Recent Awards, Grants and Publications received by Faculty, Staff and Students of Bioinformatics Computational Biology – Fall 2018

October 5, 2018
News

Recent Awards, Grants and Publications received by Faculty, Staff and Students of Bioinformatics Computational Biology – Fall 2018

GRANTS

Robert Jernigan - Biochemistry, Biophysics and Molecular Biology

Title: Protein Sequence Matching (R01)
Funding Agency: NIH
Dates: February 1, 2018-January 31, 2022
Award:  $321,552

Jeanne Serb - Ecology, Evolution and Organismal Biology
Andrew Severin (Co-PI) – Ecology, Evolution and Organismal Biology

Title: The roles of exaptive and adaptive co-option in eye evolution will explore the evolution of eyes in bivalves
Funding Agency: NSF DEB Grant
Dates: 2018/7/1 – 2022/6/30
Award:  $1,000,000

Andrew Severin (Co-PI) – Ecology, Evolution and Organismal Biology

Title: An integrated approach to enhance durability of SCN resistance for long-term, strategic SCN management (Phase II)
Funding Agency: NCSRP grant renewed (North Central Soybean Research Program)
Award: $588,719 

Amy Toth – Entomology

Title: Functional Genomics in Polistes Wasps, A Model System in Integrative Organismal Biology
Funding agency: National Science Foundation
Dates:  2018-09-01 – 2021-08-31
Award:  $815,610

Chris Tuggle – Animal Science
James Reecy (Co-PI) – Animal Science
James Koltes (Co-PI) – Animal Science

Functional Annotation of the Porcine Genome
Funding Agency:
SDA-NIFA-AFRI 2018-67015-27501
Dates: 2018-2022
Award: $2,500,000
The purpose of this project is to determine the RNA expression pattern, chromatin structure, and epigenetic marks in fetal and adult tissues, as well as flow-sorted immune cells, to annotate the regulatory and expressed regions of the porcine genome.

Geetu Tuteja – Genetics Development & Cellular Biology

Title:  Transcriptional Regulatory Networks Governing Placental Development
Funding Agency: NIH-National Institute of Child Health & Human Development|
Dates: 08/24/2018-05/31/2023
Award: $1,528,856

Justin Walley – Plant Pathology and Microbiology

Title: Elucidation of roles that protein acetylation plays in mediating plant-pathogen interactions
Funding Agency: NSF proposal # 1759023
Dates: 2018/8/1 – 2022/7/31
Award:  $677,000

Justin Walley (Co-PI) – Plant Pathology and Microbiology
Yanhai Yin (PI) – Genetics Development and Cell Biology

Title: Network-Based Discovery of Brassinosteroid Regulation of Plant Growth and Stress Responses
Funding Agency: NSF proposal # 1818160
Dates: 2018/8/15 – 2021/7/31
Award: $900,000

Lizhi Wang – Industrial and Manufacturing Systems Engineering

Title: Engineering Crops for Adaptation to Changing Environments 
Funding agency: National Science Foundation
Dates: 2018-09-01 - 2023-08-31
Award: $1,999,999 

 

PUBLICATIONS

Hao, Y. and Wu, Z., “Computation of sparse and dense equilibrium strategies of evolutionary games”, Games 9, 46-60, 2018

Jia K, Jernigan RL. SeqStruct: A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence. bioRxiv 2018, 268904; doi: https://doi.org/10.1101/268904.

Kokulapalan Wimalanathan, Iddo Friedberg, Carson M Andorf, Carolyn J Lawrence‐Dill Maize GO Annotation—Methods, Evaluation, and Review (maize‐GAMER) (2018) Plant Direct 2:4 e00052

Abdulghan, Majd, Jain, Ashish, Tuteja, Geetu "Genome-wide identification of enhancer elements in the placenta". ScienceDirect, September 2018

Mishra SK, Jernigan RL. Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics. PLoS One. 2018 Jun 20;13(6):e0199225. doi: 10.1371/journal.pone.0199225. eCollection 2018. PubMed PMID: 29924847; PubMed Central PMCID: PMC6010283. 

Purcell, C. M., Seetharam, A. S., Snodgrass, O., Ortega-García, S., Hyde, J. R., & Severin, A. J. (2018). Insights into teleost sex determination from the Seriola dorsalis genome assembly. BMC genomics19(1), 31.

Renu Srivastava, Zhaoxia Li, Giulia Russo, Jie Tang, Ran Bi, Usha Muppirala, Sivanandan Chudalayandi, Andrew SeverinMingze He, Samuel I Vaitkevicius, Carolyn J. Lawrence-Dill, Peng Liu, Ann E. Stapleton, Diane C. Bassham, Federica Brandizzi, Stephen H. Howell. "Response to Persistent ER Stress in Plants: A Multiphasic Process That Transitions Cells from Prosurvival Activities to Cell Death." The Plant Cell (2018): tpc-00153. http://www.plantcell.org/content/early/2018/05/25/tpc.18.00153

Sankar K, Mishra SK, Jernigan RL. Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models. J Phys Chem B. 2018 May 31;122(21):5409-5417. doi: 10.1021/acs.jpcb.7b11668. Epub 2018 Feb 9. PubMed PMID: 29376347.

Wang, M, Zhou, W and Wu, Z. “Equilibrium distributions of populations of biological species on networks of social sites”, Journal of Biological Dynamics, online, August 16, 2018. 

Zhou, Naihui, Zachary D Siegel, Scott Zarecor, Nigel Lee, Darwin A Campbell, Carson M Andorf, Dan Nettleton, Carolyn J Lawrence-Dill, Baskar Ganapathysubramanian, Jonathan W Kelly, Iddo Friedberg: "Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning "  (2018) PLoS computational biology 14:7  e1006337

 

OTHER

Iddo Friedberg – Veterinary Microbiology and Preventative Medicine
Recipient of the 2018 College of Veterinary Medicine Faculty Research Awards
Mid Career Achievement in Research Award

Robert Jernigan - Biochemistry, Biophysics and Molecular Biology
National 2018 PROSE award for best new textbook in the biological and life sciences for the book Protein Actions. 

Tom Peterson - Genetics, Development and Cell Biology
Recipient of the Regents Award for Faculty Excellence

Donald Sakaguchi – Genetics, Development and Cell Biology
Receives designation of Morrill Professor

Andrew Severin – Ecology, Evolution and Organismal Biology
Podcast: How to catch a fish genome with big data

GDCB graduate students place in competitions

Trevor Nolan – first place
Xinyu Fu – second place
Carla Mann – third place

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