University of Nebraska–Lincoln
Jean-Jack Riethoven
Nebraska Center ofr Biotechnology
1901 Vine Street
Lincoln, NE 68588
https://biotech.unl.edu/bioinformatics
RRID: RRID:SCR_025011
Computational - Application Development
Computational - Bioinformatics
Computational - Biostatistics
Computational - High Performance Computing
Computational - Interactive Compute/storage
Consultation
Consultations
Data Analysis
Data Analysis And Interpretation
Data Processing
Data Processing And Interpretation
Data Visualization
Genome/Transcriptome Assembly And Annotation
Genomics
High Performance Computing
Metagenomics Analysis
Metatranscriptomics
Methylation Analysis
Microbiome
Pipeline Development
Power Analysis
Proteomics Analysis
Quantitative DNA Sequence Mapping
RNA analysis
Single-Cell Analysis
Spatial / Single Cell Data Analysis
Spatial Transcriptomics
1.) 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 (2023 Sep 1). Targeting the ATF6-Mediated ER Stress Response and Autophagy Blocks Integrin-Driven Prostate Cancer Progression. Molecular cancer research : MCR, 21(9), 958-974. . ID: 37314749.
2.) Salomon JD, Qiu H, Feng D, Owens J, Khailova L, Osorio Lujan S, Iguidbashian J, Chhonker YS, Murry DJ, Riethoven JJ, Lindsey ML, Singh AB, Davidson JA (2023 May 1). Piglet cardiopulmonary bypass induces intestinal dysbiosis and barrier dysfunction associated with systemic inflammation. Disease models & mechanisms, 16(5), . . ID: 36426663.
3.) Rasquinha MT, Lasrado N, Sur M, Mone K, Qiu H, Riethoven JJ, Sobel RA, Reddy J (2022 Dec 29). A Monovalent Mt10-CVB3 Vaccine Prevents CVB4-Accelerated Type 1 Diabetes in NOD Mice. Vaccines, 11(1), . . ID: 36679922.
4.) Shafieifini M, Sun Y, Staley ZR, Riethoven JJ, Li X (2022 Oct 11). Effects of Nutrient Level and Growth Rate on the Conjugation Process That Transfers Mobile Antibiotic Resistance Genes in Continuous Cultures. Applied and environmental microbiology, 88(19), e0112122. . ID: 36094214.
5.) Zhang Y, Weh KM, Howard CL, Riethoven JJ, Clarke JL, Lagisetty KH, Lin J, Reddy RM, Chang AC, Beer DG, Kresty LA (2022 Sep 13). Characterizing isoform switching events in esophageal adenocarcinoma. Molecular therapy. Nucleic acids, 29(), 749-768. . ID: 36090744.
6.) Wang P, Lopes LD, Lopez-Guerrero MG, van Dijk K, Alvarez S, Riethoven JJ, Schachtman DP (2022 Aug 11). Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes. Journal of experimental botany, 73(14), 5052-5066. doi: 10.1093/jxb/erac202. ID: 35552399.
7.) Khan AL, Al-Harrasi A, Wang JP, Asaf S, Riethoven JM, Shehzad T, Liew CS, Song XM, Schachtman DP, Liu C, Yu JG, Zhang ZK, Meng FB, Yuan JQ, Wei CD, Guo H, Wang X, Al-Rawahi A, Lee IJ, Bennetzen JL, Wang XY (2022 Jul 15). Genome structure and evolutionary history of frankincense producing Boswellia sacra. iScience, 25(7), 104574. . ID: 35789857.
8.) Khan AL, Asaf S, Numan M, AbdulKareem NM, Imran M, Riethoven JM, Kim HY, Al-Harrasi A, Schachtman DP, Al-Rawahi A, Lee IJ (2021 Nov). Transcriptomics of tapping and healing process in frankincense tree during resin production. Genomics, 113(6), 4337-4351. doi: 10.1016/j.ygeno.2021.11.020. ID: 34798281.
