Warning: call_user_func_array() expects parameter 1 to be a valid callback, function 'yoast_breadcrumb' not found or invalid function name in /home/vaitrafficdesk/public_html/wp-content/themes/timberland/vendor/timber/timber/lib/Twig.php on line 296

Overview

Every day, we collaborate at the forefront of fundamental and translational science in pursuit of groundbreaking treatment strategies for cancer, Parkinson’s and other diseases. Through shared values and an entrepreneurial spirit, we spark innovation to multiply the impact of discovery and answer critical questions about our world.

As a reflection of this commitment, we are pleased to join the Coalition for Next Generation Life Sciences, a collaborative effort to enhance transparency by publishing outcomes data for graduate students and postdoctoral fellows. Metrics include:

  • Admissions and matriculation data of Ph.D. students
  • Median time-to-degree and completion data for Ph.D. programs
  • Demographics of Ph.D. students and postdoctoral scholars by gender, underrepresented minority status and citizenship status
  • Median time in postdoctoral status at the institution
  • Career outcomes for Ph.D. and postdoctoral alumni, classified by job sector and career type using a common taxonomy Source: Coalition for Next Generation Life Sciences

Learn more about the Coalition by visiting nglscoalition.org.

For questions about VAI graduate student data, please contact Christy Mayo at Christy.Mayo@vai.org. For questions about VAI postdoctoral fellow data, please contact Dr. Erica Gobrogge at Erica.Gobrogge@vai.org.

Peer-reviewed publications

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

2022

Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei M, Vander Scaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. Pre-print. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. bioRxiv.

Prahl J, Pierce SE, Coetzee GA, Tyson T. 2022. Alpha-synuclein negatively controls cell proliferation in dopaminergic neuronsMol Cell Neurosci 119:103702.

2021

de Oliveira LMA, Cordeiro-Spinetti E, Neves FPG, Sujii PS, Ribeiro RL, de Lyra SS, . . . Bonatelli ML. 2021. Going online in pandemic time: a DivulgaMicro workshop experienceJ Microbiol Biol Educ 22(1):22.1.79.

Sargent D, Cunningham LA, Dues DJ, Ma Y, Kordich JJ, Mercado G, Brundin P, Cowell RM, Moore DJ. 2021. Neuronal VPS35 deletion induces spinal cord motor neuron degeneration and early post-natal lethalityBrain Commun 3(3).

Booms A, Coetzee G. 2021. Functions of intracellular alpha-synuclein in microglia: Implications for Parkinson’s disease riskFront Cell Neurosci.

Bagchi A, Beddows I, Cornelius A, Robinson GW, Jewell SD. 2021. Rare cases of medulloblastoma with hypermutationCancer Rep e1521.

Dehghani N, Guven G, Kun-Rodrigues C, Gouveia C, Foster K, Hanagasi H, Lohmann E, Samanci B, Gurvit H, Bilgic B, Brás J, Guerreiro R. 2021. A comprehensive analysis of copy number variation in a Turkish dementia cohortHum Genom 15:48.

Liu Y, Molchanov V, Yang T. 2021. Enzymatic machinery of ubiquitin and ubiquitin-like modification systems in chondrocyte homeostasis and osteoarthritisCurr Rheumatol Rep 23:62.

Ruan Z*, Haley E*, Orozco I*, Sabat M, Myers R, Roth R, Du J#, Lü W#. 2021. Structures of the TRPM5 channel elucidate mechanisms of activation and inhibitionNat Struct Mol Biol.

Dehghani N, Brás J, Guerreiro R. 2021. How understudied populations have contributed to our understanding of Alzheimer’s disease geneticsBrain.

Chassé MH, Johnson BK, Boguslawski EA, Sorensen KM, Rosien JE, Kang MH, Reynolds CP, Heo L, Madaj ZB, Beddows 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 69(5)297–320.

Grit JL, Johnson BK, Dischinger PS, Essenburg CJ, Adams M, Campbell S, Pollard K, Pratilas CA, Triche TJ Jr., Graveel CR, Steensma MR. 2021. Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signalingEpi Chromatin 14(7).

2020

Machiela E, Liontis T, Dues DJ, Rudich PD, Traa A, Wyman L, Kaufman C, Cooper JF, Lew L, Nadarajan S, Senchuk MM, Van Raamsdonk JM. 2020. Disruption of mitochondrial dynamics increases stress resistance through activation of multiple stress response pathwaysFASEB J 34(6):8475–8492.

Balint B, Guerreiro R, Carmona S, Dehghani N, Latorre A, Cordivari C, Bhatia KP, Brás J. 2020. KCNN2 mutation in autosomal-dominant tremulous myoclonus-dystonia. Eur J Neurol 27(8):1471–1477.

Vaughan RMKupai A, Rothbart SB. 2020. Chromatin regulation through ubiquitin and ubiquitin-like histone modificationsTrends Biochem Sci.

Tovar EA, Sheridan R, Essenburg CJ, Dischinger PSArumugam M, Callaghan ME, Graveel CR*, Steensma MR*. 2020. Dissecting the rat mammary gland: Isolation, characterization and culture of purified mammary epithelial cells and fibroblastsBio-protocol 10(22).
*Equal contributions

Vaughan RMKupai A, Foley CA, Sagum CA, Tibben BM, Eden HE, Tiedemann RL, Berryhill CA, Patel V, Shaw KM, Krajewski K, Strahl BD, Bedford MT, Frye SV, Dickson BM, Rothbart SB. 2020. The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells. Epigenetics Chromatin 13(1):44. 

