biotech.unl.edu Open in urlscan Pro
3.90.97.115  Public Scan

Form analysis
1 forms found in the DOM

GET https://search.unl.edu/

<form class="dcf-wrapper dcf-form dcf-search-form dcf-d-flex dcf-ai-center dcf-pt-8 dcf-pb-8" id="dcf-search-form" role="search" aria-label="Site" action="https://search.unl.edu/" method="get">
  <label class="dcf-label dcf-mr-4 dcf-mb-0 unl-cream" for="dcf-search_query">Search</label>
  <div class="dcf-input-group">
    <input class="dcf-input-text dcf-search-input dcf-bg-transparent unl-cream unl-b-cream" id="dcf-search_query" name="q" type="search" required="">
    <button class="dcf-btn dcf-btn-inverse-primary" type="submit">
      <svg class="dcf-d-block dcf-h-5 dcf-w-5 dcf-fill-current" aria-hidden="true" focusable="false" height="16" width="16" viewBox="0 0 48 48">
        <path d="M18 36a17.9 17.9 0 0 0 11.27-4l15.31 15.41a2 2 0 0 0 2.84-2.82L32.08 29.18A18 18 0 1 0 18 36zm0-32A14 14 0 1 1 4 18 14 14 0 0 1 18 4z"></path>
      </svg>
      <span class="dcf-sr-only">Submit</span>
    </button>
  </div>
  <input type="hidden" name="u" value="https://biotech.unl.edu/"><input type="hidden" name="embed" value="5.0">
</form>

Text Content

Skip to main content


University of Nebraska–Lincoln
 * Visit
   Visit
      
      
    * Visit the University of Nebraska–Lincoln

 * Apply
   Apply
      
      
    * Apply to the University of Nebraska–Lincoln

 * Give
   Give
      
      
    * Give to the University of Nebraska–Lincoln

Log In

Search Search
University of Nebraska–Lincoln
Nebraska Center for Biotechnology
Menu Search Search
Log In

Email Us
 * About the Center
   * Personnel
   * Faculty Advisory Committee
   * Policy on Authorship and Acknowledgments
   * Center Newsletters
   * #BiotechMonday
 * Core Research Facilities
   * Bioinformatics
   * Flow Cytometry
   * Microscopy
   * Proteomics and Metabolomics
   * CryoEM
 * Workshops and Courses
   * CryoEM Workshop
   * Amplicon Analysis Workshop
   * Proteomics and Metabolomics Workshop
 * Scholarships, Fellowships and Awards

 * Visit
     
     
   * Visit the University of Nebraska–Lincoln
 * Apply
     
     
   * Apply to the University of Nebraska–Lincoln
 * Give
     
     
   * Give to the University of Nebraska–Lincoln

 1. Nebraska
 2. Nebraska Center for Biotechnology
 3. Core Research Facilities
 4. Bioinformatics


BIOINFORMATICS


BIOINFORMATICS
 * HOME
 * SERVICES
 * SERVICE FEES
 * INSTRUMENTS & FACILITIES
 * PERSONNEL
 * PUBLICATIONS
 * ADVISORY COMMITTEE
 * CONTACT DIRECTOR
 * SCHEDULE

APPOINTMENTS AND CONSULTATIONS

Timely consultation before starting data-heavy projects is crucial to the
success of experiments. We offer initial consultations to help you, for example,
with experimental design and power analysis of 'omics data for grant
submissions. You can also reach out to us to discuss your bioinformatics needs
for current projects. Note that these meetings are free, except for appointments
where we deal with ongoing questions and/or training which has to be paid for.
Schedule a virtual meeting today at: Schedule BCRF virtual meeting.



ELAB NOTEBOOK RESEARCHSPACE (RSPACE) AVAILABLE FOR NU USERS

This Enterprise level eLab notebook system is available for immediate use to Lab
groups of the Nebraska University community. User fees are $45 for the period up
August 2024, and accounts can be requested (a cost object is required). The
Bioinformatics Core (Biotech) and the Data and Life Sciences Core (NCIBC) have
piloted this with help of researchers at NU for three years. The system is
installed on a HIPAA-compliant cloud and is managed by NU ITS.

SERVICES


The University of Nebraska-Lincoln Bioinformatics Core Research Facility (BCRF)
is located in the Beadle Center at the east side of the City Campus. The Core
offers education, analysis, and computational services in the area of
bioinformatics and computational biology.

We provide various standard bioinformatics services (listed under Service Fees)
with a quick turnaround time and very reasonable fees.

Besides the listed services for fees, we also:

 * Help with preparing for and writing of grant proposals that include life
   sciences related computation or analyses. Free if the BCRF is included in the
   grant.
 * Collaborate on larger projects and grants (please talk to us first to request
   a quote)
 * Custom-program solutions (Python, Perl, R) for something simple as conversion
   or integration of data files, or on the other end of the spectrum develop and
   program solutions for large-scale analyses (billed per hour)
 * Give lectures in bioinformatics topics
 * Install and maintain, in collaboration with the Holland Computing Center, up
   to date software and databases in the Life Sciences (specifically
   bioinformatics) domain.
 * Provide support for bioinformatics software & analyses on the Holland
   Computing Cluster. This support is free for up to 3 hours per year per
   faculty.
 * Host (web) servers and research database-drives web sites (e.g. species
   specific genome browsers).

