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Select Publications by Lucigen Scientists

Journal Articles

2016

Molecular Diagnostic Field Test for Point-of-Care Detection of Ebola Virus Directly From Blood. Benzine JW1, Brown KM1, Agans KN2, Godiska R1, Mire CE2, Gowda K1, Converse B1, Geisbert TW2, Mead DA1, Chander Y1. J Infect Dis 2016 Oct 15;214(suppl 3):S234-S242. Epub 2016 Sep 16.
1 Lucigen Corporation
2 Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston.

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2015

Complete Genome Sequence of Thermus aquaticus Y51MC23 Phillip J. Brumm, Scott Monsma, Brendan Keough, Svetlana Jasinovica, Erin Ferguson, Thomas Schoenfeld, Michael Lodes, David A. Mead. PLoS ONE 10(10): e0138674. DOI: 10.1371/journal.pone.0138674.

SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure.McFarland KN, Liu J, Landrian I, Godiska R, Shanker S, Yu F, et al. (2015) PLoS ONE 10(8): e0135906. doi:10.1371/journal.pone.0135906

LucY: A Versatile New Fluorescent Reporter Protein. Michele E. Auldridge, et al. PLoS ONE 10(4): e0124272.  DOI: 10.1371/journal.pone.0124272.


2014

A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP) Yogesh Chander, Jim Koelbl, Jamie Puckett, Michael J. Moser, Audrey J. Klingele, Mark R. Liles, Abel Carrias, David A. Mead and Thomas W. Schoenfeld; Frontiers in Microbiology, doi: 10.3389/fmicb.2014.00395.


2013

Lateral gene transfer of Family A DNA polymerases between thermophilic viruses, Aquificae, and Apicomplexa Thomas W. Schoenfeld; Senthil Murugapiran; Jeremy A. Dodsworth; Sally Floyd; Michael Lodes; David A. Mead; Brian P. Hedlund. Molecular Biology and Evolution 2013; doi: 10.1093/molbev/mst078

Functional Inositol 1,4,5-Trisphosphate Receptors Assembled from Concatenated Homo- and Heteromeric Subunits. Kamil J. Alzayady, Larry E. Wagner, II, Rahul Chandrasekhar, Alina Monteagudo, Ronald Godiska, Gregory G. Tall, Suresh K. Joseph, and David I. Yule J Biol Chem. 2013 Oct 11; 288(41): 29772–29784. doi:  10.1074/jbc.M113.502203

The Genome Sequences of Cellulomonas fimi and ‘‘Cellvibrio gilvus’’ Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of ‘‘Cellvibrio gilvus’’ to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp. nov. Christopherson MR, Suen G, Bramhacharya S, Jewell KA, Aylward FO, et al. The PLoS ONE 2013. 8(1): e53954. doi:10.1371/journal.pone.0053954.

Evaluation of the specificity and sensitivity of a potential rapid influenza screening system.  Perez LE, Merrill GA, Delorenzo RA, Schoenfeld TW, Vats A, Moser MJ. Diagn Microbiol Infect Dis.2013 75(1):77-80.


2012

Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. Zhang HB, Scheuring CF, Zhang M, Zhang Y, Wu CC, Dong JJ, Li Y. Nat Protoc. 2012. 7(3):479-99.

Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Zhang M, Zhang Y, Scheuring CF, Wu CC, Dong JJ, Zhang HB. Nat Protoc. 2012. 7(3):467-78.

Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme. Moser MJ, DiFrancesco RA, Gowda K, Klingele AJ, Sugar DR, Stocki S, Mead DA, Schoenfeld TW. PLoS ONE. 2012 7(6):e38371.

Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.  Mead DA, Lucas S, Copeland A, Lapidus A, Cheng J-F, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang Y-J, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm PJ. Standards in Genomic Sciences 2012 6(3):366-385.  


2011

Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries. Kakirde KS, Wild J, Godiska R, Mead DA, Wiggins AG, Goodman RM, Szybalski W, Liles MR. Gene. 2011. 475(2):57-62.

Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri. Carrias A, Welch TJ, Waldbieser GC, Mead DA, Terhune JS, Liles MR. Virology Journal. 2011 8:6.

Hemicellulases and auxiliary enzymes for improved conversion of lignocellulosic biomass to monosaccharides. Gao D, Uppugundla N, Chundawat SP, Yu X, Hermanson S, Gowda K, Brumm P, Mead D, Balan V, Dale BE. Biotechnology for Biofuels. 2011 4:5.

The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist. Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ. PLoS ONE. 2011 6(4):e18814.

BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, deJong P, Wu CC, Graner A, Langridge P, Stein N. BMC Genomics. 2011. 12:247.

Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases. Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, Brunecky R, Adney WS, Himmel ME, Brumm P, Drinkwater C, Mead DA, Tringe SG, Lelie DV. Biotechnology for Biofuels. 2011 4:23.

Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7. Suen G, Stevenson DM, Bruce DC, Chertkov O, Copeland A, Cheng JF, Detter C, Detter JC, Goodwin LA, Han CS, Hauser LJ, Ivanova NN, Kyrpides NC, Land ML, Lapidus A, Lucas S, Ovchinnikova G, Pitluck S, Tapia R, Woyke T, Boyum J, Mead D, Weimer PJ. Journal of Bacteriology. 2011 193(19):5574-5575.