Dues DJ, Moore DJ. 2020. LRRK2 and protein aggregation in Parkinson’s disease: Insights from animal modelsFront Neurosci 14:719

Cunningham LA, Moore DJ. 2020. Endosomal sorting pathways in the pathogenesis of Parkinson’s diseaseProg Brain Res 252:271–306.

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 vulnerabilities. Genes (Basel) 11(3):331

Maupin KA, Dick D, Lee J, Williams BO. 2020. Loss of Lgals3 protects against gonadectomy-induced cortical bone loss in miceCalcif Tissue Int 106(3):283–229

Diegel CR, Hann S, Ayturk UM, Hu JCW, Lim KE, Droscha CJ, Madaj ZB, Foxa GE, Izaguirre I; VAI Vivarium and Transgenics Core, Robling AG, Warman ML, Williams BO. 2020. Independent validation of experimental results requires timely and unrestricted access to animal models and reagentsPLoS Genet 16(6):e1008940

Kupai AVaughan RM, Dickson BM, Rothbart SB. 2020. A degenerate peptide library approach to reveal sequence determinants of methyllysine-driven protein interactionsFront Cell Dev Biol 8:241.

Pierce SE, Booms APrahl J, van der Schans EJC, Tyson T, Coetzee GA. 2020. Post-GWAS knowledge gap: the how, where and whennpj Parkinsons 6:23.

Zhuang Y, Liu H, Zhou XE, Verma RK, de Waal PW, Jang W, Xu TH, Wang L, Meng X, Zhao G, Kang Y, Melcher K, Fan H, Lambert NA, Xu HE, Zheng C. 2020. Structure of formylpeptide receptor 2-G i complex reveals insights into ligand recognition and signaling (https://www.nature.com/articles/s41467-020-14728-9) . Nat Commun 11(1):1-12.

Ma S, Shen Q, Zhao LH, Mao C, Zhou XE, Shen DD, de Waal PW, Bi P, Li C, Jiang Y, Wang MW, Sexton PM, Wootten D, Melcher K, Zhang Y, Xu HE. 2020. Molecular basis for hormone recognition and activation of corticotropin-releasing factor receptors (https://www.sciencedirect.com/science/article/abs/pii/S1097276520300137) . Mol Cell 77(3):669–680.

Gedminas JM, Chasse MH, McBrairty M, Beddows I, Kitchen-Goosen SM, Grohar PJ. 2020. Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor.
Oncogenesis 9(4):41.

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.

de Waal PW, Shi J, You E, Wang X, Melcher K, Jiang Y, Xu HE, Dickson BM. 2020. Molecular mechanisms of fentanyl mediated β-arrestin biased signalingPLOS Comp Biol.

Flores G, Everett JH, Boguslawski EA, Oswald BM, Madaj ZB, Beddows 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

Dutka P, Mukherjee S, Gao X, Kang Y, de Waal PW, Wang L, Zhuang Y. 2019. Development of “plug and play” fiducial marks for structural studies of GPCR signaling complexes by single-particle cryo-EM (https://www.sciencedirect.com/science/article/abs/pii/S0969212619303454) . Structure 27(12):1862–1874.

Yin W, Li Z, Jin M, Yin YL, de Waal PW, Pal K, Yin Y, Gao X, He Y, Gao J, Wang X, Zhang Y, Zhou H, Melcher K, Jiang Y, Cong Y, Zhou XE, Yu X, Xu HE. 2019. A complex structure of arrestin-2 bound to a G protein-coupled receptor (https://www.nature.com/articles/s41422-019-0256-2) . Cell Res 29(12):971–983.

Choi W*, Clemente N*, Sun W, Du J#, Lü W#. 2019. The structures and gating mechanism of human calcium homeostasis modulator 2Nature.
*Co-first author
#Co-corresponding author

Colino-Sanguino Y, Cornett EM, Moulder D, Smith GC, Hrit J, Cordeiro-Spinetti EVaughan RM, Krajewski K, Rothbart SB*, Clark SJ*, Valdés-Mora F*. 2019. A read/write mechanism connects p300 Bromodomain function to H2A.Z acetylationiScience S2589-0042(19)30434-1.
*Co-corresponding authors

Dues DJ, Andrews EK, Senchuk MM, Van Raamsdonk JM. 2019. Resistance to stress can be experimentally dissociated from longevityJ Gerontol A Biol Sci Med Sci 74(8):1206–1214.

Bergsma A, Ganguly SS, Wiegand ME, Dick D, Williams BO, Miranti CK. 2019. Regulation of cytoskeleton and adhesion signaling in osteoclasts by tetraspanin CD82Bone Rep 10:100196.

Celano SL, Yco LP, Kortus MG, Solitro AR, Gunaydin H, Scott M, Spooner E, O’Hagan RC, Fuller P, Martin KR, Shumway SD, MacKeigan JP. 2019. Identification of kinases responsible for p53-dependent autophagyiScience 15:109–118.

