The Department of Biological Sciences at Purdue University provides knowledge to undergraduate and graduate students in the many facets of biocomplexity from vast ecosystems to the structure and function of individual molecules. The department conducts research in development and disease, ecology and evolutionary biology, and molecular biosciences.

This series contains publications from the Department of Biological Sciences at Purdue University.

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Submissions from 2017

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Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models., Woong Hee Shin, Xuejiao Kang, Jian Zhang, and Daisuke Kihara

Submissions from 2016

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Missing gene identification using functional coherence scores, Meghana Chitale, Ishita K. Khan, and Daisuke Kihara

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Accurate classification of RNA structures using topological fingerprints, Jiajie Huang, Kejie Li, and Michael Gribskov

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Structural Basis for Recognition of Human Enterovirus 71 by a Bivalent Broadly Neutralizing Monoclonal Antibody, Xiaohua Ye, Chen Fan, Zhiqiang Ku, Teng Zuo, Liangliang Kong, Chao Zhang, Jinping Shi, Qingwei Liu, Tan Chen, Yingyi Zhang, Wen Jiang, Linqi Zhang, Zhong Huang, and Yao Cong

Submissions from 2015

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Silencing Mist1 gene expression is essential for recovery from acute pancreatitis, Anju Karki, Sean E. Humphrey, Rebecca E. Steele, David A. Hess, Elizabeth J. Taparowsky, and Stephen F. Konieczny

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On the Origin of Protein Superfamilies and Superfolds, Abram Magner, Wojciech Szpankowski, and Daisuke Kihara

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Expression and misexpression of the MIR-183 family in the developing hearing organ of the chicken, Kaidi D. Zhang, Michelle L. Stoller, and Donna M. Fekete

Submissions from 2013

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Ultradian Metabolic Rhythm in the Diazotrophic Cyanobacterium Cyanothece sp. ATCC 51142., Jan Cerveny, Maria A. Sinetova, Luis Valledor, Louis A. Sherman, and Ladislav Nebal

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In-Depth Performance Evaluation of PFP and ESG Sequence-Based Function Prediction Methods in CAFA 2011 Experiment, Meghana Chitale, Ishita K. Khan, and Daisuke Kihara

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Lineage Analysis of the Late Otocyst Stage Mouse Inner Ear by Transuterine Microinjection of A Retroviral Vector Encoding Alkaline Phosphatase and an Oligonucleotide Library., Han Jiang, Lingyan Wang, Kevin T. Beier, Constance L. Cepko, Donna M. Fekete, and John V. Brigande

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BATF Regulates the Development and Function of IL-17 Producing iNKT Cells., Kimberly L. Jordan-Williams, Stacie Poston, and Elizabeth J. Taparowsky

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West Nile Virus Methyltransferase Domain Interacts with Protein Kinase, Julie A. Keating, Dipankar Bhattacharya, Pei-Yin Lim, Shaun Falk, Bernard Weisblum, Kristen A. Bernard, Mayuri Sharma, Richard J. Kuhn, and Rob Striker

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SipB-SipC Complex Is Essential for Translocon Formation., Sebenzile K. Myeni, Lu Wang, and Daoguo Zhou

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Essential Role of the Plasmid hik31 Operon in Regulating Central Metabolism in the Dark in Synechocystis sp. PCC 6803., Sowmya Nagarajan, Sanvesh Srivastava, and Louis A. Sherman

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A Neutralizing Monoclonal Antibody Targeting the Acid-Sensitive Region in Chikungunya Virus E2 Protects from Disease., Suganya Selvarajah, Nicole R. Sexton, Kristen M. Kahle, Rachel H. Fong, Kimberly-Anne Mattia, Joy Gardner, Kai Lu, Nathan M. Liss, Beatriz Salvador, David F. Tucker, Trevor Barnes, Manu Mabila, Xiangdong Zhou, Giada Rossini, Joseph B. Rucker, David Avram Sanders, Andreas Suhrbier, Vittorio Sambri, Alain Michault, Marcus O. Muench, Benjamin J. Doranz, and Graham Simmons

