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Scholarly Interest Report
         
Janet Louise Siefert
Senior Faculty Fellow
Senior Faculty Fellow in Statistics
 
e-mail:siefert@stat.rice.edu
 
  • B.S. (1975) University of Central Arkansas, Arkansas
  • Ph.D. Biology (1997) University of Houston, Houston
 
Primary Department
   Department of Statistics
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Department Affiliations
 
  • Institute of Biosciences and Bioengineering
  • Keck Center for Quantitative Biomedical Sciences
  •  
     
    Research Areas
     Phylogeny Reconstruction, Prokaryotic Biochemical Systems and Ecosystem Evolution, Origin of Life, RNA's and Astrobiology
     
    Selected Publications
     Refereed articles
     

    M-P Lee, Z., Poret-Peterson, A.T., Siefert, J.L., Kaul, D., Moustafa, A., Allen, A.E., Dupont, C.L., Eguiarte, L.E., Souza,V., and Elser, J.J. "Nutrient stoichiometry shapes microbial community structure in evaporitic shallow pond." Frontiers in Aquatic MicrobiolgySubmitted

     
     

    Souza, V., Eguiarte, L.E., Elser, J.J., Olmedo-Alvarez, G., Siefert, J.L. and Travisano, M. "Can we save a world? Lessons from an endangered microbial oasis in the Chihuahuan desert.." UNESCOIn Press

     
     

    Breitbart,M., Hoare,A., Nitti,A., Siefert,J., Haynes,M., Dinsdale,E., Edwards,R., Souza,V., Rohwer,F., & Hollander,D. "Metagenomic and Stable Isotopic Analyses of Modern Freshwater Microbialites in Cuatro Ciénegas, Mexico." Environmental Microbiology, 11 (2009) : 16-34.

     
     

    Siefert,J.L. "Defining the Mobilome." Methods Mol Biol, 532 (2009) : 13-27.

     
     

    Yerrapragada,S., Siefert,J.L. & Fox,G.E. "Horizontal Gene Transfer in Cyanobacterial Signature Genes." Methods Mol Biol., 532 (2009) : 339-366.

     
     

    Martin, K., Siefert, J., Yerrapragada, S., Lu, Y., McNeil, T.Z., Moreno, P.A., Weinstock, G.M., Widger, W.R. and Fox, G. "Cyanobacteria Signature Genes." Photosynthetic Research, 75 (2003) : 211-221.

     
     Articles
     

    Nitti,A., Daniels, C. A., Siefert, J., Souza, V., Hollander, D. & Breitbart, M. "Spatially Resolved Genomic, Stable Isotopic, and Lipid Analyses of a Modern Freshwater Microbialite from Cuatro Cienegas, Mexico." , 12 (2012) : 685-698.

     
     

    Siefert, J. "Discovery News, Have We Already Colonized Mars?."  (08/31/2012)

     
     

    Siefert, J.L. "Man and his spaceships: Vehicles for extraterrestrial colonization?." , 2 (2012) : 6-12.

     
     

    Siefert,J.L., Souza, V., Eguiarte, L. & Olmedo-Alvarez, G. "Microbial Stowaways: Inimitable Survivors or Hopeless Pioneers?." , 12 (2012) : 710-715.

     
     

    Souza,V., Eguiarte, L. E., Travisano, M., Elser, J. J., Rooks, C. & Siefert, J. L. "Travel, Sex, and Food: What's Speciation Got to Do with It?." , 12 (2012) : 634-640.

     
     

    Souza,V., Siefert, J. L., Escalante, A. E., Elser, J. J. & Eguiarte, L. E. "The Cuatro Cienegas Basin in Coahuila, Mexico: An Astrobiological Precambrian Park." , 12 (2012) : 641-647.

     
     

    Nitti, A., Daniels, C., Siefert, J., Souza, V., Hollander, D., and Breitbart, M. "Spatially-resolved Genomic, Molecular Organic, and Stable Isotopic Analyses of an Actively-accreting Freshwater Microbialite from Cuatro Ciénegas, Mexico. ."  (2011) In Revision

     
     

    Siefert, J.L. "Astrobiology Pioneers: How a Real Housewife Became an Astrobiologist." , 11 (2011) : 193-195.