Vaughan RM, Rothbart SB*, Dickson BM*. 2019. The finger loop of the SRA domain in the E3 ligase UHRF1 is a regulator of ubiquitin targeting and is required for maintaining DNA methylationJ Biol Chem.
*Co-corresponding authors

Booms A, Coetzee GA, Pierce SE. 2019. MCF-7 as a model for functional analysis of breast cancer risk variantsCancer Epidemiol Biomarkers Prev.

Vander Schaaf NA, Oghamian S, Park JA, Kang L, Laird PW, Lee KH. 2019. In vivo application of the REMOTE-control system for the manipulation of endogenous gene expression. J Vis Exp. 

Keaton SA, Heilman P, Bryleva EY, Madaj Z, Krzyzanowski S, Grit J, Miller ES, Jälmby M, Kalapotharakos G, Racicot K, Fazleabas A, Hansson SR, Brundin L. 2019. Altered tryptophan catabolism in placentas from women with pre-eclampsia. Int J Tryptophan Res 12:1178646919840321.

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 suicide risk. J Affect Disord 247:57–65.

Haley E, Choi W, Fan C, Sun W, Du J, Lü W. 2019. Expression and purification of the human lipid-sensitive cation channel TRPC3 for structural determination by single-particle cryo-electron microscopy. J Vis Exp (143).

Zhao LH*, Ma S*, Sutkeviciute I*, Shen DD*, Zhou XE, de Waal PW, Li CH, Kang Y, Clark LJ, Jean-Alphonse FG, White AD, Yang D, Dai A, Cai X, Chen J, Li C, Jiang Y, Watanbe T, Gradella TJ, Melcher K, Wang MW#, Vilardaga JP#, Xu HE#, Zhang Y#. 2019. Structure and dynamics of the active human parathyroid hormone receptor-1Science.
* Equal contributions
# Co-corresponding authors

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

Chen X, Kordich JK, Williams ET, Levine N, Cole-Strauss A, Marshall L, Labrie V, Ma J, Lipton JW, Moore DJ. 2019. Parkinson’s disease-linked D620N VPS35 knockin mice manifest tau neuropathology and dopaminergic neurodegenerationProc Natl Acad Sci U S A.

2018

Du M, Yaun Z, Yu H, Henderson N, Sarowar S, Zhao G, Werneburg GT, Thanassi DG, Li H. 2018. Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimDNature.

Dues DJ, Andrews EK, Senchuk MM, Van Raamsdonk JM. 2018. Resistance to stress can be experimentally dissociated from longevityJ Gerontol A Biol Sci Med Sci.

Cooper JF, Spielbauer KK, Senchuk MM, Nadarajan S, Colaiacovo MP, Van Raamsdonk JM. 2018. α-synuclein expression from a single copy transgene increases sensitivity to stress and accelerates neuronal loss in genetic models of Parkinson’s diseaseExp Neurol 310:58–69.

Martin KR, Celano SL, Solitro AR, Gunaydin H, Scott M, O’Hagan RC, Shumway SD, Fuller P, MacKeigan JP. 2018. A potent and selective ULK1 inhibitor suppresses autophagy and sensitizes cancer cells to nutrient stressiScience 8:74–84.

Maupin K, Weaver K, Bergsma A, Christie C, Zhong ZA, Yang T, Williams BO. 2018. Enhanced cortical bone expansion in Lgals3-deficient mice during agingBone Res 6:7.

Wu Z, Senchuk MM, Dues DJ, Johnson BK, Cooper JF, Lew L, Machiela E, Schaar CE, DeJonge H, Blackwell TK, Van Raamsdonk JM. 2018. Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathwaysBMC Biol 16:147.

Gu X, Bridges MD, Yan Y, de Waal PW, Zhou XE, Suino-Powell KM, Xu HE, Hubbell WL, Melcher K. 2018.  Conformational heterogeneity of the allosteric drug and metabolite (ADaM) site in AMP-activated protein kinase (AMPK)J Biol Chem293(44):16994–17007.

Harris CJ, Scheibe M, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F, Jacobsen SE. 2018. A DNA methylation reader complex that enhances gene transcriptionScience 362(6419):1182–1186.

Cornett EM, Dickson BM, Krajewski K, Spellmon N, Umstead A, Vaughan RM, Shaw KM, Versluis PP, Cowles MW, Brunzelle J, Yang Z, Vega IE, Sun ZW, Rothbart SB. 2018. A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity. Sci Adv.

Valkenburg KC, De Marzo AM, Williams BO. 2017. Deletion of tumor suppressors adenomatous polyposis coli and Smad4 in murine luminal epithelial cells causes invasive prostate cancer and loss of androgen receptor expressionOncotarget 8(46):80265-80277.

Du M, Yaun Z, Yu H, Henderson N, Sarowar S, Zhao G, Werneburg GT, Thanassi DG, Li H. 2018. Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimDNature.

Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenberg AJ. 2018. Examining the roles of H3K4 methylation states with systematically characterized antibodiesMol Cell.
*Video abstract

Cooper JF, Van Raamsdonk JM. 2018. Modeling Parkinson’s disease in C. elegansJ Parkinson’s Dis 8(1):17–32.

Krajnak K, Dahl R. 2018. A new target for Alzheimer’s disease: a small molecule SERCA activator is neuroprotective in vitro and improves memory and cognition in APP/PS1 miceBioorg Med Chem Lett 28(9):1591–1594.

Krajnak K, Dahl R. 2018. Small molecule SUMOylation activators are novel neuroprotective agentsBioorg Med Chem Lett 28(3): 405–409.

