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Benjamin R, Giacoletto CJ, FitzHugh ZT, Eames D, Buczek L, Wu X, Newsome J, Han MV, Pearson T, Wei Z, Banerjee A, Brown L, Valente LJ, Shen S, Deng HW, Schiller MR. GigaAssay - An adaptable high-throughput saturation mutagenesis assay platform. Genomics 2022; 114:110439. [PMID: 35905834 PMCID: PMC9420302 DOI: 10.1016/j.ygeno.2022.110439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/12/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022]
Abstract
High-throughput assay systems have had a large impact on understanding the mechanisms of basic cell functions. However, high-throughput assays that directly assess molecular functions are limited. Herein, we describe the "GigaAssay", a modular high-throughput one-pot assay system for measuring molecular functions of thousands of genetic variants at once. In this system, each cell was infected with one virus from a library encoding thousands of Tat mutant proteins, with each viral particle encoding a random unique molecular identifier (UMI). We demonstrate proof of concept by measuring transcription of a GFP reporter in an engineered reporter cell line driven by binding of the HIV Tat transcription factor to the HIV long terminal repeat. Infected cells were flow-sorted into 3 bins based on their GFP fluorescence readout. The transcriptional activity of each Tat mutant was calculated from the ratio of signals from each bin. The use of UMIs in the GigaAssay produced a high average accuracy (95%) and positive predictive value (98%) determined by comparison to literature benchmark data, known C-terminal truncations, and blinded independent mutant tests. Including the substitution tolerance with structure/function analysis shows restricted substitution types spatially concentrated in the Cys-rich region. Tat has abundant intragenic epistasis (10%) when single and double mutants are compared.
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Affiliation(s)
- Ronald Benjamin
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Christopher J Giacoletto
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Zachary T FitzHugh
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Danielle Eames
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Lindsay Buczek
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Xiaogang Wu
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Jacklyn Newsome
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Mira V Han
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Tony Pearson
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, GITC 4214C, University Heights, Newark, NJ 07102, USA
| | - Atoshi Banerjee
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Lancer Brown
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Liz J Valente
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Shirley Shen
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Hong-Wen Deng
- Center for Biomedical Informatics & Genomics Tulane University, 1440 Canal Street, Suite 1621, New Orleans, LA 70112, USA
| | - Martin R Schiller
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA.
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2
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Ako-Adjei D, Fu W, Wallin C, Katz KS, Song G, Darji D, Brister JR, Ptak RG, Pruitt KD. HIV-1, human interaction database: current status and new features. Nucleic Acids Res 2014; 43:D566-70. [PMID: 25378338 DOI: 10.1093/nar/gku1126] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database', available through the National Library of Medicine at http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions, serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. Each HIV-1 human protein interaction can be retrieved without restriction by web-based downloads and ftp protocols and includes: Reference Sequence (RefSeq) protein accession numbers, National Center for Biotechnology Information Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. In addition to specific HIV-1 protein-human protein interactions, included are interaction effects upon HIV-1 replication resulting when individual human gene expression is blocked using siRNA. A total of 3142 human genes are described participating in 12,786 protein-protein interactions, along with 1316 replication interactions described for each of 1250 human genes identified using small interfering RNA (siRNA). Together the data identifies 4006 human genes involved in 14,102 interactions. With the inclusion of siRNA interactions we introduce a redesigned web interface to enhance viewing, filtering and downloading of the combined data set.
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Affiliation(s)
- Danso Ako-Adjei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - William Fu
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kenneth S Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Guangfeng Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Dakshesh Darji
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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3
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Sargeant DP, Deverasetty S, Strong CL, Alaniz IJ, Bartlett A, Brandon NR, Brooks SB, Brown FA, Bufi F, Chakarova M, David RP, Dobritch KM, Guerra HP, Hedden MW, Kumra R, Levitt KS, Mathew KR, Matti R, Maza DQ, Mistry S, Novakovic N, Pomerantz A, Portillo J, Rafalski TF, Rathnayake VR, Rezapour N, Songao S, Tuggle SL, Yousif S, Dorsky DI, Schiller MR. The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. PLoS One 2014; 9:e98810. [PMID: 24886930 PMCID: PMC4041786 DOI: 10.1371/journal.pone.0098810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/06/2014] [Indexed: 12/15/2022] Open
Abstract
There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com].