     
     

    Souza, V., Siefert, J., Escalante, A.E., Elser, J, and Eguiarte, L. "The Cuatro Cienegas Basin in Coahuila, Mexico: an Astrobiological Precambrian Park. ."  (2012) In Press

     
     

    Cerritos, R., Vinuesa, P., Eguiarte, L., Herrera, L., Alcaraz, L., Olmedo, G., Siefert, J. and Souza, V. "Bacillus Coahuilensis sp. nov. a New Moderately Halophilic Species From Different Ponds in The Cuatro Cienegas Valley in Coahuila, Mexico." IJSB (2006) Submitted

     
     

    Herrera, L., Siefert, J. et al. "Bacillus Coahuilenses and Its Environment, Gene Tranfer and Geobiolgy." Nature (2006) Submitted

     
     

    Siefert, J., Fox, G., Shaw, C.A. and Kimmel, M. "Real Rates of RNA Evolution Under Selection." Nature (2006) Submitted

     
     

    Yerrapragada, S., Siefert, J. and Fox, G. "Limited Horizontal Transfer Among Cyanobacterial Signature Genes." Microbiology (2006) Submitted

     
     

    Fox, G., Siefert, J. and Yerrapragada, S. "Limited Horizontal Transfer among Cyanobacterial Signature Genes." Microbiology (2005) Submitted

     
     

    Kasting, J.F., Kharecha, P. and Siefert, J. "Predicting the Methane Flux and Productivity of the Archean Bosphere." Geobology (2005) Submitted

     
     

    Raymond, J., Siefert, J., Staples, C.R. and Blankenship, R. "The Natural History of Nitrogen Fixation." Molecular Biology and Evolution (2004) : 21:541-54.

     
     

    Siefert, J. "Life and the Evolution of Earth's Atmosphere." Science, 296 (2002) : 1066-1068.

     
     Book chapters
     

    "The Phylogeny of Bacterial Shape in Molecules in Time and Space: Bacterial Shape, Division and Phylogeny."  (2004)

     
     Other
     

    Aussman, D. "Evolutionary Thinking." Sallyport (Summer 2007)

     
     

    Aussman, D. "The Debate that Shouldn't Happen and Evolutionary Thinkging." Sallyport, Vol. 63 No. 2 (Winter 2007)

     
     

    Cerritos, R., Siefert, J., Eguiarte, L. and Souza, V. "Bacillus Coahuilensis sp. nov. a New Moderatley Halophilic Species From Different Pozas in the Cuatro Cienegas Valley in Coahuila, Mexico." IJSB

     
     

    Kiang, N., Segura, A., Tinetti, G., Vondindjee, G., Blankenship, R., Cohen, M., Siefert, J., Crisp, D. and Meadows, V. "Coveloution of Photosynthesis with the Atmosphere on Extrasolar Worlds: Pigment Spectra for Organisms Living Around M Dwarfs." Astrobiology, 7 (2007) : 252-274.

     
     

    Kiang, N., Tinetti, G., Vondindjee, G., Blankenship, R., Cohen, M., Siefert, J., Crisp, D. and Meadows, V. "Spectral Signatures of Photosynthesis II: Coevolution with Other Stars and the Atmoshere on Extrasolar Worlds." Astrobiology, 7 (2007C) : 222-251.

     
     

    Larios-Sanz, M., Travisano, M. and Siefer, J. "Exiguobacterium sp. CCB are Isolated From Multiple Pozas." 

     
     

    Siefert, J. "Desert Microbialites: Analogues to Other Worlds." ASM Microbe (Fall 2007)

     
     

    "BBC, Radio 4, with Molly Bentley." 

     
     

    "Stromatolites in Mexico, Analogues for Other Worlds." Astrobiology (January 2007)

     
     

    Fox, G., Siefert, J., Widger, B. and Martin, K. "Comparative Cyanobacterial Genomic Architeture." 

     
     

    Kasting, J. and Siefert, J. "Biogeochemistry-The Nitrogen Fix." Nature, 412 (2001) : 26-27.

     
     

    Kasting, J., Pavlov, A. and Siefert, J. "A Coupled Ecosystem-Climate Model for Predicting the Methane Concentration in the Archean Atmosphere." Origins Life Evol B, 31 (2001) : 271-285.

     
     

    Larios-Sanz, M., Fox, G., Spudich, J., Jurtshuk, P. and Siefert, J. "An Unusual Membrane Photo Responive Pigment in Marine Bacillus Isolates." 

     
     

    Renwick, A. and Siefert, J. "A Comprehensive Phylogenetic History of Nitrogenase." 

     
     

    Siefert, J. "Making New Proteins from Old Ones in an RNA World." 

     
     

    Siefert, J. and Kasting, J. "Ferredoxin: An Old Story Revisited." Journal of Molecular Evolution

     
     

    Siefert, J., Jurtshuk, Jr. P. and Fox, G. "Examining the Taxonomic Hierarchy of the Genus Bacillus." 