Yang S, Wu T, Xu TH, de Waal PW, He Y, Pu M, Chen Y, DeBruine ZJ, Zhang B, Zaidi SA, Popov P, Guo Y, Han GW, Lu Y, Suino-Powell K, Song S, Harikumar KG, Miller LJ, Katritch V, Xu HE, Shui W, Stevens RC, Melcher K, Zhao S, Xu F. 2018. Crystal structure of the Frizzled 4 receptor in a ligand-free stateNature.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. 2018. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenanceNuc Acids Res.

Pierce SE, Tyson T, Booms A, Prahl J, Coetzee GA. 2018. Parkinson’s disease genetic risk in a midbrain neuronal cell lineNeurobiol Dis 114:53–64.

Fan C*, Choi W*, Sun W, Du J, Lü W. 2018. Structure of the human lipid-gated cation channel TRPC3eLife 4;7.
*Co-first author

Yin W, Zhou XE, Yang D, de Waal PW, Want M, Dai A, Cai X, Haung CY, Liu P, Wang X, Yin Y, Liu B, Zhou Y, Wang J, Liu H, Caffrey M, Melcher K, Xu Y, Wang MW, Xu HE, Jiang Y. 2018. Crystal structure of the human 5-HT1B serotonin receptor bound to an inverse agonistCell Disc 4(12).

Williams ET, Glauser L, Tsika E, Jiang H, Islam S, Moore DJ. 2018. Parkin mediates the ubiquitination of VPS35 and modulates retromer-dependent endosomal sortingHum Mol Genet.

Peacock JD, Pridgeon MG, Tovar EA, Essenburg CJ, Bowman M, Madaj Z, 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 MR. 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.

Williams ET, Moore DJ. 2018. Deciphering the role of VPS35 in Parkinson’s diseaseJ Neurosci Res 96(8):1339–1340.

Senchuk MM, Dues DJ, Schaar CE, Johnson BK, Madaj ZB, Bowman MJ, Winn 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.

Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB. 2018. Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1Proc Natl Acad Sci U S A

Kang Y*, Kuybeda O*, de Waal PW*, Mukherjee S, Van Eps N, Dutka P, Zhou XE, Bartesaghi A, Erramilli S, Morizumi T, Gu X, Yin Y, Liu P, Jiang Y, Meng X, Zhao G, Melcher K, Ernst OP, Kossiakoff AA, Subramaniam S, Xu HE. 2018. Cryo-EM structure of human rhodopsin bound to an inhibitory G proteinNature.

2017

Cooper JF, Machiela M, Dues DJ, Spielbauer KK, Senchuk MM, Van Raamsdonk JM. 2017. Activation of the mitochondrial unfolded protein response promotes longevity and dopamine neuron survival in Parkinson’s disease modelsSci Rep 7:16441.

DeBruine ZJ, Xu HE, Melcher K. 2017. Assembly and architecture of the Wnt/β-catenin signalosome at the membraneBr J Pharmacol 174(24):4564–4574.

Dunn EM, Billquist EJ, VanderStoep AL, Bax PG, Westrate LM, McLellan LK, Peterson SC, MacKeigan JP, Putzke AP. 2017. Dual roles of Fer kinase are required for proper hematopoiesis and vascular endothelium organization during zebrafish developmentBiology (Basel) 6(4):40.

Merrill NM, Schipper JL, Karnes JB, Kauffman AL, Martin KR, MacKeigan JP. 2017. PI3K-C2α knockdown decreases autophagy and maturation of endocytic vesiclesPLoS One 12(9):e0184909.

Bryleva EY, Keaton SA, Grit J, Madaj Z, Sauro-Nagendra A, Smart L, Halstead S, Achtyes E, Brundin L.  2017. The acute-phase mediator serum amyloid A is associated with symptoms of depression and fatigueActa Psychiatr Scand 135(5):409–418.

DeBruine ZJ, Ke J, Harikumar KG, Gu X, Borowsky P, Williams BO, Xu W, Miller LJ, Xu HE, Melcher K.  2017. Wnt5a promotes frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerizationGenes Dev 31(9):916–926.

Droscha CJ, Diegel CR, Ethen NJ, Burgers TA, McDonald MJ, Maupin KA, Naidu AS, Wang PF, Teh BT, Williams BO. 2017. Osteoblast-specific deletion of Hprt2/Cdc73 results in high bone mass and increased bone turnover. Bone 98:68–78.

Gu X, Yan Y, Novick SJ, Kovach A, Goswami D, Ke J, Tan MHE, Wang L, Li X, de Waal PW, Webb MR, Griffin PR, Xu HE, Melcher K. 2017. Deconvoluting AMP-dependent kinase (AMPK) adenine nucleotide binding and sensingJ Biol Chem 292(30):12653–12666.

Thellman NM, Botting C, Madaj Z, Triezenberg SJ. 2017. An immortalized human dorsal root ganglia cell line provides a novel context to study herpes simplex virus Type-1 latency and reactivationJ Virology 91(12): 00080-17.

Thellman NM, Triezenberg SJ. 2017. Herpes simplex virus establishment, maintenance, and reactivation: in vitro modeling of latencyPathogens 6(3):28.

Tyson T, Senchuk M, Cooper JF, George S, Van Raamsdonk JM, Brundin P. 2017. Novel animal model defines genetic contributions for neuron-to-neuron transfer of α-synucleinSci Rep7:7506.

