Hajnalka E Daligault; J Chris Detter; Tracey A K Freitas; Cheryl D Gleasner; Lance D Green; Cliff S Han; Kim K McMurry; Linda J Meincke; Xiaohong Shen; Ahmet Zeytun
Genomics for key players in the N cycle from guinea pigs to the next frontier.
Methods in enzymology 2011;496():289-318.
2011: Mark W J van Passel; Ravi Kant; Erwin G Zoetendal; Caroline M Plugge; Muriel Derrien; Stephanie A Malfatti; Patrick S G Chain; Tanja Woyke; Airi Palva; Willem M de Vos; Hauke Smidt
The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
PloS one 2011;6(3):e16876.
2010: C B Walker; J R de la Torre; M G Klotz; H Urakawa; Nicolas Pinel; D J Arp; C Brochier-Armanet; Patrick S G Chain; P P Chan; A Gollabgir; J Hemp; M Hügler; E A Karr; Martin Könneke; M Shin; T J Lawton; T Lowe; Willm Martens-Habbena; L A Sayavedra-Soto; D Lang; S M Sievert; A C Rosenzweig; Gerard Manning; David A Stahl
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(19):8818-23.
2010: Anna Kielak; Jorge L M Rodrigues; Eiko E Kuramae; Patrick S G Chain; Johannes A van Veen; George A Kowalchuk
Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil.
FEMS microbiology ecology 2010;71(1):23-33.
2009: Jeffrey Foster; Stephen Beckstrom-Sternberg; Talima Pearson; James S Beckstrom-Sternberg; Patrick S G Chain; Francisco F Roberto; Jonathan Hnath; Thomas S Brettin; Paul Keim
Whole-genome-based phylogeny and divergence of the genus Brucella.
Journal of bacteriology 2009;191(8):2864-70.
2009: D R Yoder-Himes; Patrick S G Chain; Y Zhu; O Wurtzel; E M Rubin; James M Tiedje; R Sorek
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(10):3976-81.
2009: Natalie Donaher; Goro Tanifuji; Naoko T Onodera; Stephanie A Malfatti; Patrick S G Chain; Yoshiaki Hara; John M Archibald
The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate.
Genome biology and evolution 2009;1():439-48.
2008: Yasuhiro Oda; Frank W Larimer; Patrick S G Chain; Stephanie Malfatti; Maria V Shin; Lisa M Vergez; Loren Hauser; Miriam L Land; Stephan Braatsch; J Thomas Beatty; Dale A Pelletier; Amy L Schaefer; Caroline S Harwood
Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(47):18543-8.
2008: Sandra Isabel; Eric Leblanc; Maurice Boissinot; Denis Boudreau; Myrian Grondin; François J Picard; Eric A Martel; Nicholas Parham; Patrick S G Chain; Douglas E Bader; Michael Mulvey; Louis Bryden; Paul H Roy; Marc Ouellette; Michel G Bergeron
Divergence among genes encoding the elongation factor Tu of Yersinia Species.
Journal of bacteriology 2008;190(22):7548-58.
2008: Jeanette M Norton; Martin Klotz; Lisa Y Stein; Daniel J Arp; Peter J Bottomley; Patrick S G Chain; Loren J Hauser; Miriam Land; Frank W Larimer; Maria W Shin; Shawn R Starkenburg
Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.
Applied and environmental microbiology 2008;74(11):3559-72.
2008: Shawn R Starkenburg; Frank W Larimer; Lisa Y Stein; Martin Klotz; Patrick S G Chain; Luis A Sayavedra-Soto; Amisha T Poret-Peterson; Mira E Gentry; Daniel J Arp; Bess Ward; Peter J Bottomley
Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter.
Applied and environmental microbiology 2008;74(9):2852-63.
2008: Emilio Garcia; Patrick S G Chain; Jeffrey M Elliott; Alexander G Bobrov; Vladimir Motin; Olga Kirillina; Victoria Lao; Richard Calendar; Andrey A Filippov
Molecular characterization of L-413C, a P2-related plague diagnostic bacteriophage.
Virology 2008;372(1):85-96.
2008: Stefan M Sievert; Kathleen M Scott; Martin Klotz; Patrick S G Chain; Loren Hauser; James Hemp; Michael Hügler; Miriam Land; Alla Lapidus; Frank W Larimer; Susan Lucas; Stephanie Malfatti; Folker Meyer; Ian Paulsen; Qinghu Ren; Jörg Simon
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.
Applied and environmental microbiology 2008;74(4):1145-56.