     
     

    Siefert, J., Shaw, C., Fox, G. and Kimmel, M. "Ribozyme Phylogeny:A Documented Case of Vectoral Molecular Evolution." Molecular Biology and Evolution

     
     

    Hedenstierna, K.O.F., Siefert, J., Fox, G. and Murgola, E. "Co-Conservation of rRNA Tetraloop Sequences and Helix Length Suggest Involvement of the Tetraloops in Higher Order Interactions." Biochemie, 82 (2000) : 221-227.

     
     

    Siefert, J., Larios-Sanz, M., Nakamura, N., Slepecky, R., Paul, J., Moore, E., Fox, G. and Jurtshuck Jr., P. "Phylogenetic Position of Marine Bacillus Isolates From the Gulf of Mexico." Current Microbiology, 41 (2000) : 84-88.

     
    Presentations
     Invited Papers
     

    "Cuatro Cienegas: A Precambrian Park." Workshop and Fieldtrip: Geobiology in Space Exploration, Marrakesh, Morocco. (February 7-14, 2011)

     
     Invited Talks
     

    "Nutrients, Robosomes, and Genomes: A Desert Survival Test for the Growth Rate Hypothesis." ASLO Summer Meeting, Santa Fe, New Mexico, (June 5-10, 2016)

     
     

    "Life on Floating Pumice." 2012 ASLO Aquatic Sciences Meeting, Lake Biwa, Otsu, Shiga, Japan. (July 8-13, 2012) With Elser, J.J., Corman, J.R., Lee, Z.,Siefert, J.L., Bastidas, M., Cuassolo, F., Laspoumaderes, C., Souza, M.S., Balserio, E.G., Modenutti, B.E.

     
     

    "Phylogeny of cell shape: A window into origins or adaptive dead end?." 2013 Princeton Center for Theoretical Science Origin of Life, Princeton, Massachusetts. (January 21-24, 2013) With Siefert, J.L.

     
     

    "The III International Conference Biosphere Origin and Evolution." Oral Presentation: Cuatro Cienegas: A Precambrian Astrobiology Park, Crete Greece. (October 16-20, 2012)

     
     

    "What Could a Whole Earth Stromatolite Catalogue Tell Us??." 2012 ASLO Aquatic Sciences Meeting, Lake Biwa, Otsu, Shiga, Japan. (July 8-13, 2012) With Siefert, J.L., Souza, V., Eguiarte, L., and Meadows, V.

     
     

    "Cuatro Cienegas: a Precambrian Astrobiology Park." The III International conference Biosphere Origin and Evolution, Crete, Greece. (October 16-20, 2011)

     
     

    "What Could a ‘Whole Earth Stromatolite Catalogue’ Tell Us?." The First International Earth Microbiome Project Conference, Shenzhen, China. (June 13-15, 2011)

     
     

    "Bacterial IQ: Who's The Smartest Bug in The Mexican Desert?." University of Southern Florida, Florida. (January 12, 2007)

     
     Bioastronomy 2007, Molecules, Microbes and Extraterrestrial Life
     
     Genomics and Biodiversity Symposium
     
     

    "The Phosphorus Effect: Living Stromatolites in the Mexican Desert." ASM 107th General Meeting, Toronto, Canada. (May 21-25, 2007)

     
     

    "Stromatolites in the Desert: Analogues to Other Worlds." EANA Astrobiology Workshop, Lyon, France. (October 14-18, 2006)

     
     

    "Viral Metagenomics of the Stromatolites of Cuatro Cienegas." AbSciCon, Washington D.C. (March 26-30, 2006)

     
     

    "Gene Transfer." Institute of Mathematics, Polish Academy of Sciences, Bedlweo, Poland. (May 29-31, 2005)

     
     

    "Horizontal Gene Transfer: Retrospection and Beyond." Computational Molecular Biology: The Future, a Symposium at the University of Houston, University of Houston. (April 4, 2005)

     
     

    "Microbial Gene Transfer - Where, How, and Why?." Statistics Departmental Colloquium, Rice University. (April 25, 2005)

     
     

    "Real Rate of RNA Evolution." NASA NAI Research Conference, (March 2004)

     
     

    "The Phylogeny of Bacterial Shape." Bioastronomy 2004: Habitable Worlds, Reykjavik, Iceland. (July 2004)

     
     

    "Horizontal Gene Transfer and the Evolution of Nitrogen Fixation." Seventh Conference on Chemical Evolution and the Origin of Life, Trieste, Italy. (9/2003)

     
     

    "The Natural History of Nitrogen Fixation." Exobiology Principle Investigators Meeting, Seventh Triennial Science Conference, NASA, Ames. (August 25-29, 2003)

     
     