Williams ET, Chen X, Moore DJ. 2017. VPS35, the retromer complex and Parkinson’s diseaseJ Parkinsons Dis 7(2):219–233.

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 receptorsJ Biol Chem 292(24):9865–9881.

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 K, Xu HE. 2017. Identification of phosphorylation codes for arrestin recruitment by G protein–coupled receptorsCell 170(3):457–469.e13.

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

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 368: 368ra174.

Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatic regulator BRD4J Chem Phys 145(15):154113.

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 K, Xu 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 receptorsJ Biol Chem.
*Editor’s pick, cover article and F1000 Prime article

2022

Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei M, Vander Scaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. Pre-print. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. bioRxiv.

Prahl J, Pierce SE, Coetzee GA, Tyson T. 2022. Alpha-synuclein negatively controls cell proliferation in dopaminergic neuronsMol Cell Neurosci 119:103702.

2021

de Oliveira LMA, Cordeiro-Spinetti E, Neves FPG, Sujii PS, Ribeiro RL, de Lyra SS, . . . Bonatelli ML. 2021. Going online in pandemic time: a DivulgaMicro workshop experienceJ Microbiol Biol Educ 22(1):22.1.79.

Sargent D, Cunningham LA, Dues DJ, Ma Y, Kordich JJ, Mercado G, Brundin P, Cowell RM, Moore DJ. 2021. Neuronal VPS35 deletion induces spinal cord motor neuron degeneration and early post-natal lethalityBrain Commun 3(3).

Booms A, Coetzee G. 2021. Functions of intracellular alpha-synuclein in microglia: Implications for Parkinson’s disease riskFront Cell Neurosci.

Bagchi A, Beddows I, Cornelius A, Robinson GW, Jewell SD. 2021. Rare cases of medulloblastoma with hypermutationCancer Rep e1521.

Dehghani N, Guven G, Kun-Rodrigues C, Gouveia C, Foster K, Hanagasi H, Lohmann E, Samanci B, Gurvit H, Bilgic B, Brás J, Guerreiro R. 2021. A comprehensive analysis of copy number variation in a Turkish dementia cohortHum Genom 15:48.

Liu Y, Molchanov V, Yang T. 2021. Enzymatic machinery of ubiquitin and ubiquitin-like modification systems in chondrocyte homeostasis and osteoarthritisCurr Rheumatol Rep 23:62.

Ruan Z*, Haley E*, Orozco I*, Sabat M, Myers R, Roth R, Du J#, Lü W#. 2021. Structures of the TRPM5 channel elucidate mechanisms of activation and inhibitionNat Struct Mol Biol.

Dehghani N, Brás J, Guerreiro R. 2021. How understudied populations have contributed to our understanding of Alzheimer’s disease geneticsBrain.

Chassé MH, Johnson BK, Boguslawski EA, Sorensen KM, Rosien JE, Kang MH, Reynolds CP, Heo L, Madaj ZB, Beddows 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 69(5)297–320.

Grit JL, Johnson BK, Dischinger PS, Essenburg CJ, Adams M, Campbell S, Pollard K, Pratilas CA, Triche TJ Jr., Graveel CR, Steensma MR. 2021. Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signalingEpi Chromatin 14(7).

2020

Machiela E, Liontis T, Dues DJ, Rudich PD, Traa A, Wyman L, Kaufman C, Cooper JF, Lew L, Nadarajan S, Senchuk MM, Van Raamsdonk JM. 2020. Disruption of mitochondrial dynamics increases stress resistance through activation of multiple stress response pathwaysFASEB J 34(6):8475–8492.

Balint B, Guerreiro R, Carmona S, Dehghani N, Latorre A, Cordivari C, Bhatia KP, Brás J. 2020. KCNN2 mutation in autosomal-dominant tremulous myoclonus-dystonia. Eur J Neurol 27(8):1471–1477.

Vaughan RMKupai A, Rothbart SB. 2020. Chromatin regulation through ubiquitin and ubiquitin-like histone modificationsTrends Biochem Sci.

Tovar EA, Sheridan R, Essenburg CJ, Dischinger PSArumugam M, Callaghan ME, Graveel CR*, Steensma MR*. 2020. Dissecting the rat mammary gland: Isolation, characterization and culture of purified mammary epithelial cells and fibroblastsBio-protocol 10(22).
*Equal contributions

Vaughan RMKupai A, Foley CA, Sagum CA, Tibben BM, Eden HE, Tiedemann RL, Berryhill CA, Patel V, Shaw KM, Krajewski K, Strahl BD, Bedford MT, Frye SV, Dickson BM, Rothbart SB. 2020. The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells. Epigenetics Chromatin 13(1):44. 

Dues DJ, Moore DJ. 2020. LRRK2 and protein aggregation in Parkinson’s disease: Insights from animal modelsFront Neurosci 14:719

Cunningham LA, Moore DJ. 2020. Endosomal sorting pathways in the pathogenesis of Parkinson’s diseaseProg Brain Res 252:271–306.