The Bioinformatics Core Research Facility receives funding support from the
Nebraska Research Initiative (NRI), the Program of Excellence in Computational
Sciences, and the NIH via the Nebraska Center for Integrated Biomolecular
Communication (NCIBC).

SERVICE FEES

STANDARD BIOINFORMATICS SERVICES (+ DENOTES MINIMUM COST)

SERVICE DESCRIPTIONUNIV. NEBRASKA NON-PROFIT/GOVERNMENT COMMERCIAL Qa and
filtering on next-gen sequencing sample $66 $99 $198 Differential gene
expression analysis (microarray) 1) $66 $99 $198 Differential gene expression
analysis (next-gen sequences) per sample1)
Samples 1 to 10:
Sample 11 onward:
Example report
$200
$108.50
$295
$150
$591
$295 Go term enrichment analysis (per list) 1) $66 $99 $198 Ortholog/homolog
detection (between two species) $130 $190 $380

Metagenomic analysis (per sample)
Samples 1 to 50:
Sample 51 onward:
(amplicon or shotgun)
Example report for 16S



$85
$55
$190
$123
$380
$247 Phylogenetic analysis $130 + $175 + $290 + Transcriptome assembly (de-novo
or guided) $370 + $555 + $1110 + Bacterial genome assembly (de-novo or guided)
$141 + $211 + $423 + Viral/bacteriophage genome assembly (pure sample) $157 +
$235 + $471 + Viral/bacteriophage genome assembly (contaminated or sample
includes host) $370 + $555 + $1110 + Archae genome assembly (de-novo or guided)
$277 + $415 + $831 + Eukaryotic genome assembly (de-novo or guided) $1,239 +
$1,858 + $3,717 + Data deposition of microarray, next-gen, transcriptomes or
genomes (per deposition) to public database $232 $348 $696 Publication-ready
graph of any of the above analyses $66 $99 $198 1) Per analysis (not per sample)
additional cost for sparsely annotated species $200 $280 $560

CUSTOM BIOINFORMATICS SERVICES

Please note that for longer analyses (longer than 10 hours labor) it is more
cost-effective for the researcher to pay part of the salary and benefits of the
Core's staff. The minimum percentage is 2% fte, approximately a week (5 business
days) of a staff's work, and increments by 2%. Note that if payment is made for
2% fte, but staff was able to finish analysis in 3 business days, no refunds are
given but the remainder is available to you for further analysis within the same
year.

SERVICE DESCRIPTIONUNIV. NEBRASKA NON-PROFIT/GOVERNMENT COMMERCIAL Custom
programming/analysis (less than 10 hours) $90 / h $140 / h $275 / h Custom
analysis (more than 10 hours) Ask for quote

INSTRUMENTS & FACILITIES

The Bioinformatics Core Research Facility houses a high performance Linux
compute cluster dedicated to Life Sciences research. In total, the compute
cluster has approximately 350CPU cores, 1TB of RAM, and 400TB of central SAS
RAID 6 zfs disk storage.

Most of our cluster nodes have at least 8GB of RAM and are available via the
Slurm job scheduling system and are capable of running MPI jobs.

We have a dedicated 4 CPU 6-core large memory server (320 GB RAM) suitable for
larger transcriptome and genome assembly jobs. Two web servers and database
back-end machines are hosting several University database-driven research web
sites. The Core has a data transfer server with a direct fiber optic connection
at 10GB/s to the Holland Compute Center.

We do not provide access for faculty, staff, or students to our computational
cluster anymore, except indirectly via our staff or for the sole purpose of
classes or workshops taught by BCRF staff, or for the purpose of transferring
large data sets.



In additional to our own cluster, we make heavily use of the University of
Nebraska's Holland Computing Center (http://hcc.unl.edu/), on which we also
collaborate to keep life sciences software and databases up to date.

PERSONNEL

Jean-Jack M. Riethoven (Director)
BEAD E204
Phone: +1 402-472-7949
Fax: +1 402-472-3139
Email Jean-Jack

Chia Sin Liew (Bioinformatician)
BEAD E206
Phone: +1 402-472-1572
Email Chia Sin

Haowen (Max) Qiu (Bioinformatician)
BEAD E206
Phone: +1 402-472-1572
Email Max

PREVIOUS MEMBERS

Bridget Tripp, student bioinformatician (2020-2021)
Thomas Payne, bioinformatician (2018-2020)
Qidong Jia, bioinformatician (2016-2019)
Seong-il Eyun, bioinformatician (2013-2017)
Fangrui Ma, senior bioinformatician (2015-2016)
Stephanie Canny, bioinformatician (2013-2016)
Kartik Vedalaveni, student System Administrator (2010-2012)
Sridhar Acharya Malkaram, Postdoc (2008-2010)
Rong Liu, Postdoc (2008-2009)
Sabina Manandhar, student System Administrator (2008-2010)

PUBLICATIONS (CHRONOLOGICAL ORDER)

