Hot Papers

Read the latest research from our laboratories published in scientific journals.

Islet macrophages shift to a reparative state following pancreatic beta-cell death and are a major source of islet insulin-like growth factor
Dominika Nackiewicz, Meixia Dan, Madeleine Speck, Samuel Z. Chow, Yi-Chen Chen, J. Andrew Pospisilik, C. Bruce Verchere and Jan A. Ehses
2020 | iScience

Analysis of neurodegenerative disease-causing genes in dementia with Lewy bodies
Tatiana Orme, Dena Hernandez, Owen A. Ross, Celia Kun-Rodrigues, Lee Darwent, Clarie E. Shepherd, Laura Parkkinen, Olaf Ansorge, Lorraine Clark, Lawrence S. Honig, Karen Marder, . . ., Andrew Singleton, Rita Guerreiro and José Brás
2020 | Acta Neuropathologica Communications

Methionine metabolism shapes T helper cell responses through regulation of epigenetic programming
Dominic G. Roy, Jocelyn Chen, Victoria Mamane, Eric H. Ma, Brejnev M. Muhire, Ryan D. Sheldon, Tatiana Shorstova, Rutger Koning, Radia M. Johnson, Ekaterina Esaulova, Kelsey S. Williams, Sebastian Hayes, Mya Steadman, Bozena Samborska, Amanda Swain, Audrey Daigneault, Victor Chubukov, Thomas P. Roddy, William Foulkes, J. Andrew Pospisilik, Marie-Claude Bourgeois-Daigneault, Maxim N. Artymov, Michael Witcher, Connie M. Krawczyk, Catherine Larochelle and Russell G. Jones
2020 | Cell Metabolism

Dnmt3a loss and Idh2 neomorphic mutations mutually potentiate malignant hematopoiesis
Xiaotian Zhang, Xinyu Wang, Xue Qing David Wang, Jianzhong Su, Nagireddy Putluri, Ting Zhou, Ying Qu, Mira Jeong, Anna Guzman, Carina Rosas, Yun (Nancy) Huang, Arun Sreekumar, Wei Li and Margaret A. Goodell
2020 | Blood

Impaired cell fate through gain-of-function mutations in a chromatic reader
Liling Wan, Shasha Chong, Fan Xuan, Angela Liang, Xiaodong Cui, Leah Gates, Thomas S. Carroll, Yuanyuan Li, Lijuan Feng, Guochao Chen, Shu-Ping Wang, Michael V. Ortiz, Sara K. Daley, Xiaolu Wang, Hongwen Xuan, Alex Kentsis, Tom W. Muir, Robert G. Roeder, Haitao Li, Wei Li, Robert Tjian, Hong Wen and C. David Allis
2020 | Nature

Inflammation and kynurenine pathway dysregulation in postpartum women with severe and suicidal depression
Eric Achtyes, Sarah A. Keaton, LeAnn Smart, Amanda R. Burmeister, Patrick L. Heilman, Stanislaw Krzyzanowski, Madhavi Nagalla, Gilles J. Guillemin, Martha L. Escobar Galvis, Chai K. Lim, Maria Muzik, Teodor T. Postolache, Richard Leach and Lena Brundin
2020 | Brain, Behavior, and Immunity

The structures and gating mechanism of human calcium homeostasis modulator 2
Wooyoung Choi, Nicolina Clemente, Weinan Sun, Juan Du and Wei Lü
2019 | Nature

α-Synuclein conformational strains spread, see and target neuronal cells differentially after injection into the olfactory bulb
Nolwen L. Rey, Luc Bousset, Sonia George, Zachary Madaj, Lindsay Meyerdirk, Emily Schulz, Jennifer A. Steiner, Ronald Melki and Patrik Brundin
2019 | Acta Neuropathologica Communications

Integrated epigenome, exome, and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids
Jitu Wilson George, Huihui Fan, Benjamin Johnson, Tyler James Carpenter, Kelly Katherine Foy, Anindita Chatterjee, Amanda Lynn Patterson, Julie Koeman, Marie Adams, Zachary Brian Madaj, David Chesla, Erica Elizabeth Marsh, Timothy Junius Triche, Hui Shen and Jose Manuel Teixeira
2019 | Cell Reports

