Bioinformatics

Bioinformatics
BIOINFORMATICS

Services

The UNL 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 (Java, Perl, VBA) 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 $46 $70 $140
Differential gene expression analysis (microarray) 1) $46 $70 $140
Differential gene expression analysis (next-gen sequences) per comparison 1) $155 $230 $465
Go term enrichment analysis (per list) 1) $40 $60 $120
Ortholog/homolog detection (between two species) $81 $122 $245
Metagenomic analysis (per sample) $81 + $122 + $245 +
Phylogenetic analysis $81 + $122 + $245 +
Transcriptome assembly (de-novo or guided) $278 + $417 + $835 +
Bacterial genome assembly (de-novo or guided) $155 + $233 + $465 +
Viral/bacteriophage genome assembly (pure sample) $115 + $173 + $345 +
Viral/bacteriophage genome assembly (contaminated or sample includes host) $278 + $417 + $835 +
Archae genome assembly (de-novo or guided) $237 + $356 + $710 +
Eukaryotic genome assembly (de-novo or guided) $949 + $1,425 + $2,850 +
Data deposition of microarray, next-gen, transcriptomes or genomes (per deposition) to public database $196 $294 $560
Publication-ready graph of any of the above analyses $40 $60 $120
1) Per analysis (not per sample) additional cost for sparsely annotated species $200 $300 $600

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 fiscal year.
SERVICE DESCRIPTIONUNIV. NEBRASKA NON-PROFIT/GOVERNMENT COMMERCIAL
Custom programming/analysis (less than 10 hours) $40 / h $70 / h $140 / h
Custom analysis (more than 10 hours) Ask for quote
System administration per hosted server or storage cabinet (per year) $500 N/A N/A

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 250 CPU cores, 600GB 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 Sun Grid Engine 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 backend machines are hosting several UNL database-driven research web sites.

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.

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

Qidong Jia (Bioinformatician)
BEAD E206
Phone: +1 402-472-1572
Email Qidong

Previous members

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)

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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.

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.

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.

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.

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

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

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

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

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

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

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.

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.

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.

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.

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

Advisory Committee

The Bioinformatics Core advisory committee 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