Student Publications

Below is a list of publications students have published while enrolled in the Van Andel Institute Graduate School Program.

Peer-reviewed publications


Zhou XE*, He Y*, de Waal PW*, Gao X*, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher KXu HE. 2017. Identification of phosphorylation codes for arrestin recruitment by G protein-coupled receptorsCell 170(3):457–469.e13.     
*Co-first authors
**Cover of Cell

Gu X, Yan Y, Novick SJ, Kovich A, Goswami D, Ke Y, Tan MHE, Wang L, Li X, de Waal PW, Webb MR, Griffin PR, Xu HE, Melcher K. 2017. Deconvoluting AMP-dependent kinas (AMPK) adenine nucleotide binding and sensing.
J Bio Chem.

Yin Y, de Waal PW, He Y, Zhao LH, Yang D, Cai X, Jiang Y, Melcher K, Wang MW, Xu HE. 2017. Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein –coupled receptors. J Biol Chem.
*Editor’s pick, cover article and F1000 Prime article


Y Yin, de Waal Parker, He Y, Zhao LH, Yang D, Cai X, Jiang Y, Melcher K, Wang MW, Xu HE. 2017. Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein-coupled receptors. J Biol Chem.

Ghosh A, Tyson T, George S, Hildebrandt EN, Steiner JA, Madaj Z, Schulz E, Machiela E, McDonald WG, Escobar Galvis ML, Kordower JH, Van Raamsdonk JM, Colca JR, Brundin P. 2016. Mitochondrial pyruvate carrier regulates autophagy, inflammation, and neurodegeneration in experimental models of Parkinson’s diseaseSci Transl Med: 368ra174.

Dues DJ, Andrews EK, Schaar CE, Bergsma AL, Senchuk MM, Van Raamsdonk JM. 2016. Aging causes decreased resistance to multiple stresses and a failure to activate specific stress response pathways. Aging 8(4): 777–795.

Dues DJ, Cooper JF, Lillich R, Van Raamsdonk JM. 2016. Optimization of video-tracking equipment for measurement of basal slowing and other assays of movement. Worm Breeder’s Gazette.

Liu P, Jia MZ, Zhou XE, de Waal PW, Dickson BM, Liu B, Hou L, Yin YT, Kang YY, Shi Y, Melcher K, Xu HE, Jiang Y. 2016. The structural basis of the dominant negative phenotype of the Gαi1β1γ2 G203A/A326S heterotrimer. Acta Pharmacol Sin 37(9): 1259–1272. 

Machiela E, Dues DJ, Senchuk M, Van Raamsdonk JM. 2016. Oxidative stress is increased in C. elegans models of Huntington’s disease but does not contribute to polyglutamine toxicity phenotypesNeurobiol Dis 96:11.

White Y, Bagchi A, Van Ziffle J, Inguva A, Bollag G, Zhang C, Carias H, Dickens D, Loh M, Shannon K, Firestone AJ. 2016. KRAS insertion mutations are oncogenic and exhibit distinct functional properties. Nat Commun 7:10647.

Andersen NJ, Boguslawski EA, Naidu AS, Szot C, Bromberg-White JL, Kits K, Kuk CY, Holton LE, St. Croix B, Chambers CM, Duesbery NS. 2016. Anthrax toxin receptor 1 is essential for arteriogenesis in a mouse model of hindlimb ischemia. PLoS One 11(1): e0146586.

Brundin L, Sellgren CM, Lim CK, Grit J, Pålsson E, Landén M, Samuelsson M, Lundgren K, Brundin P, Fuchs D, Postolache TT, Traskman-Bendz L, Guillemin GJ, Erhardt S. 2016. An enzyme in the kynurenine pathway that governs vulnerability to suicidal behavior by regulating excitotoxicity and neuroinflammation. Transl Psych 6:e865.

Brundin L, Grit J. 2016. Ascertaining whether suicides are caused by infections. JAMA Psychiatry 73(9): 895–896.

