BIOINFORMATICS & BIOSTATISTICS CORE

Overview

The Bioinformatics and Biostatistics Core provides comprehensive, high-quality bioinformatics and statistics expertise for Van Andel Institute and external organizations.

The Core develops and maintains automated and customizable workflows for processing and analyzing many types of genomic data; supports the design of rational, robust and reproducible experiments and proposals; assists in the preparation of manuscripts, grants and presentations; and provides education and training in the use of cutting-edge software and analysis methods. The Core can contribute to many types of bioinformatics or statistical projects.

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Our Impact

We’re raising thousands to save millions.

We’re turning hope into action for the millions of people around the world affected by diseases like cancer and Parkinson’s. Find out how you can help us make a difference.

  • 171 studies published from Nov. 1, 2020 to Oct. 1, 2021
  • 68 studies in high-impact journals from Nov. 1, 2020-Oct. 1, 2021
  • 41 clinical trials launched

Services include

Statistical consulting

 

Experimental design

  • Research proposal development
  • Sample size determination
  • Randomization procedures

Manuscript preparation and data deposition

 

Genome variant identification, annotation and visualization

 

Analysis of high-throughput or genome-scale data

  • Bulk and single-cell RNA-Seq and differential gene expression
  • ChIP-Seq, ATAC-Seq, CUT&RUN
  • Spatial molecular profiling
  • Whole Genome Bisulfite Sequencing (WGBS)
  • Metabolomics and lipidomics

Systems-level bioinformatics

  • Gene Over Representation Analysis (ORA)
  • Gene Set Enrichment Analysis (GSEA)
  • Interaction networks
  • Functional enrichment analysis
  • Pathway analysis

Analysis, interpretation and presentation of data

  • Time-series
  • Tumor growth
  • Drug response

Genome assembly and annotation

 

Joint analysis of multiple genomic data sets

 

Custom application and tool development

For more information on services and pricing, please contact Bioinformatics and Biostatistics Core at bbc@vai.org.

SELECTED PUBLICATIONS

A full list of publications is available here.

2022

Wiseman AK, Tiedemann RL, Fan H, Shen H, Madaj Z, McCabe MT, Pappalardi MB, Jones PA. 2022. Chromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMTi. Commun Biol 5:528.

Paul EN, Grey JA, Carpenter TJ, Madaj ZB, Lau KH, Givan SA, Burns GW, Chandler RL, Wegienka GR, Shen H, Teixeira JM. 2022. Transcriptome and DNA methylome analyses reveal underlying mechanisms for the racial disparity in uterine fibroids. JCI Insight.

Yang CH*, Fagnocchi L*, Apostle S, Wegert V, Casani-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Brás J, Thomasen M, Grunnert LG, Vaag AA, Gillberg L, Grundberg, E, Conesa A, Körner A, PERMUTE, Pospisilik JA. 2022. Independent phenotypic plasticity axes define distinct obesity subtypesNat Metab.

*Co-first authorship
**Highlighted in News & Views
***Core members Zachary Madaj and Emily Wolfrum are part of PERMUTE

2021

Neman J, Franklin M, Madaj ZB, Deshpande K, Triche Jr TJ, Sadlik G, Carmichael JD, Chang E, Yu C, Strickland BA, Zada G. 2021. Use of predictive spatial modeling to reveal that primary cancers have distinct central nervous system topography patterns of brain metastasis . J Neurosurg.

Waldhart AN, Muhire B, Johnson B, Pettinga D, Madaj ZBWolfrum E, Dysktra H, Wegert V, Pospisilik JA, Han X, Wu N. 2021. Excess dietary carbohydrate affects mitochondrial integrity as observed in brown adipose tissueCell Rep 35(5):109488.

Carpenter BL, Remba TK, Thomas SL, Madaj ZB, Brink L, Tiedemann RL, Odendaal HJ, Jones PA. 2021. Ooctye age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA (nc886)Proc Natl Acad Sci U S A 118(12):e2026580118.

Chassé MH, Johnson BK, Boguslawski EA, Sorensen KM, Rosien JE, Kang MH, Reynolds CP, Heo L, Madaj ZBBeddows I, Foxa GE, Kitchen-Goosen SM, Williams BO, Triche TJ Jr, Grohar PJ. 2021. Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor. EMBO Mol Med 13(2):e12640.

Bagchi A, Madaj Z, Engel KB, Guan P, Rohrer DC, Valley DR, Wolfrum E, Feenstra K, Roche N, Hostetter G, Moore HM, Jewell SD. 2021. Impact of preanalytical factors on the measurement of tumor tissue biomarkers using immunohistochemistryJ Histochem Cytochem.