An AARS variant as the likely cause of Swedish type hereditary diffuse leukoencephalopathy with spheroids
Christina Sundal, Susana Carmona, Maria Yhr, Odd Almström, Maria Ljungberg, John Hardy, Carola Hedberg-Oldfors, Åsa Fred, José Brás, Anders Oldfors, Oluf Andersen and Rita Guerreiro
2019 | Acta Neuropathologica Communications

Identification of novel risk loci, causal insights, and heritable risk for Parkinson’s disease: a meta-analysis of genome-wide association studies
Mike A. Nalls, Cornelis Blauwendraat, Costanza L. Vallerga, Karl Heilbron, Sara Bandres-Ciga, Diana Chang, Manuela Tan, Demis A. Kia, Alastair J. Noyce, Angli Xue, José Brás, Emily Young, . . . Peter M. Visscher, Robert R. Graham, Andrew B. Singleton, System Genomics of Parkinson’s Disease Consortium and International Parkinson’s Disease Genomics Consortium
2019 | Lancet Neurology

Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation
Maria A. Hahn, Seung-Gi Jin, Arthur X. Li, Jiancheng Liu, Zhijun Huang, Xiwei Wu, Byung-wook Kim, Jennifer Johnson, Adrienne-Denise V. Bilbao, Shu Tao, Jacob A. Yim, Yuman Fong, Sandra Goebbels, Markus H. Schwb, Qiang Lu and Gerd P. Pfeifer
2019 | Science Advances

Metabolic profiling using stable isotope tracing reveals distinct patterns of glucose utilization by physiologically activated CD8+ T cells
Eric H. Ma, Mark J. Verway, Radia M. Johnson, Dominic G. Roy, Mya Steadman, Sebastian Hayes, Kelsey S. Williams, Ryan D. Sheldon, Bozena Samborska, Penelope A. Kosinski, Hyeryun Kim, Takla Griss, Brandon Faubert, Stephanie Condotta, Connie M. Krawczyk, Ralph J. DeBerardinis, Kelly M. Stewart, Martin J. Richer, Victor Chubukov, Thomas P. Roddy and Russell G. Jones
2019 | Immunity

Lysine methylation regulators moonlighting outside the epigenome
Cornett, Evan M., Laure Ferry, Pierre-Antoine Defossez and Scott B. Rothbart
2019 | Molecular Cell

Ctf4 organizes sister replisomes and Pol α into a replication factory
Zuanning Yuan, Roxana Georgescu, Ruda de Luna Almeida Santos, Daniel Zhang, Lin Bai, Nina Y. Yao, Gongpu Zhao, Michael E. O’Donnell and Huilin Li
2019 | eLife

Isolation of cardiomyocytes undergoing mitosis with complete cytokinesis
Hsiao-yun Y. Milliron, Matthew J. Weiland, Eric J. Kort and Stefan Jovinge
In press | Circulation Research

Role of the kynurenine pathway and the endocannabinoid system as modulators of inflammation and personality traits
Patrick Heilman, Matthew N. Hill, Mary Coussons-Read, Lena Brundin and Emil F. Coccaro
In press | Psychoneuroendocrinology

Oral vitamin C supplementation to patients with myeloid cancer treatment: normalization of plasma vitamin C induces epigenetic changes
Linn Gillberg, Andreas D. Ørskov, Ammar Nasif, Hitoshi Ohtani, Zachary Madaj, Jakob W. Hansen, Nicholas Rapin, Johanne B. Mogensen, Minmin Liu, Inge H. Dufva, Jens Lykkesfeldt, Petra Hajkova, Peter A. Jones and Kirsten Grønbaek
2019 | Clinical Epigenetics

Autoinhibition and activation mechanisms of the eukaryotic lipid flippase Drs2p–Cdc50p
Lin Bai, Amanda Kovach, Qinglong You, Hao-Chi Hsu, Gongpu Zhao and Huilin Li
2019 | Nature Communications

Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel
Yihe Huang, Becca Roth, Wei Lü and Juan Du
2019 | eLife

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
Robert M. Vaughan, Scott B. Rothbart and Bradley M. Dickson
In press | Journal of Biological Chemistry

