Paulinella chromatophora
Two cranberry cultivars
© Nicholi Vorsa
Pleopsidium© Valérie Reeb
Culex pipiensGenome Cooperative at SEBS - Home
Mission Statement:
The Genome Cooperative is a group of collaborating faculty and their lab members who share resources to enable rapid growth in genomics and genomic tools at Rutgers. Members contribute to collaborative ventures through shared funding of projects or personnel, collaborative agreements to develop novel research or teaching resources, and participate in GC events.
The Genome Cooperative is a group of collaborating faculty and their lab members who share resources to enable rapid growth in genomics and genomic tools at Rutgers. Members contribute to collaborative ventures through shared funding of projects or personnel, collaborative agreements to develop novel research or teaching resources, and participate in GC events.
GC highlight: The Genome Cooperative provides genome data to cranberry researchers at Rutgers.
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Some recent papers by members:
Bhattacharya D., Price D.C., Yoon H.S., Yang E.C., Poulton N.J., Andersen R.A., Das S.P.
Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis. Scientific Reports 2, 10 April 2012, Article number: 356 (open access).
doi
Price D.C., Chan C.X., Yoon H.S., Yang E.C., Qiu H., Weber A.P., Schwacke R., Gross J., Blouin N.A., Lane C., Reyes-Prieto A., Durnford D.G., Neilson J.A., Lang F.B., Gertraud Burger G., Steiner J.M., Löffelhardt W., Meuser J.E., Posewitz M.C., Ball S., Arias M.C., Henrissat B., Coutinho P.M., Rensing S.A., Symeonidi A., Doddapaneni H., Green B.R., Rajah V.D., Boore J., and Bhattacharya D. 2012.Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 17 February 2012: Vol. 335 no. 6070 pp. 843-847 doi
David Rotter, Karen V. Ambrose, Faith C. Belanger. Velvet bentgrass (Agrostis canina L.) is the likely ancestral diploid maternal parent of allotetraploid creeping bentgrass (Agrostis stolonifera L.). Genet Resour Crop Evol (2010) 57:1065–1077 doi|pdf
David Rotter, Arvind K. Bharti, Huaijun Michael Li, Chongyuan Luo, Stacy A. Bonos, Suleiman Bughrara, Geunhwa Jung, Joachim Messing, William A. Meyer, Stephen Rudd, Scott E. Warnke, Faith C. Belanger. Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses.
Mol Genet Genomics (2007) 278:197–209 doi| pdf
William J. Belden, Jennifer J. Loros, and Jay C. Dunlap. Execution of the Circadian Negative Feedback
Loop in Neurospora Requires the ATP-Dependent Chromatin-Remodeling Enzyme CLOCKSWITCH Molecular Cell 25, 587–600, 2007
doi|pdf
William J. Belden, Luis F. Larrondo, Allan C. Froehlich, Mi Shi, Chen-Hui Chen, Jennifer J. Loros, and Jay C. Dunlap. The band mutation in Neurospora crassa is a dominant allele of ras-1 implicating RAS signaling in circadian output. Genes Dev. 2007 21: 1494-1505. doi| pdf
Ahmed Moustafa, Bánk Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 2009. Jun 26;324(5935):1724-6. doi|pdf
Assaf Vardi, Benjamin A. S. Van Mooy, Helen F. Fredricks, Kimberly J. Popendorf, Justin E. Ossolinski, Liti Haramaty, Kay D. Bidle. Viral Glycosphingolipids Induce Lytic Infection and Cell Death in Marine Phytoplankton. Science 326, 861 (2009). doi|pdf
Kay D. Bidle, SangHoon Lee, David R. Marchant, and Paul G. Falkowski. Fossil genes and microbes in the oldest ice on Earth. Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13455-60. doi| pdf
Laura M. Cortese, Joshua Honig, Chris Miller and Stacy A. Bonos. Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers. 2010. BioEnergy Research Volume 3, Number 3, 262-271.