 1.  Le Texier, V., J.J.M. Riethoven, V. Kumanduri, C. Gopalakhrishnan, F.
     Lopez, D. Gautheret, and T.A. Thanaraj (2006). AltTrans: Transcript pattern
     variants annotated for both alternative splicing and alternative
     polyadenylation. BMC Bioinformatics 7:169.
 2.  Stamm, S., J.J.M. Riethoven, V. Le Texier, C. Gopalakhrishnan, V.
     Kumanduri, Y. Tang, N.L. Barbosa-Morais, and T.A. Thanaraj (2006). ASD: A
     Bioinformatics Resource on Alternative Splicing. Nucleic Acids Research 34:
     D46-D55.
 3.  LaRosa, P.C., J.J.M. Riethoven, H. Chen, Y. Xia, Y. Zhou, M. Chen, J.
     Miner, M.E. Fromm (2007) Trans-10, Cis-12 Conjugated Linoleic Acid
     Activates the Integrated Stress Response Pathway in Adipocytes,
     Physiological Genomics, 31 (544), 553.
 4.  Koscielny, G.,  V. Le Texier, C. Gopalakrishnan, V. Kumanduri, J.J.M.
     Riethoven, F. Nardone, E. Whitfield, C. Fallsehr, O. Hofmann, M. Knull, E.
     Harrington, S. Boue, E. Eyras, M. Plass, F. Lopez, W. Ritchie, V. Moucadel,
     T. Ara, H. Pospisil, A. Herrmann, J.G. Reich, R. Guigo, P. Bork, M. von
     Knebel Doeberitz, J. Vilo, W. Hide, R. Apweiler, T.A. Thanaraj, D.
     Gautheret (2008) ASTD: the Alternative Splicing and Transcript Diversity
     Database, Genomics 93 (3), 213-20.
 5.  Galeota, J.A., Napier J.E., Armstrong D.L., Riethoven J.J., Rogers, D.G.
     (2009) Herpesvirus infections in rock hyraxes (Procavia capensis). Journal
     of Veterinary Diagnostic Investigation 21 (4) : 531-5.
 6.  Ding, Y., Lapko, H., Ndamukong, I., Xia, Y., Al-Abdallat, A., Lalithambika,
     S., Sadder, M., Saleh, A., Fromm, M. Riethoven, J.J.,  Lu, G., Avramova, Z.
     (2009) The Arabidopsis Chromatin Modifier ATX1, the Myotubularin-like
     AtMTM, and the Response to Drought; a view from the other end of the
     pathway. Plant Signaling & Behavior, 4 (11) : 1049-58.
 7.  Jiang, S., Wang, Z., Riethoven, J.J., Xia. Y., Miner, J., Fromm, M. (Oct
     2009) Conjugated Linoleic Acid Activates AMP-Activated Protein Kinase and
     Reduces Adiposity More Effectively When Used with Metformin in Mice.
     Journal of Nutrition 139 (12) : 2244-51.
 8.  Li, C., Riethoven, J.J.M., Ma, L. (2010) Exon-primed intron-crossing (EPIC)
     markers for non-model teleost fishes. BMC Evolutionary Biology 10:90.
 9.  Belch, Y., Yang, J., Liu, Y., Malkaram, S.A., Liu, R., Riethoven, J.J.M.,
     Ladunga, I. (2010) The Transcriptional Competence of Chromatin and Weakly
     Positioned Nucleosomes. PLoS ONE 5(9): e12984.
     doi:10.1371/journal.pone.0012984
 10. van Dijk, K., Ding, Y., Malkaram, S., Riethoven, J.J.M., Liu, R., Yang, J.,
     Laczko, P., Chen, H., Xia, Y., Ladunga, I., Avramova, Z., Fromm, M. (2010)
     Dynamic changes in genome-wide Histone H3 Lysine 4 methylaton patterns in
     response to dehydration stress in Arabidopsis thaliana. BMC Plant Biology
     2010, 10:238.
 11. Jiang, S., Chen, H., Wang, Z., Riethoven, J.J.M., Xia, Y., Miner, J.,
     Fromm, M. (2010) Activated AMPK and prostaglandins are involved in the
     response to conjugated linoleic acid and are sufficient to cause lipid
     reductions in adipocytes. J Nutritional Biochemistry [E-pub ahead of
     print]. PMID 20965713
 12. Riethoven, J.J.M. Regulatory Regions in DNA: Promoters, Enhancers,
     Silencers, and Insulators, In: I. Ladunga (Eds) Computational Biology of
     Transcription Factor Binding. In the series: Methods in Molecular Biology,
     Vol. 674. USA, Humana Press, NJ. ISBN 978-1-60761-853-9. PMID 20827584
 13. Plautz, S.A., Boanca, G., Riethoven, J.J.M., Pannier, A.K. (2010)
     Intracellular Signaling Pathways in Nonviral Gene Delivery: Microarray
     Analysis of Gene Expression Profiles in Transfected Cells. Molecular
     Therapy 2011 Dec;19(12):2144-51 [Epub 2011 Aug 9] PMID 21829178
 14. Ding Y, Ndamukong I, Zhao Y, Xia Y, Riethoven J.J.M, Jones D, Divecha N,
     Avramova Z. (2012) Divergent Functions of the Myotubularin (MTM) Homologs
     AtMTM1 and AtMTM2 in Arabidopsis thaliana: Evolution of the plant MTM
     family. The Plant Journal 2012 Jun;70(5):866-878. Online:
     http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2012.04936.x/abstract
 15. Ding Y, Virlouvet L, Riethoven JJM, Fromm ME, and Avramova Z (2013). Four
     distinct types of dehydration stress memory genes in Arabidopsis thaliana.
     Accepted 19 Dec 2013. BMC Plant Biology 2013, 13:229 
     doi:10.1186/1471-2229-13-229
 16. Pashaj A, Yi X, Xia M, Canny S, Riethoven JJ, Moreau R. (2013)
     Characterization of genome-wide transcriptional changes in liver and
     adipose tissues of ZDF (fa/fa) rats fed R-α-lipoic acid by next-generation
     sequencing. Physiological Genomics PG-00138-2013R2. E-pub ahead of print 8
     Oct 2013. doi: 10.1152/physiolgenomics.00138.2013
 17. N. N. Vellichirammal , A. J. Zera, R. J. Schilder, C. Wehrkamp, J-J. M.