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Environmental pH Affects Photoautotrophic Growth of Synechocystis sp. PCC 6803 Strains Carrying Mutations in the Lumenal Proteins of PSII., Tina C. Summerfield, Tim S. Crawford, Roger Young, Jocelyn PS Chua, Rebecca Macdonald, Louis A. Sherman, and Julian J. Eaton-Rye

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Legionella pneumophila Infection of Drosophila S2 Cells Induces Only Minor Changes in Mitochondrial Dynamics., Elizabeth Wen Sun, Monica L. Wagner, Amanda Maize, Doris Kemler, Elisabeth Garland-Kuntz, Li Xu, Zhao-Qing Luo, and Peter J. Hollenbeck

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Analysis of Carbohydrate Storage Granules in the Diazotrophic Cyanobacterium Cyanothece sp. PCC 7822., David G. Welkie, Debby Sherman, William B. Chrisler, Galya Orr, and Louis A. Sherman

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Cryo-EM Structure of a Novel Calicivirus, Tulane Virus., Guimei Yu, Dongsheng Zhang, Fei Guo, Ming Tan, Xi Jiang, and Wen Jiang

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The Uptake Hydrogenase in the Unicellular Diazotrophic Cyanobacterium Cyanothece sp. Strain PCC 7822 Protects Nitrogenase From Oxygen Toxicity., Xiaohui Zhang, Debby Sherman, and Louis A. Sherman

Submissions from 2012

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Crystal Structure of Aura Virus Capsid Protease and Its Complex with Dioxane: New Insights into Capsid-Glycoprotein Molecular Contacts., Megha Aggarwal, Satya Tapas, Preeti, Anjul Siwach, Pravindra Kumar, Richard J. Kuhn, and Shailly Tomar

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Proteome Analyses of Strains Cyanothece ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp. Under Culture Conditions Resulting in Enhanced H2 Production., Uma K. Aryal, Stephen J. Callister, Sujata Mishra, Xiaohui Zhang, Janani I. Shutthanandan, Thomas E. Angel, Anil K. Shukla, Matthew E. Monroe, Ronald J. Moore, David W. Koppenhaal, Richard D. Smith, and Louis A. Sherman

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Effect of Conformation Sampling Strategies in Genetic Algorithm for Multiple Protein Docking., Juan Esquivel-Rodriguez and Daisuke Kihara

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Evaluation of Multiple Protein Docking Structures Using Correctly Predicted Pairwise Subunits., Juan Esquivel-Rodriguez and Daisuke Kihara

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Evaluation of Function Predictions by PFP, ESG, and PSI-BLAST for Moonlighting Proteins., Ishita K. Khan, Meghana Chitale, Catherine Rayon, and Daisuke Kihara

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Protein Docking Prediction Using Predicted Protein-Protein Interface., Bin Lin and Daisuke Kihara

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Structure-Function Studies of DNA Binding Domain of Response Regulator KdpE Reveals Equal Affinity Interactions at DNA Half-Sites., Anoop Narayanan, Lak N. Paul, Sakshi Tomae, Dipak N. Patil, Pravindra Kumar, and Dinesh A. Yernool

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Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells., Rushika Perera, Catherine Riley, Giorgis Isaac, Amber S. Hopf-Jannasch, Ronald J. Moore, Karl W. Weitz, Ljiljana Pasa-Tolic, Thomas O. Metz, Jiri Adamec, and Richard J. Kuhn

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Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4,5)-Bisphosphate., Roman Pleskot, Premysl Pejchar, Viktor Zarsky, Christopher J. Staiger, and Martin Potocky

