Selected publications:

• A Multiple network learning approach to capture system-wide condition-specific responses
  S Roy, T Lane, and M Werner-Washburne
  Bioinformatics doi:10.1093/bioinformatics/btr270 (2011)

  The proteomics of quiescent and non-quiescent cell differentiation in yeast stationary-
  phase cultures
  G.S. Davidson, R.M. Joe, S. Roy, O. Meirelles, C.P. Allen, M.R. Wilson, P.H. Tapia, E.E. Manzanilla, A.E. Dodson, S. Chakraborty, M.Carter, S.Young, B. Edwards, L. Sklar,  M. Werner-Washburne
  Molecular Biology of the Cell 22: 988-998 (2011)

  Encapsulation of S. cerevisiae in Poly(glycerol) Silicate Derived Matrices: Effect of Matrix
  Additives and Cell Metabolic Phase on Long-Term Viability and Rate of Gene Expression
  JC Harper, DM Lopez, EC Larkin, ME Economides, SK McIntyre, TM Alam, MS Tartis, M     Werner-Washburne, CJ Brinker, SM Brozik, DR Wheeler
  Chemistry of Materials (in press) (2011)

• Still waters run deep: Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures
  M. Werner-Washburne, S. Roy, and G.S. Davidson
  In: Aging research in yeast.  Ed. Breitenbach, Laun, and Jazwinski; Springer Verlag, Berlin (2011, in press)

• Engineering of a redox protein for DNA-directed assembly; G.R. Szilvay, S. Brocato, D. Ivnitski, C. Li, P. de la Iglesia, C. Lau, E. Chi, M. Werner-Washburne, S. Banta, P. Atanassov DOI: 10.1039/c1cc11951f
  

• Exploiting Amino Acid Composition for Predicting Protein-protein Interactions
  S. Roy, A.D. Martinez, H. Platero, T. Lane, and M. Werner-Washburne
  PLoSONE doi:10.1371/journal.pone.0007813 (2009).           

• SSD1-V regulates transcript levels of many longevity genes in budding yeast and extends
  chronological life span in purified quiescent cells
  Lihong L., Y. Lu, Li-X.Qin, Z.Bar-Joseph, M.Werner-Washburne,and  L.L. Breeden
  Molecular Biology of the Cell mbc.E09-04-0347

• Scalable learning of large networks
  Sushmita Roy, Sergey Plis, Margaret Werner-Washburne and Terran Lane
  IET Systems Biology (2009) 404-U157

• Fungal genome sequencing and bioenergy.
  S.E. Baker, J. Thykaer, W.S. Adney, T.S. Brettin, F.J. Brockman, P. D’Haeseleer, A.D. Martinez, R.M. Miller, D.S. Rokhsar, C.W. Schadt, T. Torok, G. Tuskan, J. Bennett, R.M. Berka, S.P. Briggs, J. Heitman, J.Taylor, B.G. Turgeon, M. Werner-Washburne, M.E. Himmel.  Fungal Biology Reviews 22:1-5 (2008)

• A system for generating transcription regulatory networks with combinatorial control of transcription.
  S. Roy, M. Werner-Washburne, and T. Lane.  Bioinformatics 24: 1318-1320;
  doi:10.1093/bioinformatics/btn126  (2008)

• Characterization of differentiated quiescent and non-quiescent cells in yeast stationary-
  phase cultures. A.D. Aragon, A.L. Rodriguez, O. Meirelles, S. Roy, G.S. Davidson, C. Allen, R. Joe, P. Tapia, Don Benn, and M.Werner-Washburne. Mol Biol Cell 19:1271-1280(2008) Web supplement

• A Hidden-state Markov Model for Cell Population Deconvolution
  S. Roy, T. Lane, C. Allen, A.D. Aragon, M. Werner-Washburne.  Journal of Computational
  Biology 13:174901774 (2006)

• Multivariate curve resolution of time course microarray data  
  Peter D Wentzell, Tobias K Karakach, Sushmita Roy, M Juanita Martinez, Christopher P Allen,
      and Margaret Werner-Washburne. BMC Computational Biology 7:343 (2006)