     Riethoven, J. A. Brisson (2014). De novo transcriptome assembly and
     morph-specific gene expression profiling of the wing polymorphic cricket
     Gryllus firmus. PLoS One. 2014 Jan 8;9(1):e82129. doi:
     10.1371/journal.pone.0082129
 18. Massilamany C, Gangaplara A, Jia T, Elowsky C, Kang G, Riethoven JJM, Li Q,
     Zhou Y, and Reddy J (2014). Direct staining with major histocompatibility
     complex class II dextramers permits detection of antigen-specific,
     autoreactive CD4 T cells in situ. PLoS ONE 9(1): e87519.
     doi:10.1371/journal.pone.0087519
 19. Tatineni S, Riethoven JJ, Graybosch RA, French R, Mitra A. (2014) Dynamics
     of small RNA profiles of virus and host origin in wheat cultivars
     synergistically infected by Wheat streak mosaic virus and Triticum mosaic
     virus: virus infection caused a drastic shift in the endogenous small RNA
     profile. PLoS One. 2014 Nov 3;9(11):e111577. doi:
     10.1371/journal.pone.0111577
 20. Ding Y, Virlouvet L, Liu N, Riethoven JJM, Fromm M, and Avramova Z (2014)
     Dehydration stress memory genes of Zea mays; comparison with Arabidopsis
     thaliana. PLoS ONE 11/2014; 9(11):e111577. DOI:10.1371/journal.pone.0111577
 21. Blanc G, Mozar M, Agarkova IV, Gurnon JR, Yanai-Balser G, Rowe JM, Xia Y,
     Riethoven JJ, Dunigan DD, Van Etten JL (2014) Deep RNA sequencing reveals
     hidden features and dynamics of early gene transcription in Paramecium
     bursaria chlorella virus 1. PLoS One. 2014 Mar 7;9(3):e90989. doi:
     10.1371/journal.pone.0090989. eCollection 2014.
 22. Massilamany C, Gangaplara A, Basavalingappa RH, Rajasekaran RA, Vu H,
     Riethoven JJ, Steffen D, Pattnaik AK, Reddy J. (2015) Mutations in the 5'
     NTR and the Non-Structural Protein 3A of the Coxsackievirus B3 Selectively
     Attenuate Myocarditogenicity. PLoS One. 2015 Jun 22;10(6):e0131052. doi:
     10.1371/journal.pone.0131052 PMID 26098885
 23. Virdi KS, Laurie JD, Xu YZ, Yu J, Shao MR, Sanchez R, Kundariya H, Wang D,
     Riethoven JJ, Wamboldt Y, Arrieta-Montiel MP, Shedge V, Mackenzie SA.
     (2015) Arabidopsis MSH1 mutation alters the epigenome and produces
     heritable changes in plant growth. Nat Commun. 2015 Feb 27;6:6386. doi:
     10.1038/ncomms7386
 24. Zhen Wang, Juan Armando Casas-Mollano, Jianping Xu, Jean-Jack M. Riethoven,
     Chi Zhang, and Heriberto Cerutti (2015) Osmotic stress induces
     phosphorylation of histone H3 at threonine 3 in pericentromeric regions of
     Arabidopsis thaliana. PNAS (e-pub ahead of print) doi:
     10.1073/pnas.1423325112
 25. Vellichirammal NN, Wang H, Eyun S, Moriyama EN, Coates BS, Miller NJ,
     Siegfried BD (2015) Transcriptional analysis of susceptible and resistant
     European corn borer strains and their response to Cry1F protoxin. BMC
     Genomics 16:558
 26. Wei HH, Rowe M, Riethoven JJ, Grove R, Adamec J, Jikumaru Y, Staswick P.
     Overaccumulation of γ-Glutamylcysteine in a Jasmonate-Hypersensitive
     Arabidopsis Mutant Causes Jasmonate-Dependent Growth Inhibition.  Plant
     Physiol. 2015 Oct;169(2):1371-81. doi:0.1104/pp.15.00999. Epub 2015 Aug 17.
     PMID: 26282239
 27. Nguyen, A., Beyersdorf, J., Riethoven, J.-J. and Pannier, A. K. (2016),
     High-throughput screening of clinically approved drugs that prime
     polyethylenimine transfection reveals modulation of mitochondria
     dysfunction response improves gene transfer efficiencies. Bioengineering &
     Translational Medicine. doi:10.1002/btm2.10017
 28. Basavalingappa RH, Massilamany C, Krishnan B, Gangaplara A, Kang G,
     Khalilzad-Sharghi V, Han Z, Othman S, Li Q, Riethoven JJ, Sobel RA, Steffen
     D, Reddy J (2016). Identification of an Epitope from Adenine Nucleotide
     Translocator 1 That Induces Inflammation in Heart in A/J Mice. Am J Pathol.
     2016 Dec;186(12):3160-3175. doi: 10.1016/j.ajpath.2016.08.005. PMID:
     27876151
 29. Jia, Q., G. Li, T. G. Kollner, J. Fu, X. Chen, W. Xiong, B. J.
     Crandall-Stotler, J. L. Bowman, D. J. Weston, Y. Zhang, L. Chen, Y. Xie, F.
     W. Li, C. J. Rothfels, A. Larsson, S. W. Graham, D. W. Stevenson, G. K.
     Wong, J. Gershenzon and F. Chen (2016). "Microbial-type terpene synthase
     genes occur widely in nonseed land plants, but not in seed plants." Proc
     Natl Acad Sci U S A 113(43): 12328-12333.
 30. Chen, X., T. G. Kollner, Q. Jia, A. Norris, B. Santhanam, P. Rabe, J. S.
     Dickschat, G. Shaulsky, J. Gershenzon and F. Chen (2016). "Terpene synthase
     genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae."
     Proc Natl Acad Sci U S A 113(43): 12132-12137.
 31. Kumar, S., C. Kempinski, X. Zhuang, A. Norris, S. Mafu, J. Zi, S. A. Bell,
     S. E. Nybo, S. E. Kinison, Z. Jiang, S. Goklany, K. B. Linscott, X. Chen,
     Q. Jia, S. D. Brown, J. L. Bowman, P. C. Babbitt, R. J. Peters, F. Chen and
