GENOMICS & BIOINFORMATICS SERVICE
Who We Are
Texas A&M AgriLife Genomics and Bioinformatics Service was established thru a mission directive from Dr. Craig Nessler, Director of AgriLife Research to radically improve genomic research across AgriLife, COALS, and the Texas A&M University System, addressing a central and pressing need for access to the latest genomic technologies, and world-class laboratory and bioinformatics expertise. To meet this ambitious goal, AgriLife Research brought together a team of leading genomics, bioinformatics, molecular, and computational scientists to meet the next generation sequencing (NGS) and bioinformatics needs of the TAMU system and broader scientific community.
The new AgriLife Genomic unit received start-up funds from Texas Emerging Technology Fund as part of a larger AgriLife ETF program under the leadership of Executive Associate Director of Texas A&M AgriLife Research, Dr. Bill McCutchen.
The AgriLife unit is directed by Dr. Charles D. Johnson, who was recruited from the biotech industry to develop a next generation sequencing and bioinformatics program at Texas A&M. With over 20 years of scientific research and operational leadership experience, Dr. Johnson has an established track record in genomics and bioinformatics R&D. He recruited an extraordinary team of Agrilife scientists with vast and diverse background, allowing them to quickly catalyze activity across a broad spectrum of research areas, assuring a high return for each research dollar and generating significant scientific discoveries. The group has built a collaborative network of over 700 scientists spanning the entire TAMU system, along with a growing number of private sector life science and agricultural companies.
Investments in personnel and equipment have been critical to providing genomics and bioinformatics infrastructure for student training, faculty retention and successful R&D initiatives in the areas of agriculture, life sciences, human health, and veterinary medicine.
- AgriLife gets 1st Illumina GAIIx 2009
- AgriLife gets 2nd Illumina GAIIx 2010
- Roche 454 2010
- Illumina HiSeq 2000 purchase Spring 2012
- Illumina HiSeq 2500v3 upgrade Fall 2012
- Lead AgriLife Genomic Seed Grant (470K)
- Started offering Illumina MiSeq Spring 2013
- Board of Regents approved CBGSE August 2013
- Move to Gateway facility January 2014
- Illumina MiSeq January 2014
- Lead Texas A&M Genomics Seed Grant program (600K) 2014
- Lead Genomics of Plant Water Use Seed Grant (300K) 2014
- Illumina HiSeq 2500v4 Summer 2014
- Oxford Nanopore minION system Fall 2014
- Lead Vet school graduate seed grant program fall 2015
- Lead Vector Borne Disease Genomic Seed Grant (200K) 2016
- Lead Genomics of Plant Water Use Seed Grant (220K) 2016
- Illumina HiSeq 4000 June 2016
- PacBio Sequel Auguest 2016
- OxFord Nanopore minION R9 flowcell
- Lead Vet school graduate research grant program fall 2016
- Illumina Novaseq install May 2017
- PoreCampUSA June 2017
- Plant Gene Editing Seed Grant Program (500k) Dec 2017
- Supported over 1025 researchers drawn from over 35 departments, 10 colleges, and multiple agencies across the Texas A&M System.
- Involved in over 350 state and federal grant submissions, resulting in tens of millions in new funding for scientists across the TAMU system (>$30M to date).
- Launched ten Seed Grant programs- distributing a total of $2.4M in sequencing and bioinformatics services to faculty across the system to generate preliminary data to facilitate outside grant funding. 458 seed grant proposals submitted with over 846 total participants. 106 funded projects, generating $8M in new funding from the first $400k seed grant program.
- Marker Assisted Breeding program
- Launched highly successful genomic seed grant program – produced largest response in AgriLife history
Our Vision: Become the leading genomic and bioinformatics academic service provider through superior quality service, innovation, and technical excellence.
Our Values: At the heart of everything we do are our values
Service Obsessed: Dedication to every client’s success. Striving to exceed expectation on a daily basis and provide the best serve possible. Trust and personal responsibility in all relationships.
Problem Solvers: Let us sweat the details, we’ll make it happen and not give up!” Problems are to be solved and only viewed as temporary obstacles. Innovation that matters, for TAMUS, Texas & the World.
Excellence and Pride: We strive to be the best at what we do.