Cooper JF, Dues DJ, Van Raamsdonk JM. 2016. Measuring sensitivity to oxidative stress: the superoxide-generator juglone rapidly loses potency with time. Worm Breeder’s Gazette.

Dickson BM, de Waal PW, Ramjan Z, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4. J Chem Phys. 145:154113.

Golani LK, Wallace-Povirk A, Deis SM, Wong J, Ke J, Gu X, Raghaven S, Wilson MR, Li X, Polin L, de Waal PW, White K, Kushner J, O’Connor C, Hou Z, Xu HE, Melcher K, Dann CE 3rd, Matherly LH, Gangjee A. 2016. Tumor targeting with novel 6-substituted phyrrolo [2,3-d] pyrimidine antifolates with heteroatom bridge substitutions via cellular uptake by folate receptor a and the proteon-coupled folate transporter and inhibitor of de novo purine nucleotide biosynthesis. J Med Chem 59(17):7856–7876.

Andersen NJ, Boguslawski EA, Naidu AS, Szot C, Bromberg-White JL, Kits K, Kuk CY, Holton LE, St. Croix B, Chambers CM, Duesbery NS. 2016. Anthrax toxin receptor 1 is essential for arteriogenesis in a mouse model of hindlimb ischemiaPLoS One 11(1):e0146586.

Solitro AR, MacKeigan JP. 2016. Leaving the lysosome behind: novel developments in autophagy inhibitionFuture Med Chem 8(1):73–86.

Zhou XE, Gao X, Barty A, Kang Y, He Y, Liu W, Ishchenko A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Suino-Powell KM, Boutet S, Williams GJ,Wang M, Li D, Caffrey M, Chapman HN, Spence JC, Fromme P, Weierstall U, Stevens RC, Cherezov V, Melcher K, Xu HE. 2016. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complexSci Data 3:160021.


Andersen NJ, Boguslawski EA, Kuk CY, Chambers CM, Duesbery NS.  2015. Combined inhibition of MEK and mTOR has a synergic effect on angiosarcoma tumorgraftsInt J Oncol 47(1):71–80.

Cooper JF, Dues DJ, Spielbauer KK, Machiela E, Senchuk MM, Van Raamsdonk JM. 2015. Delaying aging is neuroprotective in Parkinson’s disease: a genetic analysis in C. elegans modelsnpj Parkinsons Dis 1:15022.

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 13:110.

Kang Y, Zhou XE Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MHE, Zhang C, Moeller A, West GM, Pascal B, Eps NV, Caro1 LN, Vishnivetskiy SA, Lee RJ, Suino-Powell KM, Gu X, Pal K, Ma J, Zhi XY, Boutet S, Williams GJ, Messerschmidt M, Gati C, Zatsepin NA, Wang D, James D, Basu S, Roy-Chowdhury S, Conrad C, Coe J, Liu H, Lisova S, Kupitz C, Grotjohann I, Fromme R, Jiang Y, Tan M, Yang H, Li J, Wang M, Zheng Z, Li D, Howe N, Zhao Y, Standfuss J, Diederichs K, Dong Y, Potter CS, Carragher B, Caffrey M, Jiang H, Chapman HN, Spence JCH, Fromme P, Weierstall U, Ernst OP, Katritch V, Gurevich VV, Griffin PR, Hubbell WL, Stevens RC, Cherezov V, Melcher K, Xu HE. 2015. Crystal structure of rhodopsin bound to arrestin determined by femtosecond X-ray laser. Nature 532:561–567.

Lamberts JR, Hildebrandt EN, Brundin P. 2015. Spreading of α-synuclein in the face of axonal transport deficits in Parkinson’s disease: a speculative synthesisNeurobiol Dis77:276–283.

Li X, Wang L, Zhou EX, Ke J, de Waal PW, Gu X, Tan MHE, Wang D, Wu D, Xu HE, Melcher K. 2015. Structural basis of AMPK regulation by adenine nucleotides and glycogenCell Res 25(1):50–66.