     J. Chappell (2016). "Molecular Diversity of Terpene Synthases in the
     Liverwort Marchantia polymorpha." Plant Cell 28(10): 2632-2650.
 32. Yuan Z, Kang G, Ma F, Lu W, Fan W, Fennessey CM, Keele BF, Li Q (2016).
     Recapitulating Cross-Species Transmission of Simian Immunodeficiency Virus
     SIVcpz to Humans by Using Humanized BLT Mice. J Virol. 2016 Aug
     12;90(17):7728-39. doi: 10.1128/JVI.00860-16. Print 2016 Sep 1.
 33. Basavalingappa RH, Massilamany C, Krishnan B, Gangaplara A, Kang G,
     Khalilzad-Sharghi V, Han Z, Othman S, Li Q, Riethoven JJ, Sobel RA, Steffen
     D, Reddy J (2016). Identification of an Epitope from Adenine Nucleotide
     Translocator 1 That Induces Inflammation in Heart in A/J Mice. Am J Pathol.
     2016 Dec;186(12):3160-3175. doi: 10.1016/j.ajpath.2016.08.005. PMID:
     27876151
 34. Eyun S, Soh HY, Posavi M, Munro J, Remfert J, Hughes DST, Murali SC, Qu J,
     Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneli H, Worley KC, Muzny DM,
     Park EO, Silva JC, Richards S, Gibbs RA, Lee CE (2017) Evolutionary history
     of chemosensory-related gene families across the Arthropoda. Molecular
     Biology and Evolution, Volume 34, Issue 8, pp 1838–1862,
     https://doi.org/10.1093/molbev/msx147
 35. Eyun, S. (2017) Phylogenomic analysis of Copepoda (Arthropoda, Crustacea)
     reveals unexpected similarities with earlier proposed morphological
     phylogenies. BMC Evolutionary Biology 17:23
     https://doi.org/10.1186/s12862-017-0883-5
 36. Wang H, Eyun S, Arora K, Tan SY, Gandra P, Moriyama E, Khajuria C,
     Jurzenski J, Li H, Donahue M, Narva K, Siegfried B (2017) Patterns of Gene
     Expression in Western Corn Rootworm (Diabrotica virgifera virgifera)
     Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on
     Next-Generation Sequencing. Toxins 2017, 9(4), 124;
     doi:10.3390/toxins9040124
 37. Quispe, C. F., A. Esmael, O. Sonderman, M. McQuinn, I. Agarkova, M. Battah,
     G. A. Duncan, D. D. Dunigan, T. P. Smith, C. De Castro, I. Speciale, F. Ma
     and J. L. Van Etten (2017). "Characterization of a new chlorovirus type
     with permissive and non-permissive features on phylogenetically related
     algal strains." Virology 500: 103-113
 38. Nissimov, J. I., A. Pagarete, F. Ma, S. Cody, D. D. Dunigan, S. A. Kimmance
     and M. J. Allen (2017). "Coccolithoviruses: A Review of Cross-Kingdom
     Genomic Thievery and Metabolic Thuggery." Viruses 9(3): 52
 39. Yuan, Z., F. Ma, A. J. Demers, D. Wang, J. Xu, M. G. Lewis and Q. Li
     (2017). "Characterization of founder viruses in very early SIV rectal
     transmission." Virology 502: 97-105.
 40. Lu, W., Y. Wan, F. Ma, R. P. Johnson and Q. Li (2017). "Distinct
     transcriptome profiles of Gag-specific CD8+ T cells temporally correlated
     with the protection elicited by SIVΔnef live attenuated vaccine." PloS one
     12(3): e0173929.
 41. Wijesena HR, Lents CA, Trenhaile-Grannemann MD, Riethoven JJ, Keel BN,
     Thorson JF, Miller PS, Johnson RK, Spangler ML, Kachman SD and Ciobanu DC
     (2017) Using Genomic Approaches to Uncover Sources of Variation in Age at
     Puberty and Reproductive Longevity in Sows. Journal of Animal Science 2017
     95: supplement2: 12-12. doi:10.2527/asasmw.2017.027. Epub ahead of print
     Apr 2017.
 42. Krishnan B, Massilaman C, Basavalingappa R, Gangaplara A, Kang G, Li Q,
     Uzal F, Strande J, Delhon G, Riethoven JJ, Steffen D, Reddy J (2017)
     Branched chain α-ketoacid dehydrogenase kinase 111-130, a T cell epitope
     that induces both autoimmune myocarditis and hepatitis in A/J mice. Immun
     Inflamm Dis. 2017 Dec;5(4):421-434. doi: 10.1002/iid3.177. Epub 2017 Jun 9.
 43. Basavalingappa, R. H., C. Massilamany, B. Krishnan, A. Gangaplara, R. A.
     Rajasekaran, M. Z. Afzal, J.-J. Riethoven, J. L. Strande, D. Steffen and J.
     Reddy (2017). β1-Adrenergic Receptor Contains Multiple IAk and IEk Binding
     Epitopes That Induce T Cell Responses with Varying Degrees of Autoimmune
     Myocarditis in A/J Mice. Frontiers in Immunology 8(1567).
     https://doi.org/10.3389/fimmu.2017.01567
 44. Krishnan, B., C. Massilamany, R. H. Basavalingappa, A. Gangaplara, R. A.
     Rajasekaran, M. Z. Afzal, V. Khalilzad-Sharghi, Y. Zhou, J. J. Riethoven,
     S. S. Nandi, P. K. Mishra, R. A. Sobel, J. L. Strande, D. Steffen and J.
     Reddy (2018). "Epitope Mapping of SERCA2a Identifies an Antigenic
     Determinant That Induces Mainly Atrial Myocarditis in A/J Mice." J Immunol
     200(2): 523-537. DOI: https://doi.org/10.4049/jimmunol.1701090
 45. Sinha R, Clarke J, Riethoven J. Metabolic Syndrome, Gut Microbiome and
     Dietary Bioactive Peptides, an Unexplored Triad. Diabesity, v. 4, n. 1, p.
     1-4, jan. 2018. ISSN 2369-0569.
     doi:http://dx.doi.org/10.15562/diabesity.2018.45.
 46. Kopf JC; Suhr MJ; Clarke J; Eyun S; Riethoven JJM; Ramer-Tait AE; Rose DJ