    "Real Rates of RNA Eeuiton and Their Relevance to an RNA World." IAU Symposium 213 "Bioastronomy 2002: Life Among the Stars, (July 2002)

     
     

    "Round Table Discussion: Genomes, Extremophiles and Evolution." ISSOL, Oaxaca, Mexico. (June 2002)

     
     Keynote Speaker
     

    "Metabolic Basis of Ecology." Gordon Keenan Graduate Research Conference, Lewiston, ME. (July 21-23, 2006)

     
     Lectures
     

    "Phylogeny of cell shape: A window into origins or adaptive dead end?." Princeton Center For Theoretical Science Origin of Life, Princeton, Massachusetts. (Jan. 21-24, 2013)

     
     Other
     

    "Nitrogenase and the Rise of O2 in the Archean." EUG Meeting, (4/2001)

     
     

    "The Role of Ferredoxin in the Rise of O2." GSA/GSL International Conference, (6/2001)

     
     

    "Molecular Phylogeny: Unveiling the Origin and Early Evolution of Life." Frontiers of Science Lecture Series, Penn State University. (1/29/2000)

     
     Posters
     

    "Soil Memory: Microbial Populations as Biosignatures for Evaluating Long Term Effects of Urbanization." ASOR Annual Meeting, San Antonio, TX, (Nov 16-19, 2016) With Gonzales, S, Larios-Sanz, M, Siefert, JL, Hill, P, Boddy, C, Hartshorn, A, Lanier, M, and Ortiz, S.

     
     

    "Horizontal Gene Transfer in the Pozas of Cuatro Cienegas." NAI2005 Biennial Meeting University of Colorado, Boulder, CO. (April 10-14, 2005)

     
     

    "Signature Genes in Cyanobacteria are Resistant to Horizontal Gene Transfer." GRC Marine Microbes, Roscoff, France. (June 2004)

     
     

    "Signature Set of Cyanobacterial Genes." GRC, Origin of Life, Ventura, CA. (1/2002)

     
     

    "The Function of Most Cyanobacterial Signature Genes at 2.1 Ga is Unknown." Royal Society Discussion Meeting,, London. (6/2002)

     
     

    "The Function of Most Cyanobacterial Signature Genes at 2.1 Ga is Unknown." Astrobiology General Meeting 2002, NASA Ames. (4/2002)

     
     Workshops
     

    "UNAM and CINVESTAV, talk and guest teacher." Cuatro Cienegas Workshop, Cuatro Cienegas, Mexico. (May 2006)

     
    Awards, Prizes, & Fellowships
     Discretionary Award, NASA (August 04)

    Positions Held
     Vice Chair/Chair Elect, Gordon Research Conference, Origin of Life. (2004 - 2004)

     Session Chair, ASM General Meeting. (2007 - 2007)

     Postdoctoral Fellow, NSF Bioinformatics. (2001 - 2001)

     Member, American Geophysical Union. (2006 - 2006)

     2nd Vice President, ISSOL. (2005 - 2005)

     Chair, ISSOL Round Table Discussion, Oaxaca, Mexico. (2002 - 2002)

     Co-Director, Science Cafe. (2005 - 2005)

     Session Chair, GSA/GSL International Conference. (2001 - 2001)

     Session Chair, AGU General Meeting. (2007 - 2007)

     Member, American Society for Microbiology. (2006 - 2006)

     Chair, ISSOL Round Table Discussion, Oaxaca, Mexico. (2003 - 2003)

     Associate Member, Penn State Astrobiology Research Center. (2004 - 2004)

     Faculty/Mentor, Keck Center for Computational Biology. (2004 - 2004)

     Gordon Research Conference, Vice Chair/Chair Elect. (2005 - 2005)

     Scientific Organizing Committee, Bioastronomy. (2007 - 2007)

     2nd Vice Presidnet, ISSOL. (2006 - 2006)

     Panel Member, National Science Foundation FIBR. (2004 - 2004)

     Associate Member, Virtual Planet Laboratory Astrobiology Research Group. (2006 - 2006)

     Penn State Astrobiology Research Center, Associate Member. (2005 - 2005)

     Panelist, National Research Council COEL. (2004 - 2004)

     Assoicate Member, Penn State Astrobiology Research Center. (2006 - 2006)

     Faculty/Mentor, Keck Center for Computational Biology. (2005 - 2005)

     COEL Panelist, National Research Council. (2005 - 2005)

     Member, Johnson Space Center Lead Team, NASA NAI. (2006 - 2006)

     NASA NAI Member, Johnson Space Center Lead Team. (2005 - 2005)

     Session Chair, Gordon Research Conference, Origin of Life. (2003 - 2003)