• Isolation of quiescent and non-quiescent cells from Saccharomyces cerevisiae stationary
  phase cultures
  Chris Allen, Sabrina Büttner, Anthony D. Aragon, Jason A. Thomas, Osorio Meirelles,
  Jason E. Jaetao, Don Benn, Stephanie W. Ruby, Marten Veenhuis, Frank Madeo, and
  Margaret Werner-Washburne
  J Cell Biology 174:89-100 (2006) Web supplement

• Cell-directed assembly of lipid-silica nanostructures providing extended cell viability
  Baca, HK; Ashley, C; Carnes, E; Lopez, D; Flemming, J; Dunphy, D; Singh, S; Chen, Z; Liu, NG; Fan, HY; et. al.
  Source: SCIENCE; JUL 21 2006; v.313, no.5785, p.337-341

• Release of sequestered mRNA is responsible for a massive, non-transcriptional increase inmRNA after oxidative stress in S. cerevisiae stationary-phase cultures Anthony D. Aragon, Gabriel A. Quiñones, Edward V. Thomas, Sushmita Roy, and Margaret Werner-Washburne Genome Biology 2006, 7:R9  doi:10.1186/gb-2006-7-2-r9 (2006) PDF ; Web supplement

• An Automated, Pressure-Driven Sampling Device for Harvesting from Liquid Cultures for
  Genomic and Biochemical Analyses. Anthony D. Aragon, Gabriel A. Quiñones, Chris Allen, Jason Thomas, Sushmita Roy, George S. Davidson, Peter D. Wentzell, Brian Millier, Jason E. Jaetao, Angelina L. Rodriguez, and Margaret Werner-Washburne Journal of Microbiological Methods doi:10.1016/j.mimet.2005.08.015. Web supplement ; PDF

• Hyperspectral Microarray Scanning: Impact on the Accuracy and Reliability of Gene Expression Data Jerilyn A. Timlin, David M. Haaland, Michael B. Sinclair, Anthony D. Aragon, M. Juanita Martinez, Margaret Werner-Washburne BMC Genomics 6 :72 PDF

• A Packed Micro Column Approach to a Cell-Based Biosensor Jeb H. Flemming, Helen K. Baca, Margaret Werner-Washburne, Susan M. Brozik, Gabriel P. López Sensors & Actuators 113: 376-381 (2005)

• Inferring genetic networks from microarray data S. Martin, G. Davidson, E. May, J-L Faulon, and M. Werner-Washburne IEEE 2004, pg. 566-569 (2004)

• Genomic analysis of stationary phase and exit in Saccharomyces cerevisiae: transcriptional profiling and analysis of essential genes. M. J. Martinez, AB Archuleta, AL Rodriquez, P Wentzell, AD Aragon, CP Allen, S Roy, and M. Werner-Washburne Molecular Biology of the Cell 15:5295-5305 Web supplement; PDF

• Sleeping Beauty: Quiescence in Saccharomyces cerevisiae Joseph V. Gray, Gregory A. Petsko, Gerald C. Johnston, Dagmar Ringe, Richard Singer, and Margaret Werner-Washburne Microbiol.
  Mol. Biol. Rev. 68: 187-206 Web supplement; PDF

• Design, Construction, Characterization, and Application of a Hyperspectral Microarray Scanner
  Michael B. Sinclair, Jerilyn A. Timlin, David M. Haaland, and Margaret Werner-Washburne
  Applied Optics 43: 2079-2088 (2004) (2004)

• Genomics in Neurospora crassa: From One-Gene-One-Enzyme to 10,000 Genes
  Edward L. Braun, Donald O. Natvig, Margaret Werner-Washburne and Mary Anne
  Nelson
  Elsevier Applied Mycology & Biotechnology series, Volume 4: Fungal Genomics 4: 295-313 (2004