     (2018) Role of whole grains versus fruits and vegetables in reducing
     subclinical inflammation and promoting gastrointestinal health in
     individuals affected by overweight and obesity: a randomized controlled
     trial. Nutrition Journal 2018 17:72
     https://doi.org/10.1186/s12937-018-0381-7
 47. Manca, S., C. P. Frisbie, C. A. LaGrange, C. A. Casey, J.-J. M. Riethoven
     and A. Petrosyan (2018). "The Role of Alcohol-induced Golgi Fragmentation
     for Androgen Receptor Signaling in Prostate Cancer." Molecular Cancer
     Research. DOI: 10.1158/1541-7786.MCR-18-0577
 48. Hovde, B. T., E. R. Hanschen, C. R. Steadman Tyler, C.-C. Lo, Y. Kunde, K.
     Davenport, H. Daligault, J. Msanne, S. Canny, S.-i. Eyun, J.-J. M.
     Riethoven, J. Polle and S. R. Starkenburg (2018). "Genomic characterization
     reveals significant divergence within Chlorella sorokiniana (Chlorellales,
     Trebouxiophyceae)." Algal Research 35: 449-461.
     https://doi.org/10.1016/j.algal.2018.09.012
 49. Petrosyan A, Frisbie C, Lushnikov A, Krasnoslobodtsev A, Stepchenkova S,
     Riethoven JJM, Clarke J (2019) Post-ER stress biogenesis of Golgi is
     governed by giantin. Cells 2019, 8(12), 1631;
     https://doi.org/10.3390/cells8121631
 50. Jia, Q., Chen, X., Köllner, T.G. et al. Terpene Synthase Genes Originated
     from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid
     Diversity in Fungi. Sci Rep 9, 9223 (2019).
     https://doi.org/10.1038/s41598-019-45532-1
 51. Arumugam R, Yalaka B, Massilamany C, Haider Ali MSS, Lasrado N, Jayaraja S,
     Riethoven JJ, Sun X, Reddy J. An evidence for surface expression of an
     immunogenic epitope of sarcoplasmic/endoplasmic reticulum calcium-ATPase2a
     on antigen-presenting cells from naive mice in the mediation of autoimmune
     myocarditis. Immunobiology. 2020 Mar;225(2):151896. doi:
     10.1016/j.imbio.2019.12.005.
 52. Jayeshbhai Chaudhari; Chia-Sin Liew; Aspen Workman; Jean-Jack Riethoven;
     David Steffen; Sarah Sillman; Hiep Vu. Host Transcriptional Response to
     Persistent Infection with a Live-Attenuated Porcine Reproductive and
     Respiratory Syndrome Virus Strain. 2020, 12, 817 .
     https://doi.org/10.3390/v12080817
 53. Basavalingappa RH, Arumugam R, Lasrado N, Yalaka B, Massilamany C,
     Gangaplara A, Riethoven JJ, Xiang SH, Steffen D, Reddy J. Viral myocarditis
     involves the generation of autoreactive T cells with multiple antigen
     specificities that localize in lymphoid and non-lymphoid organs in the
     mouse model of CVB3 infection. Mol Immunol. 2020 Aug;124:218-228. doi:
     10.1016/j.molimm.2020.06.017. Epub 2020 Jun 29. PMID: 32615275; PMCID:
     PMC7363587.
 54. Hiruni R Wijesena, Stephen D Kachman, Clay A Lents, Jean-Jack Riethoven,
     Melanie D Trenhaile-Grannemann, Tim J Safranski, Matthew L Spangler, Daniel
     C Ciobanu, Fine mapping genetic variants associated with age at puberty and
     sow fertility using SowPro90 genotyping array, Journal of Animal Science,
     Volume 98, Issue 10, October 2020, skaa293,
     https://doi.org/10.1093/jas/skaa293
 55. Liew, C., Courtney, S., de Lange, P. J. & Pelser, P. B. (2021). Taxonomic
     realignment of Senecio glaucophyllus (Asteraceae; Senecioneae) necessitates
     a new name for a widespread New Zealand species. New Zealand Journal of
     Botany, DOI: 10.1080/0028825X.2020.1866030.
 56. Chaudhari J, Liew CS, Riethoven JM, Sillman S, Vu HLX. Porcine Reproductive
     and Respiratory Syndrome Virus Infection Upregulates Negative Immune
     Regulators and T-Cell Exhaustion Markers. J Virol. 2021 Oct
     13;95(21):e0105221. doi: 10.1128/JVI.01052-21. Epub 2021 Aug 11. PubMed
     PMID: 34379512; PubMed Central PMCID: PMC8513478.
 57. Khan AL, Asaf S, Numan M, AbdulKareem NM, Imran M, Riethoven JM, Kim HY,
     Al-Harrasi A, Schachtman DP, Al-Rawahi A, Lee IJ. Transcriptomics of
     tapping and healing process in frankincense tree during resin production.
     Genomics. 2021 Nov;113(6):4337-4351. doi: 10.1016/j.ygeno.2021.11.020. Epub
     2021 Nov 16. PubMed PMID: 34798281.
 58. Pachikov AN, Gough RR, Christy CE, Morris ME, Casey CA, LaGrange CA, Bhat
     G, Kubyshkin AV, Fomochkina II, Zyablitskaya EY, Makalish TP, Golubinskaya
     EP, Davydenko KA, Eremenko SN, Riethoven JM, Maroli AS, Payne TS, Powers R,
     Lushnikov AY, Macke AJ, Petrosyan A. The non-canonical mechanism of ER
     stress-mediated progression of prostate cancer. J Exp Clin Cancer Res. 2021
     Sep 14;40(1):289. doi: 10.1186/s13046-021-02066-7. PubMed PMID: 34521429;
     PubMed Central PMCID: PMC8439065.
 59. Abid, M.S.R., Qiu, H., Tripp, B.A., de Lima Leite, A., Roth, H.E., Adamec,
     J., Powers, R., Checco, J.W. Peptidomics analysis reveals changes in small
     urinary peptides in patients with interstitial cystitis/bladder pain