Machiela E, Popkie A, Sempere LF. 2015. Individual noncoding RNA variations: their role in shaping and maintaining the epigenetic landscape. In Personalized Epigenetics, Trygve Tollefsbol, ed. Waltham, Massachusetts: Academic Press, pp. 84–122.

Peacock PD, 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.

Schaar CE, Dues DJ, Spielbauer KK, Machiela ECooper JF, Senchuk M, Hekimi S, Van Raamsdonk JM. 2015. Mitochondrial and cytoplasmic ROS have opposing effects on lifespanPLoS Genet 11(2): e1004972.

Uchtmann K, Park ER, Bergsma A, Segula J, Edick MJ, Miranti CK. 2015. Homozygous loss of mouse tetraspanin CD82 enhances integrin αIIbβ3 expression and clot retraction in plateletsExp Cell Res 339(2):261–269.

Valkenburg KC, Hostetter G, Williams BO. 2015. Concurrent hepsin overexpression and adenomatous polyposis coli deletion causes invasive prostate carcinoma in mice. Prostate 75(14):1579–1585.

Zarif JC, Lamb LE, Schulz VV, Nollet EA, Miranti CK. 2015. Androgen receptor non-nuclear regulation of prostate cancer cell invasion mediated by Src and matriptaseOncotarget 6(9):6862–6876.

Zhao LH, Zhou XE, Yi W, Wu Z, Liu Y, Kang YY, Hou L, de Waal PW, Li S, Jiang Y, Scaffidi A, Flematti GR, Smith SM, Lam VQ, Griffin PR, Wang Y, Li J, Melcher K, Xu HE. 2015. Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3Cell Res 25(11):1219–1236.

Zhong ZA, Peck A, Li S, VanOss J, Snider J, Droscha CJ, Chang TA, Williams BO. 2015. 99mTC-Methylene diphosphonate uptake at injury site correlates with osteoblast differentiation and mineralization during bone healing in miceBone Res 3:15013.


Berger PL, Frank SB, Schulz VV, Nollet EA, Edick MJ, Holly B, Chang TA, Hostetter G, Kim S, Miranti CK. 2014. Transient induction of ING4 by MYC drives prostate epithelial cell differentiation and its disruption drives prostate tumorigenesisCancer Res 74(12):3357–3368.

Burgenske DM, Monsma DJ, Dylewski D, Scott SB, Sayfie AD, Kim DG, Luchtefeld M, Martin KR, Stephenson P, Hostetter G, Dujovny N, MacKeigan JP. 2014. Establishment of genetically diverse patient-derived xenografts of colorectal cancerAm J Cancer Res 4(6):824–837.

Lanning NJ, Looyenga BD, Kauffman AL, Niemi NM, Sudderth J, DeBerardinis RJ, MacKeigan JP. 2014. A mitochondrial RNAi screen defines cellular bioenergetic determinants and identifies an adenylate kinase as a key regulator of ATP levelsCell Rep 7(3):907–917.

Niemi NM, Sacoman JL, Westrate LM, Gaither LA, Lanning NJ, Martin KR, MacKeigan JP. 2014. The pseudophosphatase MK-STYX physically and genetically interacts with the mitochondrial phosphatase PTPMT1PLoS One 9(4):e93896.

Pelle DW, Peacock JD, Schmidt CL, Kampfschulte K, Scholten DJ 2nd, Russo SS, Easton KJ, Steensma MR. 2014. Genetic and functional studies of the intervertebral disc: a novel murine intervertebral disc modelPLoS One 9(12):e112454.

Pelle DW, Ringler JW, Peacock JD, Kampfschulte K, Scholten DJ 2nd, Davis MM, Mitchell DS, Steensma MR. 2014. Targeting receptor-activator of nuclear kappaB ligand in aneurysmal bone cysts: verification of target and therapeutic responseTransl Res 164(2):139–148.