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 vulnerabilities. Genes (Basel) 11(3):331

Maupin KA, Dick D, Lee J, Williams BO. 2020. Loss of Lgals3 protects against gonadectomy-induced cortical bone loss in miceCalcif Tissue Int 106(3):283–229

Diegel CR, Hann S, Ayturk UM, Hu JCW, Lim KE, Droscha CJ, Madaj ZB, Foxa GE, Izaguirre I; VAI Vivarium and Transgenics Core, Robling AG, Warman ML, Williams BO. 2020. Independent validation of experimental results requires timely and unrestricted access to animal models and reagentsPLoS Genet 16(6):e1008940

Kupai AVaughan RM, Dickson BM, Rothbart SB. 2020. A degenerate peptide library approach to reveal sequence determinants of methyllysine-driven protein interactionsFront Cell Dev Biol 8:241.

Pierce SE, Booms APrahl J, van der Schans EJC, Tyson T, Coetzee GA. 2020. Post-GWAS knowledge gap: the how, where and whennpj Parkinsons 6:23.

Zhuang Y, Liu H, Zhou XE, Verma RK, de Waal PW, Jang W, Xu TH, Wang L, Meng X, Zhao G, Kang Y, Melcher K, Fan H, Lambert NA, Xu HE, Zheng C. 2020. Structure of formylpeptide receptor 2-G i complex reveals insights into ligand recognition and signaling (https://www.nature.com/articles/s41467-020-14728-9) . Nat Commun 11(1):1-12.

Ma S, Shen Q, Zhao LH, Mao C, Zhou XE, Shen DD, de Waal PW, Bi P, Li C, Jiang Y, Wang MW, Sexton PM, Wootten D, Melcher K, Zhang Y, Xu HE. 2020. Molecular basis for hormone recognition and activation of corticotropin-releasing factor receptors (https://www.sciencedirect.com/science/article/abs/pii/S1097276520300137) . Mol Cell 77(3):669–680.

Gedminas JM, Chasse MH, McBrairty M, Beddows I, Kitchen-Goosen SM, Grohar PJ. 2020. Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor.
Oncogenesis 9(4):41.

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.

de Waal PW, Shi J, You E, Wang X, Melcher K, Jiang Y, Xu HE, Dickson BM. 2020. Molecular mechanisms of fentanyl mediated β-arrestin biased signalingPLOS Comp Biol.

Flores G, Everett JH, Boguslawski EA, Oswald BM, Madaj ZB, Beddows 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

Dutka P, Mukherjee S, Gao X, Kang Y, de Waal PW, Wang L, Zhuang Y. 2019. Development of “plug and play” fiducial marks for structural studies of GPCR signaling complexes by single-particle cryo-EM (https://www.sciencedirect.com/science/article/abs/pii/S0969212619303454) . Structure 27(12):1862–1874.

Yin W, Li Z, Jin M, Yin YL, de Waal PW, Pal K, Yin Y, Gao X, He Y, Gao J, Wang X, Zhang Y, Zhou H, Melcher K, Jiang Y, Cong Y, Zhou XE, Yu X, Xu HE. 2019. A complex structure of arrestin-2 bound to a G protein-coupled receptor (https://www.nature.com/articles/s41422-019-0256-2) . Cell Res 29(12):971–983.

Choi W*, Clemente N*, Sun W, Du J#, Lü W#. 2019. The structures and gating mechanism of human calcium homeostasis modulator 2Nature.
*Co-first author
#Co-corresponding author

Colino-Sanguino Y, Cornett EM, Moulder D, Smith GC, Hrit J, Cordeiro-Spinetti EVaughan RM, Krajewski K, Rothbart SB*, Clark SJ*, Valdés-Mora F*. 2019. A read/write mechanism connects p300 Bromodomain function to H2A.Z acetylationiScience S2589-0042(19)30434-1.
*Co-corresponding authors

Dues DJ, Andrews EK, Senchuk MM, Van Raamsdonk JM. 2019. Resistance to stress can be experimentally dissociated from longevityJ Gerontol A Biol Sci Med Sci 74(8):1206–1214.

Bergsma A, Ganguly SS, Wiegand ME, Dick D, Williams BO, Miranti CK. 2019. Regulation of cytoskeleton and adhesion signaling in osteoclasts by tetraspanin CD82Bone Rep 10:100196.

Celano SL, Yco LP, Kortus MG, Solitro AR, Gunaydin H, Scott M, Spooner E, O’Hagan RC, Fuller P, Martin KR, Shumway SD, MacKeigan JP. 2019. Identification of kinases responsible for p53-dependent autophagyiScience 15:109–118.

Vaughan RM, Rothbart SB*, Dickson BM*. 2019. The finger loop of the SRA domain in the E3 ligase UHRF1 is a regulator of ubiquitin targeting and is required for maintaining DNA methylationJ Biol Chem.
*Co-corresponding authors

Booms A, Coetzee GA, Pierce SE. 2019. MCF-7 as a model for functional analysis of breast cancer risk variantsCancer Epidemiol Biomarkers Prev.

Vander Schaaf NA, Oghamian S, Park JA, Kang L, Laird PW, Lee KH. 2019. In vivo application of the REMOTE-control system for the manipulation of endogenous gene expression. J Vis Exp. 

Keaton SA, Heilman P, Bryleva EY, Madaj Z, Krzyzanowski S, Grit J, Miller ES, Jälmby M, Kalapotharakos G, Racicot K, Fazleabas A, Hansson SR, Brundin L. 2019. Altered tryptophan catabolism in placentas from women with pre-eclampsia. Int J Tryptophan Res 12:1178646919840321.