     syndrome. Sci Rep 12, 8289 (2022).
     https://doi.org/10.1038/s41598-022-12197-2
 60. Wang P, Lopes LD, Lopez-Guerrero MG, van Dijk K, Alvarez S, Riethoven JJ,
     Schachtman DP. Natural variation in root exudation of GABA and DIMBOA
     impacts the maize root endosphere and rhizosphere microbiomes. J Exp Bot.
     2022 May 11:erac202. doi: 10.1093/jxb/erac202. Epub ahead of print. PMID:
     35552399.
 61. Khan AL, Al-Harrasi A, Wang J, Asaf S, Riethoven JJM, Shehzad T, Liew C,
     Song X, Schachtman DP, et al. Genome Structure and Evolutionary History of
     Frankincense producing Boswellia sacra. iScience: 104574 2022. doi:
     10.1016/j.isci.2022.104574
 62. Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven,
     Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy,
     Andrew C. Chang, David G. Beer, Laura A. Kresty, Characterizing Isoform
     Switching Events in Esophageal Adenocarcinoma, Molecular Therapy - Nucleic
     Acids, 2022, ISSN 2162-2531, https://doi.org/10.1016/j.omtn.2022.08.018.
 63. Shafieifini M, Sun Y, Staley ZR, Riethoven JJ, Li X. Effects of Nutrient
     Level and Growth Rate on the Conjugation Process That Transfers Mobile
     Antibiotic Resistance Genes in Continuous Cultures. Appl Environ Microbiol.
     2022 Sep 12:e0112122. doi: 10.1128/aem.01121-22. Epub ahead of print. PMID:
     36094214.
 64. de Lange, P. J., Pelser, P. B., Liew, C.-S., & Marshall, A. J. (2022).
     Senecio pokohinuensis (Asteraceae), a new combination for an endemic
     species of Mokohinau Islands, Hauraki Gulf (Tikapa Moana o Hauraki),
     northern Te Ika a Maui/North Island, Aotearoa/New Zealand. Ukrainian
     Botanical Journal, 79(3), 125-129. https://doi.org/10.15407/ukrbotj79.125
 65. Walker, K., Kalra, D.., Lowdon, R.., …, Liew, C.-S., …, Busby, B. (2022)
     The third international hackathon for applying insights into large-scale
     genomic composition to use cases in a wide range of organisms [version 1;
     peer review: 1 approved, 3 approved with reservations]. F1000Research,
     11:530. https://doi.org/10.12688/f1000research.110194.1
 66. Mousavi S, Qiu H, Heinis FI, Abid MSR, Andrews MT, Checco JW. Short-Term
     Administration of Common Anesthetics Does Not Dramatically Change the
     Endogenous Peptide Profile in the Rat Pituitary. ACS Chem Neurosci. 2022
     Sep 20. doi: 10.1021/acschemneuro.2c00359. Epub ahead of print. PMID:
     36126283.
 67. Salomon JD, Qiu H, Feng D, Owens J, Khailova L, Lujan SO, Iguidbashian J,
     Chhonker YS, Murry DJ, Riethoven JJ, Lindsey ML, Singh AB, Davidson JA.
     Piglet cardiopulmonary bypass induces intestinal dysbiosis and barrier
     dysfunction associated with systemic inflammation. Dis Model Mech. 2022 Nov
     25:dmm.049742. doi: 10.1242/dmm.049742. Epub ahead of print. PMID:
     36426663.
 68. Rasquinha MT, Lasrado N, Sur M, Mone K, Qiu H, Riethoven J-J, Sobel RA,
     Reddy J. A Monovalent Mt10-CVB3 Vaccine Prevents CVB4-Accelerated Type 1
     Diabetes in NOD Mice. Vaccines. 2023; 11(1):76.
     https://doi.org/10.3390/vaccines11010076
 69. Sakallioglu IT, Tripp B, Kubik J, Casey CA, Thomes P, Powers R. Multiomics
     Approach Captures Hepatic Metabolic Network Altered by Chronic Ethanol
     Administration. Biology. 2023; 12(1):28.
     https://doi.org/10.3390/biology12010028
 70. Mousavi S, Qiu H, Andrews MT*, Checco JW*. “Peptidomic analysis reveals
     seasonal neuropeptide and peptide hormone changes in the hypothalamus and
     pituitary of a hibernating mammal” ACS Chem. Neurosci. (2023) Article ASAP.
     DOI:10.1021/acschemneuro.3c00268
 71. Macke AJ, Pachikov AN, Divita TE, Morris ME, LaGrange CA, Holzapfel MS,
     Kubyshkin AV, Zyablitskaya EY, Makalish TP, Eremenko SN, Qiu H, Riethoven
     JM, Hemstreet GP, Petrosyan A. Targeting the ATF6-mediated ER stress
     response and autophagy blocks integrin-driven prostate cancer progression.
     Mol Cancer Res. 2023 Jun 14:MCR-23-0108. doi:
     10.1158/1541-7786.MCR-23-0108. Epub ahead of print. PMID: 37314749.
 72. VanOrmer M, Thompson M, Thoene M, Riethoven J-J, Natarajan SK, Hanson C, et
     al. (2024) The impact of iron supplementation on the preterm neonatal gut
     microbiome: A pilot study. PLoS ONE 19(2): e0297558.
     https://doi.org/10.1371/journal.pone.0297558
 73. Sun Y, Staley ZR, Woodbury B, Riethoven J-J, Li X. Composting reduces the
     risks of resistome in beef cattle manure at the transcriptional level. Appl
     Environ Microbiol. 2024 Mar 6:e0175223. doi: 10.1128/aem.01752-23. Epub
     ahead of print. PMID: 38445903.
 74. Abid, M.S.R., Qiu, H., Checco, J.W. (2024). Label-Free Quantitation of
     Endogenous Peptides. In: Schrader, M., Fricker, L.D. (eds) Peptidomics.
     Methods in Molecular Biology, vol 2758. Humana, New York, NY.
     https://doi.org/10.1007/978-1-0716-3646-6_7