Scholten DJ 2nd, Timmer CM, Peacock J, Pelle DWWilliams BO, Steensma MR. 2014. Down regulation of Wnt signaling mitigates hypoxia-induced chemoresistance in human osteosarcoma cellsPLoS One 9(10):e111431.

Valkenburg KC, Yu X, DeMarzo AM, Spiering TJ, Matusik RJ, Williams BO. 2014. Activation of Wnt/β-catenin signaling in a subpopulation of murine prostate luminal epithelial cells induces high grade prostate intraepithelial neoplasia. Prostate 74(15):1506–1520.

Westrate LM, Drocco JA, Martin KR, Hlavacek WS, MacKeigan JP. 2014. Mitochondrial morphological features are associated with fission and fusion eventsPLoS One 9(4):e95265.

Westrate LM, Sayfie AD, Burgenske DM, MacKeigan JP. 2014. Persistent mitochondrial hyperfusion promotes G2/M accumulation and caspase-dependent cell death. PLoS One 9(3):e91911.


Martin KR, Barua D, Kauffman, AL, Westrate LM, Posner RG, Hlavacek WS, MacKeigan JP. 2013. Computational model for autophagic vesicle dynamics in single cellsAutophagy 9(1):74–92.

Maupin KADroscha CJ, Williams BO. 2013. A comprehensive overview of skeletal phenotypes associated with alterations in Wnt/β-catenin signaling in humans and miceBone Res 1(1):27–71.

Monks NR, Cherba DM, Kamerling SG, Simpson H, Rusk AW, Carter D, Eugster E, Mooney M, Sigler R, Steensma MR, Grabinski T, Marotti KR, Webb CP. 2013. A multi-site feasibility study for personalized medicine in canines with osteosarcoma. J Transl Med 11:158.

Mooney M, Bond J, Monks N, Eugster E, Cherba D, Berlinski P, Kamerling S, Marotti K, Simpson H, Rusk T, Tembe W, Legendre C, Benson H, Liang W, Webb CP. 2013. Comparative RNA-seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiarisPLoS One 8(4):e61088.

Niemi NM, Lanning NJ, Westrate LM, MacKeigan JP. 2013. Downregulation of the mitochondrial phosphatase PTPMT1 is sufficient to promote cancer cell deathPLoS One 8(1):e53803.

Niemi NM, MacKeigan JP. 2013. Mitochondrial phosphorylation in apoptosis: flipping the death switchAntioxid Redox Signal 19(6):572–582.

Valkenburg KC, Steensma MR, Williams BO, Zhong Z. 2013. Skeletal metastasis: treatments, mouse models, and the Wnt signalingChin J Cancer 32(7):380–396.


Westrate LM, MacKeigan JP. 2012. PINK1. In Encyclopedia of Signaling Molecules, Sangdun Choi, ed. New York: Springer, p. 1429.

Niemi NM, MacKeigan JP. 2012. MK-STYX. In Encyclopedia of Signaling Molecules, S. Choi, ed.  New York: Springer, pp. 1089–1093.


Niemi, Natalie M., Nathan J. Lanning, Jeff A. Klomp, Stephen W. Tait, Yong Xu, Karl J. Dykema, Leon O. Murphy, L. Alex Gaither, H. Eric Xu, Kyle A. Furge, Douglas R. Green, and Jeffrey P. MacKeigan.  2011.  MK-STYX, a catalytically inactive phosphatase regulating mitochondrial dependent apoptosis.  Molecular and Cellular Biology 31(7): 1357–1368.

Roos, Frederik C., Andrew J. Evans, Walburgis Brenner, Bill Wondergem, Jeffery[sic] Klomp, Pardeep Heir, Olga Roche, Christian Thomas, Heiko Schimmel, Kyle A. Furge, Bin T. Teh, Joachim W. Thüroff, Christian Hampel, and Michael Ohh.  2011.  Deregulation of E2-EPF ubiquitin carrier protein in papillary renal cell carcinoma.  American Journal of Pathology 178(2): 853–860.