2020

Grit JL, Pridgeon MG, Essenburg CJ, Wolfrum E, Madaj ZB, Turner L, Wulfkuhle J, Petricoin EF 3rd, Graveel CR, Steensma MR. 2020. Kinome profiling of NF1-related MPNSTs in response to kinase inhibition and doxorubicin reveals therapeutic vulnerabilitiesGenes (Basel) 11(3):331

Marshall LL, Killinger BA, Ensink E, Li P, Li KX, Cui W, Lubben N, Weiland M, Wang X, Gordevicius J, Coetzee GA, Ma J, Jovinge S, Labrie V. 2020. Epigenomic analysis of Parkinson’s disease neurons identifies Tet2 loss as neuroprotectiveNat Neuro.

Diegel CR, Hann S, Ayturk UM, Hu JCW, Lim K, Droscha CJ, Madaj ZB, Foxa GE, Izaguirre I, VAI Vivarium and Transgenics Core, Paracha N, Pidhaynyy B, Dowd TL, Robling AG, Warman ML, Williams BO. 2020. An osteocalcin-deficient mouse strain without endocrine abnormalitiesPLOS Genet.

Flores G, Everett JH, Boguslawski EA, Oswald BM, Madaj ZBBeddows I, Dikalov S, Adams M, Klumpp-Thomas CA, Kitchen-Goosen SM, Martin SE, Caplen NJ, Helman LJ, Grohar PJ. 2020. CDK9 blockade exploits context-dependent transcriptional changes to improve activity and limit toxicity of mithramycin for Ewing sarcomaMol Cancer Ther.

2019

George JW, Fan H, Johnson B, Carpenter TJ, Foy KK, Chatterjee A, Patterson AL, Koeman J, Adams M, Madaj ZB, Chesla D, Marsh EE, Triche TJ, Shen H, Teixeira JM. 2019. Integrated epigenome, exome, and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroidsCell Rep.

Chatterjee D, Sanchez DS, Quansah E, Rey NL, George S, Becker K, Madaj ZB, Steiner JA, Ma J, Escobar Galvis ML, Kordower JH, Brundin P. 2019. Loss of one engrailed1 allele enhances induced alpha-synucleinopathy J Parkinsons Dis 9(2):315–326.

Keaton SA, Madaj ZB, Heilman P, Smart L, Grit J, Gibbons R, Postolache TT, Roaten K, Achtyes ED, Brundin L. 2019. An inflammatory profile linked to increased suicided riskJ Affect Disord 247:57 65.

Harlow ML*, Chassé MH*, Boguslawski EA, Sorensen KM, Gedminas MJ, Goosen JM, Rothbart SB, Taslim C, Lessnick SL, Peck A, Madaj ZBBowman MJ, Grohar PJ. 2019. Trabectedin inhibits EWS-FLI1 and evicts SWI/SNF from chromatin in a schedule-dependent mannerClin Cancer Res.
*Equal contributions

2018

Carpenter BL*, Zhou W, Madaj Z, DeWitt AK, Ross JP, Grønbaek K, Liang G, Clark SJ, Molloy PL, Jones PA. 2018. Mother-child transmission of epigenetic information by tunable polymorphic imprintingProc Natl Acad Sci U S A.
*Co-first authors

Liu M, Thomas SL, DeWitt AK, Zhou W, Madaj ZB, Ohtani H, Baylin SB, Liang G, Jones PA. 2018. Dual inhibition of DNA and histone methyltransferases increases viral mimicry in ovarian cancer cellsCancer Res 78(20):5754–5766.

deCarvalho AC, Kim H, Poisson LM, Winn ME, Mueller C, Cherba D, Koeman J, Seth S, Protopopov A, Felicella M, Zheng S, Multani A, Jiang Y, Zhang J, Nam DH, Petricoin EF, Chin L, Mikkelsen T, Verhaak RGW. 2018. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastomaNat Genet 50(5):708–717.

Rey NL, George S, Steiner JA, Madaj Z, Luk KC, Trojanowski JQ, Lee VM, Brundin P. 2018. Spread of aggregates after olfactory bulb injection of α-synuclein fibrils is associated with early neuronal loss and is reduced long termActa Neuropathol 135(1):65–83.

Killinger BA*, Madaj Z*, Sikora JW, Rey N, Haas AJ, Vepa Y, Lindqvist D, Chen H, Thomas PM, Brundin P, Brundin L, Labrie V. 2018. The veriform appendix impacts the risk of developing Parkinson’sSci Transl Med 10(465):eaar5280.

Mukherjee A, Patterson AL, George JW, Carpenter TJ, Madaj ZB, Hostetter G, Risinger JI, Teixeira JM. 2018. Nuclear PTEN localization contributes to DNA damage response in endometrial adenocarcinoma and could have a diagnostic benefit for therapeutic management of the diseaseMol Cancer Ther.