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Affiliation(s)
- David P. Sargeant
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sandeep Deverasetty
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Christy L. Strong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Izua J. Alaniz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Alexandria Bartlett
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Nicholas R. Brandon
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Steven B. Brooks
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Frederick A. Brown
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Flaviona Bufi
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Monika Chakarova
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Roxanne P. David
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Karlyn M. Dobritch
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Horacio P. Guerra
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Michael W. Hedden
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Rma Kumra
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Kelvy S. Levitt
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Kiran R. Mathew
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Ray Matti
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Dorothea Q. Maza
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sabyasachy Mistry
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Nemanja Novakovic
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Austin Pomerantz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Josue Portillo
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Timothy F. Rafalski
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Viraj R. Rathnayake
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Noura Rezapour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sarah Songao
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sean L. Tuggle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sandy Yousif
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - David I. Dorsky
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Martin R. Schiller
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
- * E-mail:
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4
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Sargeant DP, Hedden MW, Deverasetty S, Strong CL, Alaniz IJ, Bartlett AN, Brandon NR, Brooks SB, Brown FA, Bufi F, Chakarova M, David RP, Dobritch KM, Guerra HP, Levit KS, Mathew KR, Matti R, Maza DQ, Mistry S, Novakovic N, Pomerantz A, Rafalski TF, Rathnayake V, Rezapour N, Ross CA, Schooler SG, Songao S, Tuggle SL, Wing HJ, Yousif S, Schiller MR. The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system. PLoS One 2014; 9:e92877. [PMID: 24675726 PMCID: PMC3968042 DOI: 10.1371/journal.pone.0092877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 02/27/2014] [Indexed: 11/19/2022] Open
Abstract
We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/
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Affiliation(s)
- David P. Sargeant
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Michael W. Hedden
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sandeep Deverasetty
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Christy L. Strong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Izua J. Alaniz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Alexandria N. Bartlett
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Nicholas R. Brandon
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Steven B. Brooks
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Frederick A. Brown
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Flaviona Bufi
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Monika Chakarova
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Roxanne P. David
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Karlyn M. Dobritch
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Horacio P. Guerra
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Kelvy S. Levit
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Kiran R. Mathew
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Ray Matti
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Dorothea Q. Maza
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sabyasachy Mistry
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Nemanja Novakovic
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Austin Pomerantz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Timothy F. Rafalski
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Viraj Rathnayake
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Noura Rezapour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Christian A. Ross
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Steve G. Schooler
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sarah Songao
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sean L. Tuggle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Helen J. Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Sandy Yousif
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | - Martin R. Schiller
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
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Zhao Y, Jiang F, Liu P, Chen W, Yi K. Catechins containing a galloyl moiety as potential anti-HIV-1 compounds. Drug Discov Today 2012; 17:630-5. [DOI: 10.1016/j.drudis.2012.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 02/16/2012] [Accepted: 02/28/2012] [Indexed: 01/19/2023]
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6
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Mi T, Merlin JC, Deverasetty S, Gryk MR, Bill TJ, Brooks AW, Lee LY, Rathnayake V, Ross CA, Sargeant DP, Strong CL, Watts P, Rajasekaran S, Schiller MR. Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. Nucleic Acids Res 2012; 40:D252-60. [PMID: 22146221 PMCID: PMC3245078 DOI: 10.1093/nar/gkr1189] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 12/21/2022] Open
Abstract
Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease.
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Affiliation(s)
- Tian Mi
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Jerlin Camilus Merlin
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Sandeep Deverasetty
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Michael R. Gryk
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Travis J. Bill
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Andrew W. Brooks
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Logan Y. Lee
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Viraj Rathnayake
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Christian A. Ross
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - David P. Sargeant
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Christy L. Strong
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Paula Watts
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Sanguthevar Rajasekaran
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
| | - Martin R. Schiller
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269-2155, School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Pkwy., Las Vegas, NV 89154-4004 and Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030-3305, USA
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