Bioinformatics

Bioinformatics
BIOINFORMATICS

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
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  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.

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