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Role of Trehalose in Salinity and Temperature Tolerance in the Model Halophilic Bacterium Chromohalobacter salexigens., Mercedes Reina-Bueno, Montserrat Argondona, Manuel Salvador, Javier Rodriguez-Moya, Fernando Iglesias-Guerra, Laszlo Csonka, Joaquin J. Nieto, and Carmen Vargas

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Constructing Patch-Based Ligand-Binding Pocket Database for Predicting Function of Proteins., Lee Sael and Daisuke Kihara

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Drosophila Activated Cdc42 Kinase Has an Anti-Apoptotic Function., Jessica A. Schoenherr, J Michelle Drennan, Juan S. Martinez, Madhusudana Rao Chikka, Mark C. Hall, Henry C. Chang, and James C. Clemens

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Effective Inter-Residue Contact Definitions for Accurate Protein Fold Recognition., Chao Yuan, Hao Chen, and Daisuke Kihara

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Alternate Copies of D1 are Used by Cyanobacteria Under Different Environmental Conditions., Xiaohui Zhang and Louis A. Sherman

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The Expression of irx7 in the Inner Nuclear Layer of Zebrafish Retina Is Essential for a Proper Retinal Development and Lamination., Yuqing Zhang, Yifan Yang, Caleb Trujillo, Wenxuan Zhong, and Yuk Fai Leung

Submissions from 2011

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Novel Metabolic Attributes of Cyanothece, a Group of Unicellular Nitrogen Fixing Cyanobacteria., Anindita Bandyopadhyay, Thanura Elvitigala, Eric Welsh, Jana Stöckel, Michelle Liberton, Hongtao Min, Louis A. Sherman, and Himadri B. Pakrasi

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Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association., Meghana Chitale, Shriphani Palakodety, and Daisuke Kihara

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Secreted Bacterial Effectors That Inhibit Host Protein Synthesis Are Critical for Induction of the Innate Immune Response to Virulent Legionella pneumophila., Mary F. Fontana, Simran Banga, Kevin C. Barry, Xihui Shen, Yunhao Tan, Zhao-Qing Luo, and Russell E. Vance

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Differential Gene Expression in Male and Female Rainbow Trout Embryos Prior to the Onset of Gross Morphological Differentiation of the Gonads, Matthew C. Hale, Peng Xu, Julie Scardina, Paul A. Wheeler, Gary H. Thorgaard, and Krista M. Nichols

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Cellular Expression of Smarca4 (Brg1)-Regulated Genes in Zebrafish Retinas, Monica R. Hensley, Farida Emran, Sylvia Bonilla, Liyun Zhang, Wenxuan Zhong, Paul Grosu, John E. Dowling, and Yuk Fai Leung

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A Model of Cyclic Transciptomic Behavior in the Cyanobacterium Cyanothece sp. ATCC 51142., Jason E. McDermott, Christopher S. Oehmen, Lee Ann McCue, Eric Hill, Daniel M. Choi, Jana Stöckel, Michelle Liberton, Himadri B. Pakrasi, and Louis A. Sherman

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Functions of the Duplicated hik31 Operons in Central Metabolism and Responses to Light, Dark, and Carbon Sources in Synechocystis sp. Strain PCC 6803, Sowmya Nagarajan, Debby Sherman, Isaac Shaw, and Louis A. Sherman

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Welcome to Microbial Informatics and Experimentation, Michael J. Wise and Barry L. Wanner

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Comprehensive Identification of Protein Substrates of the Dot/Icm Type IV Transporter of Legionella pneumophila., Wenhan Zhu, Simran Banga, Yunhao Tan, Cheng Zheng, Robert E. Stephenson, Jonathan Gately, and Zhao-Qing Luo

Submissions from 2010

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Vertebrate Lrig3-ErbB Interactions Occur In Vitro but Are Unlikely to Play a Role in Lrig3-Dependent Inner Ear Morphogenesis., Victoria E. Abraia, Takunori Satoh, Donna M. Fekete, and Lisa V. Goodrich