Valkenburg, Kenneth C., Carrie R. Graveel, Cassandra R. Zylstra-Diegel, Zhendong Zhong, and Bart O. Williams.  2011.  Wnt/β-catenin signaling in normal and cancer stem cells.  Cancers 3(2): 2050–2079.

Valkenburg, Kenneth C., and Bart O. Williams.  2011.  Mouse models of prostate cancer.  Prostate Cancer 2011: 22 pp.


Klomp JA, Teh BT, Furge KA. 2010. An integrated oncogenomic approach: from genes to pathway analysis. In An Omics Perspective on Cancer Research, William C.S. Cho, ed. New York: Springer, p. 31.


Wolters NM,
MacKeigan JP. 2009. Applications of RNA interference in drug discovery.  In A Practical Guide to Assay Development and High-Throughput Screening in Drug Discovery, T. Chen, ed. London: Taylor and Francis, pp. 157–168.


Elis W, Triantafellow E, Wolters NM, Sian KR, Caponigro G, Borawski J, Gaither LA, Murphy LO,. Finan PM, MacKeigan JP.  2008. Down-regulation of class II phosphoinositide 3-kinase α expression below a critical threshold induces apoptotic cell deathMol Cancer Res 6(4): 614–623.

Wolters NM, MacKeigan JP. 2008. From sequence to function: using RNAi to elucidate mechanisms of human diseaseCell Death Differ 15(5): 809–819.


Wolters NM, MacKeigan JP. 2007. MK-STYX. UCSD-Nature Molecule Pages

Non peer-reviewed publications


Cooper, Jason, Kevin Maupin, and Nathan Merrill.  2015.  Origins of Cancer Symposium 2015: posttranslational modifications and cancer.  Genes & Cancer 6(7–8): 303–306.


Howard, Andrew M., Eric A. Nollet, and Nikki M. Thellman.  2014.  Origins of Cancer Symposium report: beyond the tumor cell.  Genes & Cancer 5(11–12): 375–377.

Miranti, Cindy K., Alexis Bergsma, and Annemiek B. van Spriel.  2014.  Tetraspanins as master organizers of the plasma membrane.  In Cell Membrane Nanodomains: From Biochemistry to Nanoscopy, Alessandra Cambi and Diane S. Lidke, eds.  Boca Raton, FL: CRC Press, pp. 59–86.


Nollet, Eric A., and Cindy K. Miranti.  2013.  Integrin and matrix regulation of autophagy and mitophagy.  In Autophagy, Yannick Bailly, ed.  New York: InTech, pp. 465–485.

Burgenske, Dani M., and Kenneth C. Valkenburg.  2013.  Origins of Cancer Symposium report.  Genes & Cancer 4(11–12): 457–459.


Westrate, Laura, and Jeffrey P. MacKeigan.  2012.  PINK1.  In Encyclopedia of Signaling Molecules, Sangdun Choi, ed.  New York: Springer, p. 1429.

Niemi, Natalie M., and Jeffrey P. MacKeigan.  2012.  MK-STYX.  In Encyclopedia of Signaling Molecules, S. Choi, ed.  New York: Springer, pp. 1089–1093.


Klomp, Jeff A., Bin T. Teh, and Kyle A. Furge.  2010.  An integrated oncogenomic approach: from genes to pathway analysis.  In An Omics Perspective on Cancer Research, William C.S. Cho, ed.  New York: Springer, p. 31.


Wolters, Natalie M., and Jeffrey P. MacKeigan.  2009.  Applications of RNA interference in drug discovery.  In A Practical Guide to Assay Development and High-Throughput Screening in Drug Discovery, T. Chen, ed.  London: Taylor and Francis, pp. 157–168.