Patient-derived xenografts of central nervous system metastasis reveal expansion of aggressive minor clones
Ben Yi, Tew, Christophe Legendre, Mark A. Schroeder, Tim Triche, Jr., Gerald C. Gooden, Yizhou Huang, Loren Butry, Daniel J. Ma, Kyle Johnson, Rae Anne Martinez, Mariaelena Pierobon, Emanuel F. Petricoin, Joyce O’Shaughnessy, Cindy Osborne, Coya Tapia, David N. Buckley, Jennifer Glen, Mark Bernstein, Jann N. Sarkaria, Steven A. Toms and Bodour Salhia
In press | Neuro-Oncology

Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson’s disease
Sonia George, Nolwen L. Rey, Trevor Tyson, Corinne Esquibel, Lindsay Meyerdirk, Emily Schulz, Steven Pierce, Amanda R. Burnmeister, Zachary B. Madaj, Jennifer A. Steiner, Martha L. Escobar Galvis, Lena Brundin and Patrik Brundin
2019 | Molecular Neurodegeneration

Protein interactions at oxidized 5-methylcytosine bases
Gerd P. Pfeifer, Piroska E. Szabó and Jikui Song
In press | Journal of Molecular Biology

Isoform-specific destabilization of the active site reveals a molecular mechanism of intrinsic activation of KRas G13D
Christian W. Johnson, Yi-Jang Lin, Derion Reid, Jillian Parker, Spiro Pavlopoulos, Patrick Dischinger, Carrie Graveel, Andrew J. Aguirre, Matthew Steensma, Kevin M. Haigis and Carla Mattos
2019 | Cell Reports

Notch3 promotes prostate cancer-induced bone lesion development via MMP-3
Sourik S. Ganguly, Galen Hostetter, Lin Tang, Sander B. Frank, Kathylynn Saboda, Rohit Mehra, Lisha Wang, Xiaohong Li, Evan T. Keller and Cindy K. Miranti
In press | Oncogene

Before and after: comparison of legacy and harmonized TCGA Genomic Data Commons’ data
Galen F. Gao, Joel S. Parker, Sheila M. Reynolds, Tiago D. Silva, Liang-Bo Wang, Wanding Zhou, Rehan Akbani, Matthew Bailey, Saianand Balu, Benjamin P. Berman, et al.
2019 | Cell Systems

Structure-based design of a hyperthermostable AgURicase for hyperuricemia and gout therapy
Yi Shi, Ting Wang, X. Edward Zhou, Qiu-feng Liu, Yi Jiang and H. Eric Xu
In press | Acta Pharmacologica Sinica

Single cell expression analysis reveals anatomical and cell cycle–dependent transcriptions shifts during heart development
Guang Li, Lei Tian, William Goodyer, Eric J. Kort, Jan Willem Buikema, Adele Xu, Joseph Wu, Stefan Jovinge and Sean M. Wu
In press | Development

A novel mass spectrometry platform for multiplexed N-glycoprotein biomarker discovery from patient biofluids by antibody panel based N-glycan imaging
Alyson P. Black, Hongyan Liang, Connor A. West, Mengjun Wang, Harmin P. Herrera, Brian B. Haab, Peggi M. Angel, Richard R. Drake and Anand S. Mehta
2019 | Analytical Chemistry

Chromatin architecture as an essential determinant of dendritic cell function
Giselle M. Boukhaled, Mario Corrado, Hannah Guak and Connie M. Krawczyk
2019 | Frontiers in Immunology

Structure of the eukaryotic protein O-mannosyltransferase Pmt1-Pmt2 complex
Lin Bai, Amanda Kovach, Qinglong You, Alanna Kenny and Huilin Li
In press | Nature Structural & Molecular Biology

MCF-7 as a model for functional analysis of breast cancer risk variants 
Alix Booms, Gerhard A. Coetzee and Steven E. Pierce 
In press | Cancer Epidemiology, Biomarkers and Prevention

Assembly of gold nanoparticles into chiral superstructures driven by circularly polarized light
Ji-Young Kim, Jihyeon Yeom, Gongpu Zhao, Heather Calcaterra, Jiyoun Munn, Peijun Zhang and Nicholas Kotov
In press | Journal of the American Chemical Society

Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms
Peipei Li, Lee Marshall, Gabriel Oh, Jennifer L. Jakubowski, Daniel Groot, Yu He, Ting Wang, Arturas Petronis and Viviane Labrie 
2019 | Nature Communications

EHMT2 and SETDB1 protect the maternal pronucleus from 5mC oxidation
Tie-Bo Zeng, Li Han, Nicholas Pierce, Gerd P. Pfeifer and Piroska E. Szabó 
In press | Proceedings of the National Academy of Sciences U.S.A.