Functional annotation of Fibrobacter succinogenes S85 carbohydrate active enzymes. Brumm P, Mead D, Boyum J, Drinkwater C, Deneke J, Gowda K, Stevenson D, Weimer P. Appl Biochem Biotechnol. 2011. 163(5):649-57.

Mining Dictyoglomus turgidum for enzymatically active carbohydrases. Brumm P, Hermanson S, Hochstein B, Boyum J, Hermersmann N, Gowda K, Mead D. Appl Biochem Biotechnol. 2011. 163(2):205-14.


2010

Strategy for identification of novel fungal and bacterial glycosyl hydrolase hybrid mixtures that can efficiently saccharify pretreated lignocellulosic biomass. Gao D, Chundawat S, Liu T, Hermanson S, Gowda K, Brumm P, Dale BE, Balan V. Bioenergy Research. 2010. 3(1):67-8.

Functional viral metagenomics and the next generation of molecular tools. Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D. Trends in Microbiology. 2010. 18(1):20

Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli. Godiska R, Mead D, Dhodda V, Wu C, Hochstein R, Karsi A, Usdin K, Entezam A, Ravin N. Nucleic Acids Research. 2010. 38(6): e88.

ExCyto PCR Amplification. Dhodda V, Godiska R, VanWye JD, Mead D, Hochstein R, Sheets L, Zande SV, Niebauer C, Crawford DL, Oleksiak MF. PLoS ONE. 2010. 5(9): e12629.


2009

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D. PLoS ONE. 2009. 4(1):e4169.

Complete and Draft Genome Sequences of Six Members of the Aquificales. Reysenbach AL, Hamamura N, Podar M, Griffiths E, Ferreira S, Hochstein R, Heidelberg J, Johnson J, Mead D, Pohorille A, Sarmiento M, Schweighofer K, Seshadri R, Voytek MA. Journal of Bacteriology. 2009. 191(6):1992-1993.

Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species. Wu C, Proestou D, Carter D, Nicholson E, Santos F, Zhao S, Zhang HB, Goldsmith MR. BMC Genomics. 2009. 10:283

One-plasmid tunable coexpression for mycobacterial protein–protein interaction studies. Chang Y, Mead D, Dhodda V, Brumm P, Fox BG. Protein Science 2009. 18(11): 2316-2325.


2008

Assembly of Viral Metagenomes from Yellowstone Hot Springs. Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, Mead D. Applied and Environmental Microbiology. 2008. 74(13):4164-4174.

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures. Pride DT, Schoenfeld T. BMC Genomics. 2008. 9:420.

Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Srinivasiah S, Bhavsar J, Thapar K, Liles M, Schoenfeld T, Wommack KE. Res Microbiol.2008. 159:349.


2004

Phage Community Dynamics in Hot Springs. Breitbart M, Wegley L, Leeds S, Schoenfeld T, Rohwer F. Applied and Environmental Microbiology. 2004. 70(3):1633-1640.


2002

"Genomic analysis of uncultured marine viral communities." Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. Proceedings of the National Academy of Sciences of the United States of America. 2002. 99(22):14250-14255.


Book Chapters

  • Schoenfeld T, Mead D. (2011). "Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution." In de Bruijn, Frans J. Editor, Handbook of Molecular Microbial Ecology II: Metagenomics in different habitats (pp. 45-63). Hoboken, NJ: Wiley-Blackwell.

  • Schoenfeld T, Hermersmann N, Moser M, Renneckar D, Dhodda V, Mead D. (2011). "Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing." In de Bruijn, Frans J. Editor, Handbook of Molecular Microbial Ecology II: Metagenomics in different habitats (pp. 563-577). Hoboken, NJ: Wiley-Blackwell.

  • Wommack KE, Bench SR, Bhavsar J, Mead D, Hanson T. (2009). "Isolation independent methods of characterizing phage communities: Characterizing a metagenome." In Bacteriophages: Methods and Protocols (A. Kropinski, M. Cloike eds.) Humana Press.

  • Samuels M, Leamon J, Rothberg J, Godiska G, Schoenfeld T, Mead D. (2009). "New Paradigms in Droplet Based Microfluidics and DNA Amplification." In Automation in Genomics and Proteomics: An Engineering CaseBased Approach (G Alterovitz, M Ramoni, R Beson ed.) Wiley.

  • Godiska R, Mead DA, Dhodda V, Hochstein R, Karsi A, Ravin N, Wu C. (2008). Bias-Free Cloning of “Unclonable” DNA for Simplified Genomic Finishing. In DNA Sequencing III: Dealing with Difficult Templates. (J. Kieleczawa, ed.), Jones and Bartlett Publishers, Sudbury, MA.

  • Godiska R, Patterson M, Schoenfeld T, Mead DA. (2005). “Beyond pUC: Vectors for Cloning Unstable DNA.” In DNA Sequencing: Optimizing the Process and Analysis. (J. Kieleczawa, ed.), Jones and Bartlett Publishers, Sudbury, MA.


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