ADVISORY COMMITTEE

The Bioinformatics Core advisory committee meets once a year (or more as needed)
and consists of the following faculty:

Jennifer Clarke, Ph.D.
Phone: (402) 472-2512
Email: jclarke3@unl.edu
Visit Faculty Webpage

Daniel Ciobanu, Ph.D.
Phone: (402) 472-8066
Email: dciobanu@unl.edu
Visit Faculty Webpage

Juan Cui, PhD
Phone: (402) 472-5023
Email: jcui@unl.edu
Visit Faculty Webpage

CONTACT THE CORE STAFF

For technical help with bioinformatics software and databases, and analyses
using them on the Holland Computing Cluster, we are glad to help out for up to 3
hours gratis per year per faculty. Please use the email listed below to initiate
such help; one of us will contact you within a business day. For larger or
scientific help, or to initiate discussion on projects, please contact the
Director directly instead.

Email Bioinformatics Technical Support

CONTACT THE DIRECTOR

Jean-Jack M. Riethoven
BEAD E204
Phone: +1 402-472-7949
Fax: +1 402-472-3139

Email Jean-Jack






CONTACT US

N300 Beadle Center
1901 Vine St
Lincoln, NE 68588-0665

402-472-1384

402-472-3139


RELATED LINKS

 * Agronomy & Horticulture
 * Beadle Business Center
 * Room Reservations
 * Biochemistry
 * Biological Sciences
 * Center for Plant Science Innovation
 * IANR
 * Plant Pathology
 * UNL Events Calendar


CAMPUS LINKS

 * Directory
 * Employment
 * Events
 * Libraries
 * Maps
 * News
 * Office of the Chancellor
 * Report an Incident
   


POLICIES & REPORTS

 * Accessibility Statement
 * Institutional Equity and Compliance
 * Notice of Nondiscrimination
 * Privacy Policy
 * Safety at Nebraska
 * Student Information Disclosures

UNL web framework and quality assurance provided by the Web Developer Network ·
QA Test
University of Nebraska–Lincoln
Established 1869 · Copyright 2024

Some parts of this site work best with JavaScript enabled.

Email Us




SEARCH FORM

Search
Submit
Close