Characterization of guided entry of tail-anchored proteins 3 homologues in Mycobacterium tuberculosis
Kuan Hu, Ashley T. Jordan, Susan Zhang, Avantika Dhabaria, Amanda Kovach, Margarita Rangel, Beatrix Ueberheide, Huilin Li and K. Heran Darwin 
In press | Journal of Bacteriology

Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF
Yi Zhang, Younghoon Jang, Ji-Eun Lee, JaeWoo Ahn, Longxia Xu, Michael R. Holden, Evan M. Cornett, Krzysztof Krajewski, Barbara J. Klein, Shu-Ping Wang, Yali Dou, Robert G. Roeder, Brian D. Strahl, Scott B. Rothbart, Xiaobing Shi, Kai Ge and Tatiana G. Kutateladze 
2019 | Nature Communications

Peri-infarct upregulation of the oxytocin receptor in vascular dementia
Erin C. McKay, John S. Beck, Sok Kean Khoo, Karl J. Dykema, Sandra L. Cottingham, Mary E. Winn, Henry L. Paulson, Andrew P. Lieberman, and Scott E. Counts 
2019 | Journal of Neuropathology and Experimental Neurology

Structure and dynamics of the active human parathyroid hormone receptor-1
Li-Hua Zhao, Shanshan Ma, Ieva Sutkeviciute, Dan-Dan Shen, X. Edward Zhou, Parker W. de Waal, Chen-Yao Li, Yanyong Kang, Lisa J. Clark, Frederic G. Jean-Alphonse, Alex D. White, Dehua Yang, Antao Dai, Xiaoqing Cai, Jian Chen, Cong Li, Yi Jiang, Tomoyuki Watanabe, Thomas J. Gardella, Karsten Melcher, Ming-Wei Wang, Jean-Pierre Vilardaga, H. Eric Xu, and Yan Zhang 
2019 | Science

PRMT1 loss sensitizes cells to PRMT5 inhibition
Gao, Guozhen, Liang Zhang, Oscar D. Villarreal, Wei He, Dan Su, Ella Bedford, Phoebe Moh, Jianjun Shen, Xiaobing Shi, Mark T. Bedford and Han Xu
In press | Nucleic Acids Research

The efficacy and safety of Sendai viral reprogramming of mouse primary cells using human vectors
Laura Tarnawski, Emily Eugster, Lisa DeCamp and Stefan Jovinge 
In press | Cellular Reprogramming

In vivo application of the REMOTE-control system for the manipulation of endogenous gene expression
Nicole A. Vander Schaaf, Shirley Oghamian, Jin-A Park, Liang Kang, Peter W. Laird and KwangHo Lee
2019 | Journal of Visualized Experiments

Altered tryptophan catabolism in placentas from women with pre-eclampsia
Sarah A. Keaton, Patrick Heilman, Elena Y. Bryleva, Zachary Madaj, Stanislaw Krzyzanowski, Jamie Grit, Emily S. Miller, Maya Jälmby, Grigoros Kalapotharakos, Karen Racicot, Asgerally Fazleabas, Stefan R. Hansson and Lena Brundin
In press | International Journal of Tryptophan Research

Automated identification and quantification of signals in multichannel immunofluorescence images: the SignalFinder platform
Daniel Barnett, Johnathan Hall and Brian Haab
In press | American Journal of Pathology

Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis
Shraddha Pai, Peipei Li, Bryan Killinger, Lee Marshall, Peixin Jia, Ji Liao, Arturas Petronis, Piroska E. Szabó and Viviane Labrie
2019 | Nature Communications

The ZZ domain as a new epigenetic reader and a degradation signal sensor
Yi Zhang, Wenyi Mi, Yongming Xue, Xiaobing Shi and Tatiana G. Kutateladze
In press | Critical Reviews in Biochemistry and Molecular Biology

Parkinson’s disease-linked D620N VPS35 knockin mice manifest tau neuropathology and dopaminergic neurodegeneration
Xi Chen, Jennifer K. Kordich, Erin T. Williams, Nathan Levine, Allyson Cole-Strauss, Lee Marshall, Viviane Labrie, Jiyan Ma, Jack W. Lipton and Darren J. Moore 
2019 | Proceedings of the National Academy of Sciences U.S.A.