doi| pdf
Christine Kubik, Joshua Honig, William A. Meyer and Stacy A. Bonos. Genetic Diversity of Creeping Bentgrass Cultivars Using SSR Markers. International Turfgrass Society Research Journal Volume 11, 2009. pdf
Yana Bromberg, John Overton, Christian Vaisse, Rudolph L. Leibel, and Burkhard Rost. 2009. In silico mutagenesis: a case study of the melanocortin 4 receptor. The FASEB Journal article fj.08-127530. doi| pdf
Yana Bromberg, Guy Yachdav and Burkhard Rost. SNAP predicts effect of mutations on protein function. Bioinformatics. 2008 Oct 15;24(20):2397-8. doi| pdf
Cadhla Firth, Michael A. Charleston, Siobain Duffy, Beth Shapiro and Edward C. Holmes. Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2. Journal of Virology, Dec. 2009, p. 12813–12821 Vol. 83, No. 24. doi| pdf
Gordon W Harkins, Wayne Delport, Siobain Duffy, Natasha Wood, Adérito L Monjane, Betty E Owor, Lara Donaldson, Salem Saumtally, Guy Triton, Rob W Briddon, Dionne N Shepherd, Edward P Rybicki, Darren P Martin and Arvind Varsani. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virology Journal 2009, 6:104. doi| pdf
Dina M. Fonseca, A. K. Widdel, M. Hutchinson, S.E. Spichiger and L. D. Kramer. Fine-scale spatial and temporal population genetics of Aedes japonicus, a new US mosquito, reveal multiple introductions. Molecular Ecology (2010) 19, 1559–1572.
doi| pdf
Dina M. Fonseca, Julie L. Smith, Heung-Chul Kim, Motoyoshi Mogi. Population genetics of the mosquito Culex pipiens pallens reveals sex-linked asymmetric introgression by Culex quinquefasciatus. Infection, Genetics and Evolution 9 (2009) 1197–1203. doi| pdf
Andrzej Z. Pietrzykowski, Ryan M. Friesen, Gilles E. Martin, Sylvie I. Puig, Cheryl L. Nowak, Patricia M. Wynne,
Hava T. Siegelmann, and Steven N. Treistman. Posttranscriptional Regulation of BK Channel Splice Variant Stability by miR-9 Underlies Neuroadaptation to Alcohol Neuron 59, 274–287, July 31, 2008.
doi| pdf
Andrzej Z. Pietrzykowski, Gilles E. Martin, Sylvie I. Puig, Thomas K. Knott, Jose R. Lemos, and Steven N. Treistman. Alcohol Tolerance in Large-Conductance, Calcium-Activated Potassium Channels of CNS Terminals Is Intrinsic and Includes Two Components: Decreased Ethanol Potentiation and Decreased Channel Density J. Neurosci., September 22, 2004; 24(38):8322– 8332. doi| pdf
Jeanmaire Molina and Lena Struwe. 2009. Utility of secondary structure in phylogenetic reconstructions using nrDNA ITS sequences - an example from Potalieae (Gentianaceae: Asteridae). Systematic Botany 34: 414-428. doi
Lena Struwe, Scott Haag, Einar Heiberg, and Jason R. Grant. 2009. Andean speciation and vicariance in neotropical Macrocarpaea (Gentianaceae-Helieae). Annals of Missouri Botanical Garden 96: 450-469. doi
Kerry O'Donnell, Deanna A. Sutton, Michael G. Rinaldi, Brice A. J. Sarver, S. Arunmozhi Balajee, Hans-Josef Schroers, Richard C. Summerbell, Vincent A. R. G. Robert, Pedro W. Crous, Ning Zhang, Takayuki Aoki, Kyongyong Jung, Jongsun Park, Yong-Hwan Lee, Seogchan Kang, Bongsoo Park, and David M. Geiser. Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections. Journal of Clinical Microbiology, Oct. 2010, p. 3708–3718 Vol. 48, No. 10. doi| pdf
Ning Zhang, Kerry ÓDonnell, Deanna A. Sutton, F. Ameena Nalim, Richard C. Summerbell, Arvind A. Padhye, and David M. Geiser. Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. Journal of Clinical Microbiology, June 2006, p. 2186–2190 Vol. 44, No. 6. doi| pdf
