Genomics & Bioinformatics Service

Providing Genomics and Bioinformatics Service to the Texas A&M AgriLife, the Texas A&M System, Texas, and the World

To start a sequencing project please contact Dr. Charlie Johnson

GENOMICS & BIOINFORMATICS SERVICE

Providing Next Generation Sequencing and Bioinformatics Services
Go to Sequencing

Sequencing

We have already sequenced more than 100 different species (not counting metagenomic projects), over 1000 samples/month processed and we add about one new project every day.

Go to Library preparation

Library preparation

A key element of NGS is the high-quality library preparation. The protocols and equipment used by our team can accommodate a range of needs.

Go to Bioinformatics Analysis and Processing

Bioinformatics Analysis and Processing

Our quantitative and computational analytical unit sits at the cutting edge of bioinformatics research — we use the latest tools and develop improvements to correct short comings with these tools.

To start a project, contact Dr. Johnson for a quote and make arrangements with Dr. Metz to drop off samples

Who We Are

Established to radically improve genomic research across AgriLife, TAMU, and the Texas A&M University System

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.

Texas A&M AgriLife Director, Genomics and Bioinformatics 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: Fundamentally change agriculture genomics at Texas A&M University by accelerating genomic research across Texas and the world by embodying the Aggie Core Values of Service, Excellence, Leadership, Loyalty, Respect, Integrity.

Selfless service: We put the customer at the center of everything we do. We strive to exceed expectations and provide the best possible service to our clients every day.

Excellence : We work tirelessly to provide the latest and best equipment and methodologies to our clients.

Leadership: “At Texas A&M you learn first to follow, then to develop and practice your leadership skills, and finally you become someone others want to follow.” 

Loyalty: Two-way process: Faithfulness owed by a pledge or promise. Let us earn your trust over time.

Respect: Respect is not given, but earned. We strive to earn your respect daily

Integrity: Aggie Code of Honor states: 'Aggies do not lie, cheat or steal nor tolerate those that do', Enough said

To start a sequencing project please contact Dr. Charlie Johnson

OUR TEAM

The AgriLife unit is directed by Dr. Charles D. Johnson, who 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.

To start a project, contact Dr. Johnson for a quote and make arrangements with Dr. Metz to drop off samples

To start a project, contact Dr. Johnson for a quote and make arrangements with Dr. Metz to drop off samples

Names in bold are TxGen personnel – ready to support your next research project and/or grant. Journal Papers

2021

    • Chenggen Chu, Shichen Wang,, Li Paetzold, Zhen Wang, Kele Hui, Jackie C. Rudd, Qingwu Xue, Amir M. H. Ibrahim, Richard Metz, Charles D. Johnson, Charles M. Rush, Shuyu Liu. RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’ doi: https://doi.org/10.1038/s41598-021-83372-0
      Felix D Guerrero, Noushin Ghaffari, Kylie G Bendele, Richard P Metz, C Michael Dickens, Philip D Blood, Jason Tidwell, Robert J Miller, Adalberto A Pérez de León, Pete D Teel, Charles D Johnson. Raw Pacific Biosciences and Illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus. Data In Brief. Volume 35, 2021, 106852, ISSN 2352-3409, https://doi.org/10.1016/j.dib.2021.106852

2020

    • Yan Yang, Smit Dhakal, Chenggen Chu, Shichen Wang, Qingwu Xue, Jackie C. Rudd, Amir M.H. Ibrahim, Kirk Jessup, Jason Baker, Maria Pilar Fuentealba, Ravindra Devkota, Shannon Baker, Charles D. Johnson, Richard Metz, Shuyu Liu. Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112 doi: https://doi.org/10.1101/2020.07.27.222703 2020
      Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh, Bryce E. Nickels, Craig D. Kaplan. Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”doi: https://doi.org/10.1101/810127 2020Anne N Thorndike ,Jessica L McCurley ,Emily D Gelsomin ,Eric B Rimm,Yuchiao Chang,Bianca Porneala,Emma Anderson, Charles D. Johnson, Douglas E Levy. MP07: Automated, Personalized Feedback and Behavioral Nudges to Improve Workplace Food Choices and Prevent Weight Gain: Choosewell 365 Randomized Controlled Trial. 2 Mar 2020https://doi.org/10.1161/circ.141.suppl_1.MP07Circulation. 2020;141:AMP07 Christopher M Seabury, David L Oldeschulte, Eric K Bhattarai, Dhruti Legare, Pamela J Ferro, Richard P Metz, Charles D Johnson, Mitchell A Lockwood, Tracy A Nichols. Accurate Genomic Predictions for Chronic Wasting Disease in US White-Tailed Deer G3: Genes, Genomes, Genetics April 1, 2020 vol. 10 no. 4 1433-1441; https://doi.org/10.1534/g3.119.401002 Nancy H Ing, Kranti Konganti, Noushin Ghaffari, Charles D Johnson, David W Forrest, Charles C Love, Dickson D Varner. Identification and quantification of coding and long non‐coding RNAs in stallion spermatozoa separated by density 03 April 2020 https://doi.org/10.1111/andr.12791 Song, Q., Joshi, M., Wang, S. et al. Comparative Analysis of Root Transcriptome Profiles of Sesame (Sesamum indicum L.) in Response to Osmotic Stress. J Plant Growth Regul (2020). https://doi.org/10.1007/s00344-020-10230-0 Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M Visbisky, Scott L Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William KM Lai, Richard P Metz, Charles D Johnson, Sing-Hoi Sze, B Franklin Pugh, Bryce E Nickels, Craig D Kaplan. Genome Biol 21, 132 (2020). https://doi.org/10.1186/s13059-020-02040-0

2019

2018

    • 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

2017

    • 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)

2016

    • 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
    • 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

2015

  • Yvette A. Halley, David L. Oldeschulte, Eric K. Bhattarai, Joshua Hill, Richard P. Metz, Charles D. Johnson, Steven M. Presley, Rebekah E. Ruzicka, Dale Rollins, Markus J. Peterson, William J. Murphy, Christopher M. Seabury. (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

More Publications

To start a sequencing project please contact Dr. Charlie Johnson

NEW TxGen location

Building location:
TxGen (Genomics and Bioinformatics Service)
1500 Research Parkway
Suit 250
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.

For mailing information go here.

Google Map: http://bit.ly/TxGenMap

Aggie Map https://aggiemap.tamu.edu/?bldg=1605

 

To start a project, contact Dr. Johnson for a quote and make arrangements with Dr. Metz to drop off samples