Senchuk MM, Dues DJ, Schaar CE, Johnson BKMadaj ZBBowman MJWinn ME, Van Raamsdonk JM. 2018. Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegansPLoS Genet 14(3):e1007268.

Beddows I, Rose LE. 2018. Factors determining hybridization rates in plants: A case study in Michigan Perspec Plant Ecol Sys 34:51–60.

Peacock JD, Pridgeon MG, Tovar EA, Essenburg CJ, Bowman MJMadaj ZB, Koeman J, Boguslawski EA, Grit J, Dodd RD, Khachaturov V, Cardona DM, Chen M, Kirsch DG, Maina F, Dono R, Winn ME, Graveel CR, Steensma. 2018. Genomic status of MET potentiates sensitivity to MET and MEK inhibition in NF1-related malignant peripheral nerve sheath tumorsCancer Res 78(13):3672–3687.

2017

Waldhart AN, Dykstra H, Peck AS, Boguslawski EA, Madaj ZB, Wen J, Veldkamp K, Hollowell M, Zheng B, Cantley LC, McGraw TE, Wu N. 2017. Phosphorylation of TXNIP by AKT mediates acute influx of glucose in response to insulinCell Rep 19(10):2005–2013.

Dues DJ, Schaar CJ, Johnson BKBowman MJWinn ME, Senchuk MM, Van Raamsdonk JM. 2017. Uncoupling of oxidative stress resistance and lifespan in long-lived isp-1 mitochondrial mutants in Caenorhabditis elegansFree Radic Biol Med 108:362–373.

Martin KR, Zhou W, Bowman MJ, Shih J, Au KS, Dittenhafer-Reed KE, Sisson KA, Koeman J, Weisenberger DJ, Cottingham SL, DeRoos ST, Devinsky O, Winn ME, Cherniak AD, Shen H, Northrup H, Krueger DA, MacKeigan JP. 2017. The genomic landscape of tuberous sclerosis complexNat Commun 8:15816. 

2016

Harlow ML, Maloney N, Roland J, Guillen Navarro MJ, Easton MK, Kitchen-Goosen SM, Boguslawski EA, Madaj ZBJohnson BKBowman MJ, D’Incalci M, Winn ME, Turner L, Hostetter G, Galmarini CM, Aviles PM, Grohar PJ. 2016. Lurbinectedin inactivates the Ewing sarcoma oncoprotein EWS-FLI1 by redistributing it within the nucleusCancer Res 76(22):6657–6668.

Osgood CL, Tantawy MN, Maloney N, Madaj ZB, Peck A, Boguslawkski E, Jess J, Buck J, Winn ME, Manning HC, Grohar PJ. 2016. 18F-FLT positron emission tomography (PET) is a pharmacodynamic marker for EWS-FLI1 activity and Ewing sarcomaSci Rep 6:33926.

Osgood CL, Maloney N, Kidd CG, Kitchen-Goosen S, Segars L, Gebregiorigis M, Woldemichael GM, He M, Sankar S, Lessnick SL, Kang M, Smith M, Turner L, Madaj ZBWinn ME, Núnez LE, González-Sabin J, Helman LJ, Moris F, Grohar PJ. 2016. Identification of mithramycin analogues with improved targeting of the EWS-FLI1 transcription factorClin Cancer Res 22(16):4105–4118.

2015

Foley JM, Scholten DJ 2nd, Monks NR, Cherba D, Monsma DJ, Davidson P, Dylewski D, Dykema K, Winn ME, Steensma MR. 2015. Anoikis-resistant subpopulations of human osteosarcoma display significant chemoresistance and are sensitive to targeted epigenetic therapies predicted by expression profilingJ Transl Med 13(1):110.

Peacock JD, Dykema KJ, Toriello HV, Mooney MR, Scholten DJ 2nd, Winn ME, Borgman A, Duesbery NS, Hiemenga JA, Liu C, Campbell S, Nickoloff BP, Williams BO, Steensma MR. 2015. Oculoectodermal syndrome is a mosaic RASopathy associated with KRAS alterationsAm J Med Genet A 167(7):1429–1435.

Scott A. Givan, Ph.D.

Director, Bioinformatics and Biostatistics Core

Tim Triche, Jr., Ph.D.

Associate Professor, Department of Epigenetics

Translational Biological Informatics

Daisy Fu, Ph.D.

Bioinformatics Scientist, Bioinformatics and Biostatistics Core

Kin Lau, Ph.D

Bioinformatics Research Scientist, Bioinformatics and Biostatistics Core

Zach Madaj

Zach Madaj, M.S.

Biostatistician, Bioinformatics and Biostatistics Core

Emily Wolfrum, MPH

Biostatistician, Bioinformatics and Biostatistics Core