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.
Submissions from 2021
Plant DNA Repair and Agrobacterium T−DNA Integration, Stanton B. Gelvin
Embryonic and Neonatal Mouse Cochleae Are Susceptible to Zika Virus Infection, Vidhya Munnamalai, Nabilah H. Sammudin, Caryl A. Young, Ankita Thawani, Richard J. Kuhn, and Donna M. Fekete
Submissions from 2018
Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization, Saif Hasan, Chengqun Sun, Arthur S. Kim, Yasunori Watanabe, Chun-Liang Chen, Thomas Klose, Geeta Buda, Max Crispin, Michael S. Diamond, William B. Klimstra, and Michael G. Rossmann
Zika Virus Can Strongly Infect and Disrupt Secondary Organizers in the Ventricular Zone of the Embryonic Chicken Brain, Ankita Thawani, Devika Sirohi, Richard J. Kuhn, and Donna Fekete
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis, Sheng Wang, Jeffrey D. Mandell, Yogesh Kumar, Nawei Sun, Montana T. Morris, Juan Arbelaez, Cara Nasello, Shan Dong, Clif Duhn, Xin Zhao, Zhiyu Yang, Shanmukha S. Padmanabhuni, Dongmei Yu, Robert A. King, Andrea Dietrich, Najah Khalifa, Niklas Dahl, Alden Y. Huang, Benjamin M. Neale, Giovanni Coppola, Carol A. Mathews, Jeremiah M. Scharf, Tourette International Collaborative Genetics Study (TIC Genetics), Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE), Tourette Association of America International Consortium for Genetics (TAAICG), Thomas V. Fernandez, Joseph D. Buxbaum, Silvia De Rubeus, Dorothy E. Grice, Jinchuan Xing, Gary A. Heiman, Jay A. Tischfield, Peristera Paschou, A Jeremy Wilsey, and Matthew W. State
MicroRNA-223 Suppresses the Canonical NF-kB Pathway in Basal Keratinocytes to Dampen Neutrophilic Inflammation, Wenqing Zhou, Arpita S. Pal, Alan Yi-Hui Hsu, Theodore Gurol, Xiaoguang Zhu, Sara E. Wirbisk-Hershberger, Jennifer L. Freeman, Andrea L. Kasinski, and Qing Deng
Submissions from 2017
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
Sexual Differences in Prevalence of a New Species of Trypanosome Infecting Túngara Frogs, Ximena Bernal and C Miguel Pinto
Missing gene identification using functional coherence scores, Meghana Chitale, Ishita K. Khan, and Daisuke Kihara
Accurate classification of RNA structures using topological fingerprints, Jiajie Huang, Kejie Li, and Michael Gribskov
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
RNA-guided CRISPR-Cas technologies for genome-scale investigation of disease processes, Sean E. Humphrey and Andrea L. Kasinski
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
On the Origin of Protein Superfamilies and Superfolds, Abram Magner, Wojciech Szpankowski, and Daisuke Kihara
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 2014
PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions, Bingjie Hu, Xiaolei Zhu, Lyman Monroe, Mark G. Bures, and Daisuke Kihara
Submissions from 2013
Ultradian Metabolic Rhythm in the Diazotrophic Cyanobacterium Cyanothece sp. ATCC 51142., Jan Cerveny, Maria A. Sinetova, Luis Valledor, Louis A. Sherman, and Ladislav Nebal
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
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
BATF Regulates the Development and Function of IL-17 Producing iNKT Cells., Kimberly L. Jordan-Williams, Stacie Poston, and Elizabeth J. Taparowsky
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
SipB-SipC Complex Is Essential for Translocon Formation., Sebenzile K. Myeni, Lu Wang, and Daoguo Zhou
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
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
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
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
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
Cryo-EM Structure of a Novel Calicivirus, Tulane Virus., Guimei Yu, Dongsheng Zhang, Fei Guo, Ming Tan, Xi Jiang, and Wen Jiang
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
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
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
Effect of Conformation Sampling Strategies in Genetic Algorithm for Multiple Protein Docking., Juan Esquivel-Rodriguez and Daisuke Kihara
Evaluation of Multiple Protein Docking Structures Using Correctly Predicted Pairwise Subunits., Juan Esquivel-Rodriguez and Daisuke Kihara
Evaluation of Function Predictions by PFP, ESG, and PSI-BLAST for Moonlighting Proteins., Ishita K. Khan, Meghana Chitale, Catherine Rayon, and Daisuke Kihara
Protein Docking Prediction Using Predicted Protein-Protein Interface., Bin Lin and Daisuke Kihara
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