2007: Lisa Y Stein; Daniel J Arp; Paul M Berube; Patrick S G Chain; Loren Hauser; Mike S.M. Jetten; Martin Klotz; Frank W Larimer; Jeanette M Norton; Huub J M Op den Camp; Maria Shin; Xueming Wei
Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation.
Environmental microbiology 2007;9(12):2993-3007.
2007: Krassimira R Hristova; Radomir Schmidt; Anu Y Chakicherla; Tina C Legler; Janice Wu; Patrick S G Chain; Kate M Scow; Staci R Kane
Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol.
Applied and environmental microbiology 2007;73(22):7347-57.
2007: Staci R Kane; Anu Y Chakicherla; Patrick S G Chain; Radomir Schmidt; Maria W Shin; Tina C Legler; Kate M Scow; Frank W Larimer; Susan M Lucas; Paul M Richardson; Krassimira R Hristova
Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1.
Journal of bacteriology 2007;189(5):1931-45.
2007: Emilio Garcia; Patricia L Worsham; Scott Bearden; Stephanie Malfatti; Dorothy Lang; Frank W Larimer; Luther E Lindler; Patrick S G Chain
Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union.
Advances in experimental medicine and biology 2007;603():17-22.
2007: Daniel J Arp; Patrick S G Chain; Martin Klotz
The impact of genome analyses on our understanding of ammonia-oxidizing bacteria.
Annual review of microbiology 2007;61():503-28.
2006: Anna Brotcke; David S Weiss; Charles C Kim; Patrick S G Chain; Stephanie Malfatti; Emilio Garcia; Denise M Monack
Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis.
Infection and immunity 2006;74(12):6642-55.
2006: Patrick S G Chain; Vincent J Denef; Konstantinos T Konstantinidis; Lisa M Vergez; Loreine Agulló; Valeria Latorre Reyes; Loren Hauser; Macarena Córdova; Luis Gómez; Myriam González; Miriam Land; Victoria Lao; Frank W Larimer; John J LiPuma; Eshwar Mahenthiralingam; Stephanie Malfatti; Christopher J Marx; Jacob Parnell; Alban Ramette; Paul Richardson; Michael Seeger; Daryl Smith; Theodore Spilker; Woo Jun Sul; Tamara V Tsoi; Luke E Ulrich; Igor B Zhulin; James M Tiedje
Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(42):15280-7.
2006: Martin Klotz; Daniel J Arp; Patrick S G Chain; Amal F El-Sheikh; Loren Hauser; Norman G Hommes; Frank W Larimer; Stephanie Malfatti; Jeanette M Norton; Amisha T Poret-Peterson; Lisa M Vergez; Bess B Ward
Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707.
Applied and environmental microbiology 2006;72(9):6299-315.
2006: Patrick S G Chain; Ping Hu; Stephanie Malfatti; Lyndsay Radnedge; Frank W Larimer; Lisa M Vergez; Patricia L Worsham; May C Chu; Gary L Andersen
Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen.
Journal of bacteriology 2006;188(12):4453-63.
2006: Konstantinos Mavromatis; C Kuyler Doyle; Athanasios Lykidis; Natalia Ivanova; M P Francino; Patrick S G Chain; M Shin; Stephanie Malfatti; Frank W Larimer; Alex Copeland; John C Detter; Miriam Land; Paul M Richardson; Xue-Jie Yu; David H Walker; Jere W McBride; Nikos Kyrpides
The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies.
Journal of bacteriology 2006;188(11):4015-23.
2006: Shawn R Starkenburg; Patrick S G Chain; Luis A Sayavedra-Soto; Loren Hauser; Miriam Land; Frank W Larimer; Stephanie Malfatti; Martin Klotz; Peter J Bottomley; Daniel J Arp; William J Hickey
Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255.
Applied and environmental microbiology 2006;72(3):2050-63.
2006: Harry R Beller; Patrick S G Chain; Tracy E Letain; Anu Y Chakicherla; Frank W Larimer; Paul M Richardson; Matthew A Coleman; Ann P Wood; Donovan P Kelly
The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans.
Journal of bacteriology 2006;188(4):1473-88.
2006: Gabriela G Loots; Patrick S G Chain; Shalini Mabery; Amy Rasley; Emilio Garcia; Ivan Ovcharenko
Array2BIO: from microarray expression data to functional annotation of co-regulated genes.
BMC bioinformatics 2006;7():307.