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Disruption of Zebrafish Cyclin G-Associated Kinase (GAK) Function Impairs the Expression of Notch-Dependent Genes During Neurogenesis and Causes Defects in Neuronal Development., Ting Bai, Jamie L. Seebald, Kyu-Eui Kim, Hong-Mei Ding, Daniel P. Szeto, and Henry C. Chang

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High Rates of Photobiological H2 Production by a Cyanobacteriium Under Aerobic Conditions., Anindita Bandyopadhyay, Jana Stöckel, Louis A. Sherman, and Himadri B. Pakrasi

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Functional Enrichment Analyses and Construction of Functional Similarity Networks with High Confidence Function Prediction by PFP., Troy Hawkins, Meghana Chitale, and Daisuke Kihara

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Genetic Transformation and Mutagenesis Via ssDNA in the Unicellular, Diazotrophic Cyanobacteria of the Genus Cyanothece., Hongtao Min and Louis A. Sherman

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Hydrogen Production by the Unicellular Diazotrophic Cyanobacterium Cyanothece ATCC sp. Strain 51142 Under Continuous Light., Hongtao Min and Louis A. Sherman

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The Escherichia Coli K-12 ORFeome: a Resource for Comparative Molecular Microbiology, Seesandra V. Rajagopala, Natsuko Yamamoto, Adrienne E. Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge David Mendez-Rios, Jonathan Franc-Koh, Meher Preethi Boorgula, Kazutoshi Fujita, Ken-ichirou Suzuki, James C. Hu, Barry L. Wanner, Hirotada Mori, and Peter Uetz

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Improved Protein Surface Comparison and Application to Low-Resolution Protein Structure Data., Lee Sael and Daisuke Kihara

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Involvement of TIP60 Acetyltransferase in Intracellular Salmonella Replication., Xueqin Wang, Dongju Li, Di Qu, and Daoguo Zhou

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Inhibition of Host Vacuolar H+-ATPase Activity by a Legionella pneumophila Effector., Li Xu, Xihui Shen, Andrew Bryan, Simran Banga, Michele S. Swanson, and Zhao-Qing Luo

Submissions from 2009

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The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion., Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li-jun Ma, Etienne G.J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker, Michael Gribskov, Martijn Rep, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora, Mark L. Farman, Eric U. Selker, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini, and Hans D. VanEtten

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Role of MrgA in Peroxide and Light Stress in the Cyanobacterium Synechocystis sp. PCC 6803., Jamie S. Foster, Stephanie A. Havemann, Abhay Singh, and Louis A. Sherman

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Next-Generation Pyrosequencing of Gonad Transcriptomes in the Polyploid Lake Sturgeon (Acipenser fulvescens): the Relative Merits of Normalization and Rarefaction in Gene Discovery., Matthew C. Hale, Cory R. McCormick, James R. Jackson, and J. Andrew DeWoody

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Protein-Protein Interactions of Tandem Affinity Purified Protein Kinases from Rice., Jai S. Rohila, Mei Chen, Shuo Chen, Johann Chen, Ronald L. Cerney, Christopher Dardick, Patrick Canlas, Hiroaki Fujii, Michael Gribskov, Siddhartha Kanrar, Lucas Knoflicek, Becky Stevenson, Mingtang Xie, Xia Xu, Xianwu Zheng, Jian-Kang Zhu, Pamela Ronald, and Michael E. Fromm

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Transcriptional Analysis of the Unicellular, Diazotrophic Cyanobacterium Cyanothece ATCC 51142 Grown Under Short Day/Night Cycles., Jörg Toepel, Jason McDermott, Tina C. Summerfield, and Louis A. Sherman

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Application of 3D Zernike descriptors to shape-based ligand similarity searching, Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, and Daisuke Kihara

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Application of 3D Zernike Descriptors to Shape-Based Ligand Similarity Searching., Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, and Daisuke Kihara

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Protein-Protein Docking Using Region-Based 3D Zernike Descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, and Daisuke Kihara