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 suicide risk. J Affect Disord 247:57–65.

Haley E, Choi W, Fan C, Sun W, Du J, Lü W. 2019. Expression and purification of the human lipid-sensitive cation channel TRPC3 for structural determination by single-particle cryo-electron microscopy. J Vis Exp (143).

Zhao LH*, Ma S*, Sutkeviciute I*, Shen DD*, Zhou XE, de Waal PW, Li CH, Kang Y, Clark LJ, Jean-Alphonse FG, White AD, Yang D, Dai A, Cai X, Chen J, Li C, Jiang Y, Watanbe T, Gradella TJ, Melcher K, Wang MW#, Vilardaga JP#, Xu HE#, Zhang Y#. 2019. Structure and dynamics of the active human parathyroid hormone receptor-1Science.
* Equal contributions
# Co-corresponding authors

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

Chen X, Kordich JK, Williams ET, Levine N, Cole-Strauss A, Marshall L, Labrie V, Ma J, Lipton JW, Moore DJ. 2019. Parkinson’s disease-linked D620N VPS35 knockin mice manifest tau neuropathology and dopaminergic neurodegenerationProc Natl Acad Sci U S A.

2018

Du M, Yaun Z, Yu H, Henderson N, Sarowar S, Zhao G, Werneburg GT, Thanassi DG, Li H. 2018. Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimDNature.

Dues DJ, Andrews EK, Senchuk MM, Van Raamsdonk JM. 2018. Resistance to stress can be experimentally dissociated from longevityJ Gerontol A Biol Sci Med Sci.

Cooper JF, Spielbauer KK, Senchuk MM, Nadarajan S, Colaiacovo MP, Van Raamsdonk JM. 2018. α-synuclein expression from a single copy transgene increases sensitivity to stress and accelerates neuronal loss in genetic models of Parkinson’s diseaseExp Neurol 310:58–69.

Martin KR, Celano SL, Solitro AR, Gunaydin H, Scott M, O’Hagan RC, Shumway SD, Fuller P, MacKeigan JP. 2018. A potent and selective ULK1 inhibitor suppresses autophagy and sensitizes cancer cells to nutrient stressiScience 8:74–84.

Maupin K, Weaver K, Bergsma A, Christie C, Zhong ZA, Yang T, Williams BO. 2018. Enhanced cortical bone expansion in Lgals3-deficient mice during agingBone Res 6:7.

Wu Z, Senchuk MM, Dues DJ, Johnson BK, Cooper JF, Lew L, Machiela E, Schaar CE, DeJonge H, Blackwell TK, Van Raamsdonk JM. 2018. Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathwaysBMC Biol 16:147.

Gu X, Bridges MD, Yan Y, de Waal PW, Zhou XE, Suino-Powell KM, Xu HE, Hubbell WL, Melcher K. 2018.  Conformational heterogeneity of the allosteric drug and metabolite (ADaM) site in AMP-activated protein kinase (AMPK)J Biol Chem293(44):16994–17007.

Harris CJ, Scheibe M, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F, Jacobsen SE. 2018. A DNA methylation reader complex that enhances gene transcriptionScience 362(6419):1182–1186.

Cornett EM, Dickson BM, Krajewski K, Spellmon N, Umstead A, Vaughan RM, Shaw KM, Versluis PP, Cowles MW, Brunzelle J, Yang Z, Vega IE, Sun ZW, Rothbart SB. 2018. A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity. Sci Adv.

Valkenburg KC, De Marzo AM, Williams BO. 2017. Deletion of tumor suppressors adenomatous polyposis coli and Smad4 in murine luminal epithelial cells causes invasive prostate cancer and loss of androgen receptor expressionOncotarget 8(46):80265-80277.

Du M, Yaun Z, Yu H, Henderson N, Sarowar S, Zhao G, Werneburg GT, Thanassi DG, Li H. 2018. Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimDNature.

Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenberg AJ. 2018. Examining the roles of H3K4 methylation states with systematically characterized antibodiesMol Cell.
*Video abstract

Cooper JF, Van Raamsdonk JM. 2018. Modeling Parkinson’s disease in C. elegansJ Parkinson’s Dis 8(1):17–32.

Krajnak K, Dahl R. 2018. A new target for Alzheimer’s disease: a small molecule SERCA activator is neuroprotective in vitro and improves memory and cognition in APP/PS1 miceBioorg Med Chem Lett 28(9):1591–1594.

Krajnak K, Dahl R. 2018. Small molecule SUMOylation activators are novel neuroprotective agentsBioorg Med Chem Lett 28(3): 405–409.

Yang S, Wu T, Xu TH, de Waal PW, He Y, Pu M, Chen Y, DeBruine ZJ, Zhang B, Zaidi SA, Popov P, Guo Y, Han GW, Lu Y, Suino-Powell K, Song S, Harikumar KG, Miller LJ, Katritch V, Xu HE, Shui W, Stevens RC, Melcher K, Zhao S, Xu F. 2018. Crystal structure of the Frizzled 4 receptor in a ligand-free stateNature.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. 2018. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenanceNuc Acids Res.

Pierce SE, Tyson T, Booms A, Prahl J, Coetzee GA. 2018. Parkinson’s disease genetic risk in a midbrain neuronal cell lineNeurobiol Dis 114:53–64.