Price D.C., Chan C.X., Yoon H.S., Yang E.C., Qiu H., Weber A.P., Schwacke R., Gross J., Blouin N.A., Lane C., Reyes-Prieto A., Durnford D.G., Neilson J.A., Lang F.B., Gertraud Burger G., Steiner J.M., Löffelhardt W., Meuser J.E., Posewitz M.C., Ball S., Arias M.C., Henrissat B., Coutinho P.M., Rensing S.A., Symeonidi A., Doddapaneni H., Green B.R., Rajah V.D., Boore J., and Bhattacharya D. 2012.Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 17 February 2012: Vol. 335 no. 6070 pp. 843-847 doi
David Rotter, Karen V. Ambrose, Faith C. Belanger. Velvet bentgrass (Agrostis canina L.) is the likely ancestral diploid maternal parent of allotetraploid creeping bentgrass (Agrostis stolonifera L.). Genet Resour Crop Evol (2010) 57:1065–1077 doi
|pdf
David Rotter, Arvind K. Bharti, Huaijun Michael Li, Chongyuan Luo, Stacy A. Bonos, Suleiman Bughrara, Geunhwa Jung, Joachim Messing, William A. Meyer, Stephen Rudd, Scott E. Warnke, Faith C. Belanger. Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses.
Mol Genet Genomics (2007) 278:197–209 doi| pdf
William J. Belden, Jennifer J. Loros, and Jay C. Dunlap. Execution of the Circadian Negative Feedback
Loop in Neurospora Requires the ATP-Dependent Chromatin-Remodeling Enzyme CLOCKSWITCH Molecular Cell 25, 587–600, 2007
doi|pdf
William J. Belden, Luis F. Larrondo, Allan C. Froehlich, Mi Shi, Chen-Hui Chen, Jennifer J. Loros, and Jay C. Dunlap. The band mutation in Neurospora crassa is a dominant allele of ras-1 implicating RAS signaling in circadian output. Genes Dev. 2007 21: 1494-1505. doi| pdf
Ahmed Moustafa, Bánk Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya. Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 2009. Jun 26;324(5935):1724-6. doi|pdf
Assaf Vardi, Benjamin A. S. Van Mooy, Helen F. Fredricks, Kimberly J. Popendorf, Justin E. Ossolinski, Liti Haramaty, Kay D. Bidle. Viral Glycosphingolipids Induce Lytic Infection and Cell Death in Marine Phytoplankton. Science 326, 861 (2009). doi|pdf
Kay D. Bidle, SangHoon Lee, David R. Marchant, and Paul G. Falkowski. Fossil genes and microbes in the oldest ice on Earth. Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13455-60. doi| pdf
Laura M. Cortese, Joshua Honig, Chris Miller and Stacy A. Bonos. Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers. 2010. BioEnergy Research Volume 3, Number 3, 262-271.
doi| pdf
Christine Kubik, Joshua Honig, William A. Meyer and Stacy A. Bonos. Genetic Diversity of Creeping Bentgrass Cultivars Using SSR Markers. International Turfgrass Society Research Journal Volume 11, 2009. pdf
Yana Bromberg, John Overton, Christian Vaisse, Rudolph L. Leibel, and Burkhard Rost. 2009. In silico mutagenesis: a case study of the melanocortin 4 receptor. The FASEB Journal article fj.08-127530. doi| pdf
Yana Bromberg, Guy Yachdav and Burkhard Rost. SNAP predicts effect of mutations on protein function. Bioinformatics. 2008 Oct 15;24(20):2397-8. doi| pdf
Cadhla Firth, Michael A. Charleston, Siobain Duffy, Beth Shapiro and Edward C. Holmes. Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2. Journal of Virology, Dec. 2009, p. 12813–12821 Vol. 83, No. 24. doi| pdf
Gordon W Harkins, Wayne Delport, Siobain Duffy, Natasha Wood, Adérito L Monjane, Betty E Owor, Lara Donaldson, Salem Saumtally, Guy Triton, Rob W Briddon, Dionne N Shepherd, Edward P Rybicki, Darren P Martin and Arvind Varsani. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virology Journal 2009, 6:104. doi| pdf
Dina M. Fonseca, A. K. Widdel, M. Hutchinson, S.E. Spichiger and L. D. Kramer. Fine-scale spatial and temporal population genetics of Aedes japonicus, a new US mosquito, reveal multiple introductions. Molecular Ecology (2010) 19, 1559–1572.
