GENOMICS & BIOINFORMATICS SERVICE
Who We Are
Texas A&M AgriLife Genomics and Bioinformatics Service was established thru a mission directive from 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 Mission: Become the leading genomic and bioinformatics academic service provider through superior quality service, innovation, and technical excellence.
Our Vision: Fundamentally change Agriculture Genomics
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.
Illumina Inc. highlighted the work AgriLife and TxGen in the videos below (>6,200 views) Agriculture Throughout the World is Benefiting from the Latest NGS Technologies- interview with Dr. Johnson Sequencing Complex Plant Genomes at Texas A&M AgriLife https://youtu.be/eecnhlhAn9w Empowering Agrigenomics Across the Globe https://youtu.be/UfBR6FJnQ_o Featured 2019 PAG video https://youtu.be/wSFtVRHe5-k Using the iSeq™ 100 Sequencing System Read more about Illumina Videos and interview[…]
Come Celebrate! October 29th, 2019 The Genomics and Bioinformatics Service (TxGen), part of Texas A&M AgriLife Research, celebrates its 10th year of service to the Texas A&M community, Texas, and scientists around the world with the opening of our new sequencing and bioinformatics facility in the Texas A&M West Campus Research Park. You are invited Read more about Come Celebrate with Us[…]
We are in the process of packing and moving into our new facilities at the Texas A&M Reserach Park, Centeq Building. Please excuse any delays in responding to your emails. We expect to be back to normal operations by the first week in May. Building Address: New Address for TxGen Room 250 Centeq Building A Read more about TxGen Moving Back to Campus[…]
In our continuing commitment to the Aggie core value of excellence, Texas A&M AgriLife Genomic and Bioinformatics Service is pleased to announce our new NovaSeq pricing. We have recently added a 2nd Illumina NovaSeq system to our facility. As a consequence, we are able to offer researchers a significant reduction in the cost of sequencing. Read more about New NovaSeq Pricing (25Feb2019)[…]
2018 was a landmark sequencing year for @TXGEN and this year is shaping up to be even bigger. We added a 2nd @illumina NovaSeq to meet the growing demand and in collaboration with @PerkinElmer_AG are slashing total sequencing project costs by 40%, or more for 2019. We were named a Center of Excellence by PerkinElmer. Read more about Launching new NovaSeq Service. up to 40% reduction in cost of sequencing[…]
2018 was a landmark sequencing year for @TXGEN and this year is shaping up to be even bigger. We added a 2nd @illumina NovaSeq to meet the growing demand and in collaboration with @PerkinElmer_AG are slashing total sequencing project costs by 40%, or more for 2019. pic.twitter.com/wfouiIT7sd — Charlie Johnson (@BioMath) February 1, 2019 Dr. Read more about Twitter Feed Week of Feb 20,1019[…]
Howdy! We are pleased to invite you to the second 2-day Official Software Carpentry Workshop at Texas A&M University. Texas A&M AgriLife Genomics and Bioinformatics Service, TAMU High Performance Research Computing, TAMU Libraries, TAMU Departments of Atmospheric Sciences, ECE and EEB Departments are collaborating to organize and hold this workshop. This hands-on workshop is an Read more about Second 2-Day Official Software Carpentry Workshop at Texas A&M University[…]
Texas A&M AgriLife Genomics and Bioinformatics Service (TxGene) and the Texas A&M University High Performance Research Computing (HPRC) are offering four bioinformatics short courses. Limited seating is available and registration is required. These short courses are free of charge and available to anyone at Texas A&M. Topic: Introduction to Next Generation Sequencing, Dr. Michael Dickens Read more about Spring 2019 Bioinformatics Training[…]
Plant and Animal Genomics (PAG) 2019, San Diego California PerkinElmer Workshop at PAG2019 TUESDAY, JANUARY 15TH |1:30 PM TOWN & COUNTRY, ROYAL PALM SALON 5-6 Link to Flyer: https://goo.gl/bxFw8E
Texas A&M AgriLife receives sponsored support for agrigenomics lab from PerkinElmer
Names in bold are TxGen personnel – ready to support your next research project and/or grant.
Dhruva K. Chakravorty, Marinus “Maikel” Pennings, Honggao Liu, Zengyu “Sheldon” Wei, Dylan M. Rodriguez, Levi T. Jordan, Donald “Rick” McMullen, Noushin Ghaffari, and Shaina D. Le. Effectively Extending Computational Training Using Informal Means at Larger Institutions 2019 Journal of Computational Science EducationDOI: https://doi.org/10.22369/issn.2153-4136/10/1/10
Joshua R. Beytebiere, Alexandra J. Trott, Ben J. Greenwell, Collin A. Osborne, Helene Vitet, Jessica Spence, Seung-Hee Yoo, Zheng Chen, Joseph S. Takahashi, Noushin Ghaffari, and, Jerome S. Menet. Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions. Genes and Development. March 1, 2019 33: 255-257; doi:10.1101/gad.324046.119
Yan Yang, Bhoja R. Basnet, Amir M.H. Ibrahim, Jackie C. Rudd, Xianming Chen, Robert L. Bowden, Qingwu Xue, Shichen Wang, Charles D. Johnson, Richard Metz, Richard Esten Mason, Dirk B. Hays, and Shuyu Liu. Developing KASP Markers on a Major Stripe Rust Resistance QTL in a Popular Wheat TAM 111 Using 90K Array and Genotyping-by-Sequencing SNPs. Crop science, vol. 59, january–february 2019
- Jan E Janečka, Brian W Davis, Sharmila Ghosh, Nandina Paria, Pranab J Das, Ludovic Orlando, Mikkel Schubert, Martin K Nielsen, Tom AE Stout, Wesley Brashear, Gang Li, Charles D Johnson, Richard P Metz, Charles C Love, Dickson D Varner, Daniel W Bellott, William J Murphy, Bhanu P Chowdhary, Terje Raudsepp Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nature Communicationsvolume 9, Article number: 2945 (2018)
- NH Ing, K Konganti, N Ghaffari, CD Johnson, DW Forrest, CC Love, DD Varner Functional RNAs in Stallion Sperm: Potential Indicators of Sperm Quality and Contributors to Fertility. Journal of Equine Veterinary Science. Volume 66, July 2018 https://doi.org/10.1016/j.jevs.2018.05.011
- 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
NEW TxGen location
TxGen (Genomics and Bioinformatics Service)
1500 Research Parkway
College Station TX 77845
Please park in the Centeq building parking lot (Lot 109), no TAMU parking permit required. We are on the 2nd floor of the A section of the Centeq building. Come up the elevator, take a right and our main office is room 250.
Google Map: http://bit.ly/TxGenMap
Aggie Map https://aggiemap.tamu.edu/?bldg=1605