• The Genome Sequence of the Filamentous Fungus Neurospora crassa
  James E. Galagan1, Sarah E. Calvo1, Katherine A. Borkovich2, Eric U. Selker3, Nick D. Read4, William FitzHugh5, Li-Jun Ma1, Serge Smirnov1, Seth Purcell1, Bushra Rehman1, Timothy Elkins1, Reinhard Engels1, Shunguang Wang1, Cydney B. Nielsen1, Jonathan Butler1, David Jaffe1, Matthew Endrizzi1, Dayong Qui1, Peter Ianakiev1, Deborah Bell-Pedersen6, Mary Anne Nelson7, Margaret Werner-Washburne7, Claude P. Selitrennikoff8, John A. Kinsey10, Edward L. Braun11, Alex Zelter4,26, Ulrich Schulte12, Gregory O. Kothe3, Gregory Jedd13, Werner Mewes9,17, Chuck Staben14, Ed Marcotte15, David Greenberg16, Alice Roy1, Karen Foley1, Jerome Naylor1, Nicole Stange-Thomann1, Robert Barrett1, Sante Gnerre1, Michael Kamal1, Manolis Kamvysselis1, Cord Bielke9, Stephen Rudd17, Dmitrij Frishman17, Svetlana Krystofova2, Carolyn Rasmussen18, Robert L. Metzenberg19, David D. Perkins19, Scott Kroken20, David Catcheside21, Weixi Li 14, Robert J. Pratt6, Stephen A. Osmani23, Colin P.C. DeSouza24, Louise Glass18, Marc J. Orbach25, J. Andrew Berglund3, Rodger Voelker3, Oded Yarden26, Mike Plamann27, Stephan Seiler27, Jay Dunlap22, Alan Radford28, Rodolfo Aramayo6, Donald O. Natvig7, Lisa A. Alex29, Gertrud Mannhaupt9, Daniel J. Ebbole30, Michael Freitag3, Ian Paulsen16, Matthew S. Sachs31, Eric S. Lander1,32, Chad Nusbaum1 & Bruce Birren1
  Nature 422: 859 - 868 (2003)
  

• Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays. M. Juanita Martinez, Anthony D. Aragon, Angelina Rodriguez, Jose Weber, David Haaland, Jerilyn Timlin, Michael Sinclair, and Margaret Werner-Washburne. Nucleic Acids Research 31:e18 (2003) PDF
  
  
• Visual comparison of multiple genome-scale datasets. Margaret Werner-Washburne¹, Brian Wylie², Kevin Boyack², Edwina Fuge¹, Judith Galbraith¹, Jose Weber¹, and George Davidson^{2 1}Biology Department, University of New Mexico; Albuquerque, NM and ² Sandia National Laboratories; Albuquerque, NM
  Genome Research 12: 1564-1573 (2002)
  
  
• Genomics of Stress Responses. A. Gasch and M. Werner-Washburne. Fungal and Integrative Genomics 12: 1564-1573 (2002)
  
  
• Signaling pathways in quiescent S. cerevisiae cells: Characterization of late-acting bcy1 alleles.
  A.R. Colina, A. Errett, M. Crawford, E. Fuge, V. Peck, and M. Werner-Washburne. Manuscript in preparation (2002)
  
  
• Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: correlation of pyridoxine-requiring phenotypes with mutations in two structural genes.
  Bean, L.E., W.H. Dvorachek, Jr., E.L. Braun, A. Errett, G.S. Saenz, M.D. Giles, M.Werner-Washburne, M.A. Nelson, and D.O. Natvig. Genetics, in press. (2001)
  
  
• The Highly Conserved, Coregulated SNO and SNZ Gene Families in Saccharomyces cerevisiae Respond to Nutrient Limitation.
  P. A. Padilla, E. K. Fuge, M. E. Crawford, A. Errett, and M.Werner-Washburne
  J. Bacteriol. 180:5718-5726 (1998)
  
  
• The role of the carboxyl-terminus of Bcy1p in stationary-phase yeast.
  V. M. Peck, M.A. Gomez, and M. Werner-Washburne.
  Current Genetics.32: 83-92(1997)
  
  
• Expressed sequences from the mycelial, conidial and sexual stages of Neurospora crassa.
  M. A. Nelson, S. Kang, E. L. Braun, M. E. Crawford, P. L. Dolan, P. M. Leonard, J Mitchell, A. M. Armijo, L. Bean, E. Blueyes, T. Cushing, A. Errett, M. Fleharty, M Gorman, K. Judson, R. Miller, J. Ortega, I. Pavlova, J. Perea, S. Todisco, R. Trujillo, J. Valentine, A. Wells, M. Werner-Washburne, S Yazzie, and DO Nativg.
  Fungal Genetics and Biology 21: 348-363 (1997)
  