Fun and Creativity: Working hard comes naturally, but fun and creativity is cultivated and protected.
Our army of amazing PerkinElmer, Inc. robots have arrived! With a capacity to process 50,000 samples a year. In combination with our Illumina NovaSeq system (Illumina’s first agricultural focused NovaSeq site) we now have an even larger capacity to support agriculture research from across Texas A&M AgriLife, Texas A&M University, Texas A&M University System, and Read more about Capacity to processing 50,000 DNA Samples a year[…]
Next set of NGS analysis courses comes to Texas A&M University, covering introduction, RNA-Seq, assembly, metagenomics and genotyping in collaboration between TxGen and TAMU HPRC. Outstanding instructors and a great group of students 👏👏👏 . Whoop for all the Aggies with the new rings on Ring day. R class next week. Organized by Noushin Ghaffari, Read more about NGS analysis workshops come to Aggieland[…]
25 Texas A&M faculty & students use their Spring Break to attend the first Software Carpentry workshop at Texas A&M University. The workshop was taught by A&M instructors. Instructors: Noushin Ghaffari, Anna Dabrowski, Ramalingam Saravanan Helpers: David Bapst, Jian Tao, Michael Dickens The attendees learned best practices for scientific programing. Participants from across the University, Read more about #1 Software Carpentry workshop at Texas A&M University[…]
Great to have K-12 STEM educators in our center this morning! introducing sequencing technologies (Dr. Josh Hill) and bioinformatics analysis (me). Interdisciplinary research interests should start early on. #stem4innovation @TXGEN @tamu_hprc pic.twitter.com/HIunO51kCy — Noushin Ghaffari (@Noushin_Gh) January 26, 2018
COLLEGE STATION – Texas A&M AgriLife Research is investing in the future of rapid crop design with improved traits through the deployment of two new labs and a half-million dollar seed grant program to jump-start the process. “We are pleased to announce a new funding opportunity that focuses on building a pipeline for genome editing Read more about Latest crop improvement technology coming to Texas A&M AgriLife Research[…]
Recruiting for a key leadership position as part of our new Illumina NovaSeq service team. We are looking to fill a critical need within our facility for a senior person with experience in NGS research, loves working with people, and has had experience in industry or a leadership position in an academic research service. Apply Read more about Recruiting key leadership position within AgriLife TxGen[…]
Bin Tian, Shichen Wang, Timothy C. Todd, Charles D. Johnson, Guiliang Tang, and Harold N. Trick Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics 2017. 2 August 2017 18:572 https://doi.org/10.1186/s12864-017-3963-4 Link David L. Oldeschulte, Yvette A. Halley, Miranda L. Wilson, Eric K. Bhattarai, Wesley Brashear, Joshua Hill, Richard Read more about New Recent Publications[…]
New blog post! Very helpful @nanopore Q&A session from June 2017 #porecampusa @txresearch https://t.co/Qez1i0mG4e — Lisa K. Johnson (@monsterbashseq) February 1, 2018 Q&A at Porecamp TAMU, June 2017: From the Ebola Outbreak to Sequencing on Mars #PoreCampUSA 2017 and @nanopore make the local TV news @pathogenomenick @Scalene @BioMickWatson @mattloose @DrT1973 https://t.co/jq1wK3v5vD — Charlie Johnson (@BioMath) June Read more about PoreCampUSA17 Twitter Feed[…]
In collaboration with CVM, we are putting a short course on a minION sequencing (handheld sequencer). Five of the top researchers working in this area will be coming to College Station in June and we are now in the process of recruiting students. http://www.txgen.tamu.edu/porecamp_usa/ PoreCamp is part of the PoreCamp series, This series was founded Read more about PoreCamp USA[…]
Names in bold are TxGen personnel – ready to support your next research project and/or grant.