9.) Chaudhari J, Liew CS, Riethoven JM, Sillman S, Vu HLX (2021 Oct 13). Porcine Reproductive and Respiratory Syndrome Virus Infection Upregulates Negative Immune Regulators and T-Cell Exhaustion Markers. Journal of virology, 95(21), e0105221. . ID: 34379512.
10.) 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 (2021 Sep 14). The non-canonical mechanism of ER stress-mediated progression of prostate cancer. Journal of experimental & clinical cancer research : CR, 40(1), 289. . ID: 34521429.
11.) Wijesena HR, Kachman SD, Lents CA, Riethoven JJ, Trenhaile-Grannemann MD, Safranski TJ, Spangler ML, Ciobanu DC (2020 Oct 1). Fine mapping genetic variants associated with age at puberty and sow fertility using SowPro90 genotyping array. Journal of animal science, 98(10), . . ID: 32888012.
12.) Basavalingappa RH, Arumugam R, Lasrado N, Yalaka B, Massilamany C, Gangaplara A, Riethoven JJ, Xiang SH, Steffen D, Reddy J (2020 Aug). 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. Molecular immunology, 124(), 218-228. . ID: 32615275.
13.) Chaudhari J, Liew CS, Workman AM, Riethoven JM, Steffen D, Sillman S, Vu HLX (2020 Jul 28). Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain. Viruses, 12(8), . . ID: 32731586.
14.) Arumugam R, Yalaka B, Massilamany C, Haider Ali MSS, Lasrado N, Jayaraja S, Riethoven JJ, Sun X, Reddy J (2020 Mar). 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, 225(2), 151896. . ID: 31870642.
15.) Frisbie CP, Lushnikov AY, Krasnoslobodtsev AV, Riethoven JM, Clarke JL, Stepchenkova EI, Petrosyan A (2019 Dec 13). Post-ER Stress Biogenesis of Golgi Is Governed by Giantin. Cells, 8(12), . . ID: 31847122.
16.) Manca S, Frisbie CP, LaGrange CA, Casey CA, Riethoven JM, Petrosyan A (2019 Jan). The Role of Alcohol-Induced Golgi Fragmentation for Androgen Receptor Signaling in Prostate Cancer. Molecular cancer research : MCR, 17(1), 225-237. . ID: 30224543.
17.) Kopf JC, Suhr MJ, Clarke J, Eyun SI, Riethoven JM, Ramer-Tait AE, Rose DJ (2018 Jul 30). 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, 17(1), 72. . ID: 30060746.
18.) Krishnan B, Massilamany C, Basavalingappa RH, Gangaplara A, Rajasekaran RA, Afzal MZ, Khalilzad-Sharghi V, Zhou Y, Riethoven JJ, Nandi SS, Mishra PK, Sobel RA, Strande JL, Steffen D, Reddy J (2018 Jan 15). Epitope Mapping of SERCA2a Identifies an Antigenic Determinant That Induces Mainly Atrial Myocarditis in A/J Mice. Journal of immunology (Baltimore, Md. : 1950), 200(2), 523-537. . ID: 29229678.
19.) Wijesena HR, Lents CA, Riethoven JJ, Trenhaile-Grannemann MD, Thorson JF, Keel BN, Miller PS, Spangler ML, Kachman SD, Ciobanu DC (2017 Sep). GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows. Journal of animal science, 95(9), 4196-4205. doi: 10.2527/jas2016.1334. ID: 28992028.
20.) Basavalingappa RH, Massilamany C, Krishnan B, Gangaplara A, Rajasekaran RA, Afzal MZ, Riethoven JJ, Strande JL, Steffen D, Reddy J (2017). β1-Adrenergic Receptor Contains Multiple IA(k) and IE(k) Binding Epitopes That Induce T Cell Responses with Varying Degrees of Autoimmune Myocarditis in A/J Mice. Frontiers in immunology, 8(), 1567. . ID: 29209317.
The UNL Bioinformatics Core Research Facility (BCRF_ helps researchers, both in academic institutions and for-profits, with the analysis of 'omics data and the integration thereof. We offer, inter alia, gene expression analysis, single-cell/nuclei RNA-seq analysis, transcriptome and genome assembly with gene prediction and annotation, and statistical analysis.