  
• Stationary phase in the yeast Saccharomyces cerevisiae.
  Edwina K. Fuge and Margaret Werner-Washburne
  in Yeast Stress Responses, ed. Stefan Hohmann and W. H Mager.
  Molecular Biology Intelligence Unit, R.G. Landes Company, Austin, TX, pp. 53-74 (1997)
  
  
• A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family.
  Edward L. Braun, Edwina K. Fuge, Pamela A. Padilla, and Margaret Werner-Washburne.
  J Bact 178:6865-6872 (1996)
  
  
• Stationary Phase in Saccharomyces cerevisiae.
  Margaret Werner-Washburne, E. L. Braun, M.E. Crawford, and V.M.Peck.
  Molecular Microbiology 19:1159-1166 (1996)
  
  
• Protein synthesis in long-term stationary phase cultures of Saccharomyces cerevisiae.
  Edwina K. Fuge, Edward L. Braun, and Margaret Werner-Washburne.
  Journal of Bacteriology 176:5802-5813. (1994)
  
  
• Stationary phase in the yeast Saccharomyces cerevisiae.
  M. Werner-Washburne, E. Braun, G.C. Johnston, and R. A. Singer.
  Microbiological Reviews 57:383-401. (1993)
  
  
• Isolation and characterization of AAP1; a gene encoding an alanine/arginine aminopeptidase in yeast.
  Dan Caprioglio, Christopher Padilla, and Margaret Werner-Washburne.
  Journal of Biological Chemistry 268:14310-14315. (1993)
  
  
• Heat-shock mediated cell-cycle blockage and G1 cyclin expression in the yeast Saccharomyces cerevisiae.
  A.Rowley, B. Butler, M. Werner-Washburne, G.C. Johnston, and R.A. Singer.
  Molecular and Cellular Biology 13:1034-1041. (1992)
  
  
• The translation machinery and 70 kilodalton heat shock protein cooperate in protein synthesis.
  R. J. Nelson, T. Ziegelhoffer, C. Nicolet, M. Werner-Washburne, and E. A. Craig.
  Cell 71: 97-105.(1992)
  
  
• Bcy1, the regulatory protein of cAMP- dependent protein kinase, is differentially modified in response to the physiological status of the cell.
  M. Werner-Washburne, David Brown, and Edward Braun.
  Journal of Biological Chemistry 266:19704-19709. (1991)
  
  
• Yeast Hsp70 RNA levels vary in response to the physiological status of the cell.
  M. Werner-Washburne, J. Becker, J. Kosic-Smithers, and E. A. Craig.
  J. Bacteriol. 171: 2680-2688. ( 1989)
  
  
• Expression of members of the S.cerevisiae HSP70 multigene family.
  M. Werner-Washburne and E.A.Craig.
  Genome 31 :684-689. ( 1989)
  
  
• SSC1, an essential member of the yeast HSP70 multigene family, encodes a mitochondrial protein.
  E.A. Craig, J. Kramer, J. Shilling, M. Werner-Washburne, S. Holmes, J. Kosic-Smithers, and C.M. Nicolet.
  Molec. Cell Biol .9:3000-3008. (1989)
  
  
• A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides.
  R. Deshaies, B.D. Koch, M. Werner-Washburne, E. Craig, and R. Schekman.
  Nature 332:800-805. (1988)
  
  
• Complex interactions among members of an essential subfamily of Hsp70 genes in yeast.
  M. Werner-Washburne, D.Stone, and E.A. Craig.
  Mol. Cell Biol. 7: 2568-2577.(1987)
  
  
• L-Aspartate transport into pea chloroplasts. Kinetic and inhibitor evidence for multiple transport systems.
  M. Werner-Washburne and K. Keegstra.
  Plant Physiol. 78: 221-227. (1985)
  
  
• Precursors to two chloroplast proteins bind to the outer chloroplast membrane prior to import.
  K. Cline, M. Werner-Washburne, T.H. Lubben, and K. Keesgtra.
  J.Biol. Chem. 260: 3691-3696. (1985)
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