doi| pdf
Dina M. Fonseca, Julie L. Smith, Heung-Chul Kim, Motoyoshi Mogi. Population genetics of the mosquito Culex pipiens pallens reveals sex-linked asymmetric introgression by Culex quinquefasciatus. Infection, Genetics and Evolution 9 (2009) 1197–1203. doi| pdf
Andrzej Z. Pietrzykowski, Ryan M. Friesen, Gilles E. Martin, Sylvie I. Puig, Cheryl L. Nowak, Patricia M. Wynne,
Hava T. Siegelmann, and Steven N. Treistman. Posttranscriptional Regulation of BK Channel Splice Variant Stability by miR-9 Underlies Neuroadaptation to Alcohol Neuron 59, 274–287, July 31, 2008. doi
| pdf
Andrzej Z. Pietrzykowski, Gilles E. Martin, Sylvie I. Puig, Thomas K. Knott, Jose R. Lemos, and Steven N. Treistman. Alcohol Tolerance in Large-Conductance, Calcium-Activated Potassium Channels of CNS Terminals Is Intrinsic and Includes Two Components: Decreased Ethanol Potentiation and Decreased Channel Density J. Neurosci., September 22, 2004; 24(38):8322– 8332. doi| pdf
Jeanmaire Molina and Lena Struwe. 2009. Utility of secondary structure in phylogenetic reconstructions using nrDNA ITS sequences - an example from Potalieae (Gentianaceae: Asteridae). Systematic Botany 34: 414-428. doi
Lena Struwe, Scott Haag, Einar Heiberg, and Jason R. Grant. 2009. Andean speciation and vicariance in neotropical Macrocarpaea (Gentianaceae-Helieae). Annals of Missouri Botanical Garden 96: 450-469. doi
Kerry O'Donnell, Deanna A. Sutton, Michael G. Rinaldi, Brice A. J. Sarver, S. Arunmozhi Balajee, Hans-Josef Schroers, Richard C. Summerbell, Vincent A. R. G. Robert, Pedro W. Crous, Ning Zhang, Takayuki Aoki, Kyongyong Jung, Jongsun Park, Yong-Hwan Lee, Seogchan Kang, Bongsoo Park, and David M. Geiser. Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections. Journal of Clinical Microbiology, Oct. 2010, p. 3708–3718 Vol. 48, No. 10. doi| pdf
Ning Zhang, Kerry ÓDonnell, Deanna A. Sutton, F. Ameena Nalim, Richard C. Summerbell, Arvind A. Padhye, and David M. Geiser. Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. Journal of Clinical Microbiology, June 2006, p. 2186–2190 Vol. 44, No. 6. doi| pdf
If you are interested in joining the Genome Cooperative please contact:
Debashish Bhattacharya
Tel: (848) 932-6218
Email: Bhattacharya@AESOP.Rutgers.edu
102 Foran Hall, 59 Dudley Rd
New Brunswick, NJ 08901
Debashish Bhattacharya
Tel: (848) 932-6218
Email: Bhattacharya@AESOP.Rutgers.edu
102 Foran Hall, 59 Dudley Rd
New Brunswick, NJ 08901
Aedes japonicus, the most recently introduced mosquito to the US (first caught here in 1998). 
Lichens such as Pleopsidium pictured here are famous for containing a large numberof mobile genetic elements (group I introns) in their rDNA genes.
Two cranberry cultivars are shown in this figure: the red fruit is from #35 and the yellow fruit from a seedling of the wild-pollinated "yellow bell".
Culex pipiens is the primary urban vector of West Nile virus in the United States.