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
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
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
Constructing Patch-Based Ligand-Binding Pocket Database for Predicting Function of Proteins., Lee Sael and Daisuke Kihara
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
Effective Inter-Residue Contact Definitions for Accurate Protein Fold Recognition., Chao Yuan, Hao Chen, and Daisuke Kihara
Alternate Copies of D1 are Used by Cyanobacteria Under Different Environmental Conditions., Xiaohui Zhang and Louis A. Sherman
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
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
Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association., Meghana Chitale, Shriphani Palakodety, and Daisuke Kihara
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
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
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
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
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
Welcome to Microbial Informatics and Experimentation, Michael J. Wise and Barry L. Wanner
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
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
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
High Rates of Photobiological H2 Production by a Cyanobacteriium Under Aerobic Conditions., Anindita Bandyopadhyay, Jana Stöckel, Louis A. Sherman, and Himadri B. Pakrasi
Functional Enrichment Analyses and Construction of Functional Similarity Networks with High Confidence Function Prediction by PFP., Troy Hawkins, Meghana Chitale, and Daisuke Kihara
Genetic Transformation and Mutagenesis Via ssDNA in the Unicellular, Diazotrophic Cyanobacteria of the Genus Cyanothece., Hongtao Min and Louis A. Sherman
Hydrogen Production by the Unicellular Diazotrophic Cyanobacterium Cyanothece ATCC sp. Strain 51142 Under Continuous Light., Hongtao Min and Louis A. Sherman
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
Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches, Lee Sael and Daisuke Kihara
Improved Protein Surface Comparison and Application to Low-Resolution Protein Structure Data., Lee Sael and Daisuke Kihara
Involvement of TIP60 Acetyltransferase in Intracellular Salmonella Replication., Xueqin Wang, Dongju Li, Di Qu, and Daoguo Zhou
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
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
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
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
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
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
Application of 3D Zernike descriptors to shape-based ligand similarity searching, Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, and Daisuke Kihara
Application of 3D Zernike Descriptors to Shape-Based Ligand Similarity Searching., Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, and Daisuke Kihara
Protein-Protein Docking Using Region-Based 3D Zernike Descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, and Daisuke Kihara
Protein-protein docking using region-based 3D Zernike descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, and Daisuke Kihara
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
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
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
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
Bioinformatics Research in the Asia Pacific: A 2007 Update, Shoba Ranganathan, Michael Gribskov, and Tin Wee Tan
Global Transcriptional Response of the Alkalitolerant Cyanobacterium Synechocystis sp. Strain PCC 6803 to pH 10., Tina C. Summerfield and Louis A. Sherman
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
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
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
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
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
Wiggle—Predicting Functionally Flexible Regions from Primary Sequence., Jenny Gu, Michael R. Gribskov, and Philip E. Bourne
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, Jianjun Hu, Yifeng D. Yang, and Daisuke Kihara
EMD: an Ensemble Algorithm for Discovering Regulatory Motifs in DNA Sequences., Jianjun Hu, Yifeng D. Yang, and Daisuke Kihara
Establishing Bioinformatics Research in the Asia Pacific, Shoba Ranganathan, Martti Tammi, Michael Gribskov, and Tin Wee Tan
Submissions from 2003
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