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Protein-protein docking using region-based 3D Zernike descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, and Daisuke Kihara

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Tape-Arabidopsis Sandwich - a Simpler Arabidopsis Protoplast Isolation Method, Fu-Hui Wu, Shu-Chen Shen, Lan-Ying Lee, Shu-Hong Lee, Ming-Tsar Chan, and Choun-Sea Lin

Submissions from 2008

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The Clathrin-Binding Motif and the J-Domain of Drosophila Auxilin are Essential for Facilitating Notch Ligand Endocytosis., Vasundhara Kandachar, Ting Bai, and Henry C. Chang

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Structural Studies of West Nile Virus in Complex with Neutralizing Antibodies., Richard J. Kuhn, Bärbel Kaufmann, Shee Mei Lok, Mick Cherrier, Rushika Perera, Dagmar Sedlak, Grant E. Nybakken, Paul R. Chipman, Wei Zhang, Michael S. Diamond, Daved H. Fremont, and Michael G. Rossmann

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Vectors for Multi-Color Bimolecular Fluorescence Complementation to Investigate Protein-Protein Interactions in Living Plant Cells, Lan-Ying Lee, Mei-Jane Fang, Lin-Yun Kuang, and Stanton B. Gelvin

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Bioinformatics Research in the Asia Pacific: A 2007 Update, Shoba Ranganathan, Michael Gribskov, and Tin Wee Tan

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Global Transcriptional Response of the Alkalitolerant Cyanobacterium Synechocystis sp. Strain PCC 6803 to pH 10., Tina C. Summerfield and Louis A. Sherman

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Sequence Information Encoded in DNA that May Influence Long-Range Chromatin Structure Correlates with Human Chromosome Functions., Taichi E. Takasuka, Alfred Cioffi, and Arnold Stein

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Differential transcriptional analysis of the cyanobacterium Cyanothece sp. ATCC 51142 during light-dark and continuous-light growth., Jörg Toepel, Eric Welsh, Tina C. Summerfield, Himadri B. Pakrasi, and Louis A. Sherman

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The Genome of Cyanothece 51142, a Unicellular Diazotrophic Cyanobacterium Important in the Marine Nitrogen Cycle., Eric A. Welsh, Michelle Liberton, Jana Stöckel, Thomas Loh, Chunyan Wang, Aye Wollam, Robert S. Fulton, Sandra W. Clifton, Jon M. Jacobs, Rajeev Aurora, Louis A. Sherman, Richard D. Smith, Richard K. Wilson, and Himadri B. Pakrasi

Submissions from 2007

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Restricted Cell Elongation in Arabidopsis Hypocotyls is Associated with a Reduced Average Pectin Esterification Level, Paul Derbyshire, Maureen C. McCann, and Keith Roberts

Submissions from 2006

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Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density., Matthew L. Baker, Wen Jiang, William J. Wedemeyer, Frazer J. Rixon, David Baker, and Wah Chiu

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Wiggle—Predicting Functionally Flexible Regions from Primary Sequence., Jenny Gu, Michael R. Gribskov, and Philip E. Bourne

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EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, Jianjun Hu, Yifeng D. Yang, and Daisuke Kihara

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EMD: an Ensemble Algorithm for Discovering Regulatory Motifs in DNA Sequences., Jianjun Hu, Yifeng D. Yang, and Daisuke Kihara

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Establishing Bioinformatics Research in the Asia Pacific, Shoba Ranganathan, Martti Tammi, Michael Gribskov, and Tin Wee Tan

Submissions from 2003

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The Construction and Use of Bacterial DNA Microarrays Based on an Optimized Two-Stage PCR Strategy., Bradley L. Postier, Hong-Liang Wang, Abhay Singh, Lori Impson, Heather L. Andrews, Jessica Klahn, Hong Li, George Risinger, David Pesta, Michael Deyholos, David W. Galbraith, Louis A. Sherman, and Robert L. Burnap