Fan C*, Choi W*, Sun W, Du J, Lü W. 2018. Structure of the human lipid-gated cation channel TRPC3eLife 4;7.
*Co-first author

Yin W, Zhou XE, Yang D, de Waal PW, Want M, Dai A, Cai X, Haung CY, Liu P, Wang X, Yin Y, Liu B, Zhou Y, Wang J, Liu H, Caffrey M, Melcher K, Xu Y, Wang MW, Xu HE, Jiang Y. 2018. Crystal structure of the human 5-HT1B serotonin receptor bound to an inverse agonistCell Disc 4(12).

Williams ET, Glauser L, Tsika E, Jiang H, Islam S, Moore DJ. 2018. Parkin mediates the ubiquitination of VPS35 and modulates retromer-dependent endosomal sortingHum Mol Genet.

Peacock JD, Pridgeon MG, Tovar EA, Essenburg CJ, Bowman M, Madaj Z, 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 MR. 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.

Williams ET, Moore DJ. 2018. Deciphering the role of VPS35 in Parkinson’s diseaseJ Neurosci Res 96(8):1339–1340.

Senchuk MM, Dues DJ, Schaar CE, Johnson BK, Madaj ZB, Bowman MJ, Winn 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.

Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB. 2018. Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1Proc Natl Acad Sci U S A

Kang Y*, Kuybeda O*, de Waal PW*, Mukherjee S, Van Eps N, Dutka P, Zhou XE, Bartesaghi A, Erramilli S, Morizumi T, Gu X, Yin Y, Liu P, Jiang Y, Meng X, Zhao G, Melcher K, Ernst OP, Kossiakoff AA, Subramaniam S, Xu HE. 2018. Cryo-EM structure of human rhodopsin bound to an inhibitory G proteinNature.

2017

Cooper JF, Machiela M, Dues DJ, Spielbauer KK, Senchuk MM, Van Raamsdonk JM. 2017. Activation of the mitochondrial unfolded protein response promotes longevity and dopamine neuron survival in Parkinson’s disease modelsSci Rep 7:16441.

DeBruine ZJ, Xu HE, Melcher K. 2017. Assembly and architecture of the Wnt/β-catenin signalosome at the membraneBr J Pharmacol 174(24):4564–4574.

Dunn EM, Billquist EJ, VanderStoep AL, Bax PG, Westrate LM, McLellan LK, Peterson SC, MacKeigan JP, Putzke AP. 2017. Dual roles of Fer kinase are required for proper hematopoiesis and vascular endothelium organization during zebrafish developmentBiology (Basel) 6(4):40.

Merrill NM, Schipper JL, Karnes JB, Kauffman AL, Martin KR, MacKeigan JP. 2017. PI3K-C2α knockdown decreases autophagy and maturation of endocytic vesiclesPLoS One 12(9):e0184909.

Bryleva EY, Keaton SA, Grit J, Madaj Z, Sauro-Nagendra A, Smart L, Halstead S, Achtyes E, Brundin L.  2017. The acute-phase mediator serum amyloid A is associated with symptoms of depression and fatigueActa Psychiatr Scand 135(5):409–418.

DeBruine ZJ, Ke J, Harikumar KG, Gu X, Borowsky P, Williams BO, Xu W, Miller LJ, Xu HE, Melcher K.  2017. Wnt5a promotes frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerizationGenes Dev 31(9):916–926.

Droscha CJ, Diegel CR, Ethen NJ, Burgers TA, McDonald MJ, Maupin KA, Naidu AS, Wang PF, Teh BT, Williams BO. 2017. Osteoblast-specific deletion of Hprt2/Cdc73 results in high bone mass and increased bone turnover. Bone 98:68–78.

Gu X, Yan Y, Novick SJ, Kovach A, Goswami D, Ke J, Tan MHE, Wang L, Li X, de Waal PW, Webb MR, Griffin PR, Xu HE, Melcher K. 2017. Deconvoluting AMP-dependent kinase (AMPK) adenine nucleotide binding and sensingJ Biol Chem 292(30):12653–12666.

Thellman NM, Botting C, Madaj Z, Triezenberg SJ. 2017. An immortalized human dorsal root ganglia cell line provides a novel context to study herpes simplex virus Type-1 latency and reactivationJ Virology 91(12): 00080-17.

Thellman NM, Triezenberg SJ. 2017. Herpes simplex virus establishment, maintenance, and reactivation: in vitro modeling of latencyPathogens 6(3):28.

Tyson T, Senchuk M, Cooper JF, George S, Van Raamsdonk JM, Brundin P. 2017. Novel animal model defines genetic contributions for neuron-to-neuron transfer of α-synucleinSci Rep7:7506.

Williams ET, Chen X, Moore DJ. 2017. VPS35, the retromer complex and Parkinson’s diseaseJ Parkinsons Dis 7(2):219–233.

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 receptorsJ Biol Chem 292(24):9865–9881.

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 K, Xu HE. 2017. Identification of phosphorylation codes for arrestin recruitment by G protein–coupled receptorsCell 170(3):457–469.e13.

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

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 368: 368ra174.

Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB. 2016. A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatic regulator BRD4J Chem Phys 145(15):154113.

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 K, Xu 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 receptorsJ Biol Chem.
*Editor’s pick, cover article and F1000 Prime article

Non peer-reviewed publications

2015

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

2014

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.

2013

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.

2012

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.

2010

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.

2009

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.