2005: Patrick S G Chain; Diego COMERCI; Marcelo E Tolmasky; Frank W Larimer; Stephanie Malfatti; Lisa M Vergez; Fernan Aguero; Miriam Land; Rodolfo A Ugalde; Emilio Garcia
Whole-genome analyses of speciation events in pathogenic Brucellae.
Infection and immunity 2005;73(12):8353-61.
2005: Helene Feil; William S Feil; Patrick S G Chain; Frank W Larimer; Genevieve DiBartolo; Alex Copeland; Athanasios Lykidis; Stephen Trong; Matt Nolan; Eugene Goltsman; James Thiel; Stephanie Malfatti; Joyce E Loper; Alla Lapidus; John C Detter; Miriam Land; Paul M Richardson; Nikos Kyrpides; Natalia Ivanova; Steven E Lindow
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(31):11064-9.
2005: Pär Larsson; Petra C F Oyston; Patrick S G Chain; May C Chu; Melanie Duffield; Hans-Henrik Fuxelius; Emilio Garcia; Greger Hälltorp; Daniel Johansson; Karen E Isherwood; Peter Karp; Eva Larsson; Ying Liu; Stephen L Michell; Joann Prior; Richard Prior; Stephanie Malfatti; Anders Sjöstedt; Kerstin Svensson; Nick Thompson; Lisa Vergez; Jonathan K Wagg; Brendan W Wren; Luther E Lindler; Siv G E Andersson; Mats Forsman; Richard Titball
The complete genome sequence of Francisella tularensis, the causative agent of tularemia.
Nature genetics 2005;37(2):153-9.
2004: Patrick S G Chain; Elisabeth Carniel; Frank W Larimer; Jane Lamerdin; P O Stoutland; Warren Regala; Anca M Georgescu; Lisa M Vergez; Miriam Land; Vladimir Motin; Robert R Brubaker; J Fowler; J Hinnebusch; Michael Marceau; C Medigue; Michel Simonet; Viviane Chenal-Francisque; B Souza; D Dacheux; Jeffrey M Elliott; Anne Derbise; Loren Hauser; Emilio Garcia
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(38):13826-31.
2004: Frank W Larimer; Patrick S G Chain; Loren Hauser; Jane Lamerdin; Stephanie Malfatti; Long Do; Miriam Land; Dale A Pelletier; J Thomas Beatty; Andrew S Lang; F Robert Tabita; Janet L Gibson; Thomas Hanson; Cedric E Bobst; Janelle L Torres y Torres; Caroline Peres; Faith H Harrison; Jane Gibson; Caroline S Harwood
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris.
Nature biotechnology 2004;22(1):55-61.
2003: Emilio Garcia; Jeffrey M Elliott; Erlan Ramanculov; Patrick S G Chain; May C Chu; Ian J Molineux
The genome sequence of Yersinia pestis bacteriophage phiA1122 reveals an intimate history with the coliphage T3 and T7 genomes.
Journal of bacteriology 2003;185(17):5248-62.
2003: Gabrielle Rocap; Frank W Larimer; Jane Lamerdin; Stephanie Malfatti; Patrick S G Chain; Nathan A Ahlgren; Andrae Arellano; Maureen Coleman; Loren Hauser; Wolfgang Hess; Zackary I Johnson; Miriam Land; Debbie Lindell; Anton F Post; Warren Regala; Manesh Shah; Stephanie L Shaw; Claudia Steglich; Matthew B Sullivan; Claire S Ting; Andrew C Tolonen; Eric A Webb; Erik R Zinser; Sallie W Chisholm
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.
Nature 2003;424(6952):1042-7.
2003: Brian Palenik; B Brahamsha; Frank W Larimer; Miriam Land; Loren Hauser; Patrick S G Chain; Jane Lamerdin; Warren Regala; Eric E Allen; J McCarren; Ian Paulsen; A Dufresne; Frédéric Partensky; E A Webb; John B Waterbury
The genome of a motile marine Synechococcus.
Nature 2003;424(6952):1037-42.
2003: Patrick S G Chain; Stefan Kurtz; Enno Ohlebusch; Tom R Slezak
An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges.
Briefings in bioinformatics 2003;4(2):105-23.
2003: Patrick S G Chain; Jane Lamerdin; Frank W Larimer; Warren Regala; Victoria Lao; Miriam Land; Loren Hauser; Alan B Hooper; Martin Klotz; Jeanette Norton; Luis A Sayavedra-Soto; David M Arciero; Norman Hommes; Mark Whittaker; Daniel J Arp
Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea.
Journal of bacteriology 2003;185(9):2759-73.