Student Publications

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 neurons. Mol Cell Neurosci 119:103702.

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 experience. J 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 lethality. Brain Commun 3(3).

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

Bagchi A, Beddows I, Cornelius A, Robinson GW, Jewell SD. 2021. Rare cases of medulloblastoma with hypermutation. Cancer 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 cohort. Hum Genom 15:48.

Liu Y, Molchanov V, Yang T. 2021. Enzymatic machinery of ubiquitin and ubiquitin-like modification systems in chondrocyte homeostasis and osteoarthritis. Curr 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 inhibition. Nat Struct Mol Biol.

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

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 immunohistochemistry. J 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 signaling. Epi Chromatin 14(7).

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 pathways. FASEB 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 RM, Kupai A, Rothbart SB. 2020. Chromatin regulation through ubiquitin and ubiquitin-like histone modifications. Trends Biochem Sci.

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

Vaughan RM, Kupai 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 models. Front Neurosci 14:719

Cunningham LA, Moore DJ. 2020. Endosomal sorting pathways in the pathogenesis of Parkinson’s disease. Prog 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 mice. Calcif 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 reagents. PLoS Genet 16(6):e1008940

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

Pierce SE, Booms A, Prahl J, van der Schans EJC, Tyson T, Coetzee GA. 2020. Post-GWAS knowledge gap: the how, where and when. npj 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 abnormalities. PLOS 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 signaling. PLOS 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 sarcoma. Mol Cancer Ther.

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 2. Nature.
*Co-first author
#Co-corresponding author

Colino-Sanguino Y, Cornett EM, Moulder D, Smith GC, Hrit J, Cordeiro-Spinetti E, Vaughan RM, Krajewski K, Rothbart SB*, Clark SJ*, Valdés-Mora F*. 2019. A read/write mechanism connects p300 Bromodomain function to H2A.Z acetylation. iScience 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 longevity. J 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 CD82. Bone 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 autophagy. iScience 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 methylation. J Biol Chem.
*Co-corresponding authors

Booms A, Coetzee GA, Pierce SE. 2019. MCF-7 as a model for functional analysis of breast cancer risk variants. Cancer 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-1. Science. 
* 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 manner. Clin 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 neurodegeneration. Proc Natl Acad Sci U S A.

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 FimD. Nature.

Dues DJ, Andrews EK, Senchuk MM, Van Raamsdonk JM. 2018. Resistance to stress can be experimentally dissociated from longevity. J 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 disease. Exp 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 stress. iScience 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 aging. Bone 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 pathways. BMC 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 transcription. Science 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 expression. Oncotarget 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 FimD. Nature.

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 antibodies. Mol Cell.
*Video abstract

Cooper JF, Van Raamsdonk JM. 2018. Modeling Parkinson’s disease in C. elegans. J 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 mice. Bioorg Med Chem Lett 28(9):1591–1594.

Krajnak K, Dahl R. 2018. Small molecule SUMOylation activators are novel neuroprotective agents. Bioorg 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 state. Nature.

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 maintenance. Nuc Acids Res.

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

Fan C*, Choi W*, Sun W, Du J, Lü W. 2018. Structure of the human lipid-gated cation channel TRPC3. eLife 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 agonist. Cell 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 sorting. Hum 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 tumors. Cancer Res 78(13):3672–3687.

Williams ET, Moore DJ. 2018. Deciphering the role of VPS35 in Parkinson’s disease. J 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 elegans. PLoS 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 UHRF1. Proc 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 protein. Nature.

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 models. Sci Rep 7:16441.

DeBruine ZJ, Xu HE, Melcher K. 2017. Assembly and architecture of the Wnt/β-catenin signalosome at the membrane. Br 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 development. Biology (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 vesicles. PLoS 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 fatigue. Acta 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 dimerization. Genes 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 sensing. J 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 reactivation. J Virology 91(12): 00080-17.

Thellman NM, Triezenberg SJ. 2017. Herpes simplex virus establishment, maintenance, and reactivation: in vitro modeling of latency. Pathogens 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-synuclein. Sci Rep7:7506.

Williams ET, Chen X, Moore DJ. 2017. VPS35, the retromer complex and Parkinson’s disease. J 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 receptors. J 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 receptors. Cell 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 3^rd 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 biosynthesis. J 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 disease. Sci 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 BRD4. J 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 receptors. Cell 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 disease. Sci 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 Gα_i1β₁γ₂ 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 phenotypes. Neurobiol 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 3^rd, 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 ischemia. PLoS One 11(1):e0146586.

Solitro AR, MacKeigan JP. 2016. Leaving the lysosome behind: novel developments in autophagy inhibition. Future 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 complex. Sci 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 tumorgrafts. Int 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 models. npj 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 profiling. J 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 synthesis. Neurobiol 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 glycogen. Cell 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 alterations. Am J Med Genet A 167(7):1429–1435.

Schaar CE, Dues DJ, Spielbauer KK, Machiela E, Cooper JF, Senchuk M, Hekimi S, Van Raamsdonk JM. 2015. Mitochondrial and cytoplasmic ROS have opposing effects on lifespan. PLoS 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 platelets. Exp 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 matriptase. Oncotarget 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 DWARF3. Cell 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 mice. Bone 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 tumorigenesis. Cancer 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 cancer. Am 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 levels. Cell 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 PTPMT1. PLoS 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 model. PLoS 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 response. Transl Res 164(2):139–148.

Scholten DJ 2nd, Timmer CM, Peacock J, Pelle DW, Williams BO, Steensma MR. 2014. Down regulation of Wnt signaling mitigates hypoxia-induced chemoresistance in human osteosarcoma cells. PLoS 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 events. PLoS 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 cells. Autophagy 9(1):74–92.

Maupin KA, Droscha CJ, Williams BO. 2013. A comprehensive overview of skeletal phenotypes associated with alterations in Wnt/β-catenin signaling in humans and mice. Bone 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 familiaris. PLoS 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 death. PLoS One 8(1):e53803.

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

Valkenburg KC, Steensma MR, Williams BO, Zhong Z. 2013. Skeletal metastasis: treatments, mouse models, and the Wnt signaling. Chin 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 death. Mol Cancer Res 6(4): 614–623.

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

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

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.