- Bin Tian, Shichen Wang, Timothy C. Todd, Charles D. Johnson, Guiliang Tang, and Harold N. Trick Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics 2017. 2 August 2017 18:572 https://doi.org/10.1186/s12864-017-3963-4 Link
- David L. Oldeschulte, Yvette A. Halley, Miranda L. Wilson, Eric K. Bhattarai, Wesley Brashear, Joshua Hill, Richard P. Metz, Charles D. Johnson, Dale Rollins, Markus J. Peterson, Derek M. Bickhart, Jared E. Decker, John F. Sewell and Christopher M. Seabury. Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3: Genes, Genomes, Genetics July 17, 2017; Link
- Heidi M. Blank, Ricardo Perez, Chong He, Nairita Maitra, Richard Metz, Joshua Hill, Yuhong Lin, Charles D. Johnson, Vytas A. Bankaitis, Brian K. Kennedy, Rodolfo Aramayo and Michael Polymenis. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. 2017 DOI 10.15252/embj.201695050 | Published online 05.01.2017 The EMBO Journal (2017) e201695050 (Article ID: EMBJ788)
- Yuya Liang, Michael Baring, Shichen Wang, and Endang M. Septiningsih. Mapping QTLs for Leafspot Resistance in Peanut Using SNP-Based Next-Generation Sequencing Markers. Plant Breeding and Biotechnology 2017;5:115-22. https://doi.org/10.9787/PBB.2017.5.2.115
- Chor-Tee Tan, Hangjin Yu, Yan Yang, Xiangyang Xu, Mingshun Chen, Jackie C. Rudd, Qingwu Xue, Amir M. H. Ibrahim, Lisa Garza, Shichen Wang, Mark E. Sorrells, Shuyu Liu. Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. Theoretical and Applied Genetics 2017
- C-C. Chen, N. Ghaffari, X. Qian, and B-J. Yoon, ” Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy”, Journal Computational Biology and Chemistry, 2017
- Noushin Ghaffari, Jordi Abante, Raminder Singh, Philip D. Blood, Charles D. Johnson. Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data July 17 – 21, 2016 ISBN: 978-1-4503-4755-6
- NH Ing, K Konganti, N Ghaffari, CD Johnson, DW Forrest, CC Love, DD Varner. Sequencing of RNA from stallion sperm identifies potential markers of fertility. 2016 Journal of Equine Veterinary Science, S56eS82
- Maria F. Torres, Noushin Ghaffari, Ester A. S. Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson and Lisa J. Vaillancourt. Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction. BMC Genomics 201617:202. DOI:10.1186/s12864-016-2546-0. 8 March 2016
- Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, et al. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J. 2016; 86:195–207. http://www.ncbi.nlm.nih.gov/pubmed/26945524
(2015) Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS ONE 10(12): e0144913. doi: 10.1371/journal.pone.0144913
- Ghaffari, N.; Arshad, O.A.; Jeong, H.; Thiltges, J.; Criscitiello, M.F.; Yoon, Byung-Jun; Datta, A.; Johnson, C.D., “Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline,” Computational Biology and Bioinformatics, IEEE/ACM Transactions on , vol.PP, no.99, pp.1,1 doi: 10.1109/TCBB.2015.2446478
- Masoud Toloue , Jan Risinger , Lindsey Renken , Josh Hill , Noushin Ghaffari , Richard P Metz , Charles D. Johnson , Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification – Mixed Species Plant and Animal Genome XXIII Conference 2015.
- Guttieri MJ, Baenziger PS, Frels K, Carver B, Arnall B, Wang S, et al. Prospects for Selecting Wheat with Increased Zinc and Decreased Cadmium Concentration in Grain. Crop Sci. 2015; 55:1712. https://dl.sciencesocieties.org/publications/cs/abstracts/55/4/1712
- Jordan KW, Wang S*(co-first), Lun Y, Gardiner L-J, MacLachlan R, Hucl P, et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 2015; 16:48. http://www.ncbi.nlm.nih.gov/pubmed/25886949
- Tiwari VK, Wang S, Danilova T, Koo DH, Vrána J, Kubaláková M, et al. Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M(g) of Aegilops geniculata. Plant J. 2015; 84:733–46. http://www.ncbi.nlm.nih.gov/pubmed/26408103
AgriLife Genomics and Bioinformatics Service location
101 Gateway, Suite A
College Station TX 77845
Lab Phone: (979) 862-2143
If you are going south on Highway 6 (from TAMU), take the Nantucket exit and make a U-turn under the bridge to get onto the northbound HW6 feeder road. From the feeder road make a right turn into our complex on the right immediately after passing the business park entrance (Gateway Blvd). We are located in Suite A of this building, which is on the right hand side.
Please park in the front of the building.