Regulation of cytoskeleton and adhesion signaling in osteoclasts by tetraspanin CD82
Alexis Bergsma, Sourik S. Ganguly, Mollie E. Wiegand, Daniel Dick, Bart O. Williams and Cindy K. Miranti
In press | Bone Reports

The Biospecimen Preanalytical Variables Program: a multiassay comparison of effects of delay to fixation and fixation duration on nucleic acid quality
Carithers, Latarsha J., Agarwal Rachana, Ping Guan, Hana Odeh, Michael C. Sachs, Kelly B. Engel, Sarah R. Greytak, Mary Barcus, Conrado Soria, Chih-Jian Lih, P. Mickey Williams, Philip A. Branton, Leslie Sobin, Benjamin Fombonne, Therese Bocklage, Chris Andry, Elizabeth R. Duffy, Gabriel Sica, Rajib Dhir, Scott Jewell, Nancy Roche and Helen M. Moore
In press | Archives of Pathology and Laboratory Medicine

Epigenetic therapy in immune-oncology
Peter A. Jones, Hitoshi Ohtani, Ankur Chakravarthy and Daniel D. De Carvalho 
In press | Nature Reviews Cancer 

Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease
Gabriel Oh, Karolis Koncevičius, Sasha Ebrahimi, Matthew Carlucci, Daniel Erik Groot, Akhil Nair, Aiping Zhang, Algimantas Kriščiūnas, Edward S. Oh, Viviane Labrie, Albert H.C. Wong, Juozas Gordevičius, Peixin Jia, Miki Susic and Art Petronis 
2019 | Genome Biology

Trabectedin inhibits EWS-FLI1 and evicts SWI/SNF from chromatin in a schedule dependent manner
Matt L. Harlow, Maggie H. Chasse, Elissa A. Boguslawski, Katie M. Sorensen, Jenna M. Gedminas, Susan M. Kitchen-Goosen, Scott B. Rothbart, Cenny Taslim, Stephen L. Lessnick, Anderson S. Peck, Zachary B. Madaj, Megan J. Bowman and Patrick J. Grohar 
In press | Clinical Cancer Research 

Streamlined analysis of LINCS L1000 data with the slinky package for R
Eric J. Kort and Stefan Jovinge 
In press | Bioinformatics 

The sTRA plasma biomarker: blinded validation of improved accuracy over CA19-9 in pancreatic cancer diagnosis
Ben Staal, Ying Liu, Daniel Barnett, Peter Hsueh, Zonglin He, Chong-Feng Gao, Katie Partyka, Mark W. Hurd, Aatur D. Singhi, Richard R. Drake, Ying Huang, Anirban Maitra, Randall E. Brand and Brian B. Haab
In press | Clinical Cancer Research

Erroneous rates and false statistical confirmations from infrequent metadynamics and other equivalent violations of the hyperdynamics paradigm
Bradley M. Dickson
2019 | Journal of Chemical Theory and Computation

An inflammatory profile linked to increased suicide risk
Sarah A. Keaton, Zachary B. Madaj, Patrick Heilman, LeAnn Smart, Jamie Grit, Robert Gibbons, Teodor T. Postolache, Kimberly Roaten, Eric D. Achtyes and Lena Brundin
In press | Journal of Affective Disorders

Cold ischemia score: an mRNA assay for the detection of extended cold ischemia in formalin-fixed, paraffin-embedded tissue
William Mathieson, Kathleen Mommaerts, Johanna M. Trouet, Conny Mathay, Ping Guan, Latarsha J. Carithers, Daniel Rohrer, Dana R. Valley, Alexander Blanski, Scott Jewell, Helen M. Moore and Fay Betsou
In press | Journal of Histochemistry and Cytochemistry

Mother–child transmission of epigenetic information by tunable polymorphic imprinting 
Brittany L. Carpenter, Wanding Zhou, Zachary Madaj, Ashley K. DeWitt, Jason P. Ross, Kirsten Grønbaek, Gangning Liang, Susan J. Clark, Peter L. Molloy and Peter A. Jones 
2018 | Proceedings of the National Academy of Sciences U.S.A. 

Transposable element expression in acute myeloid leukemia transcriptome and prognosis 
Anthony R. Colombo, Timothy Triche, Jr. and Giridharan Ramsingh 
2018 | Scientific Reports   

KRAS suppression-induced degradation of MYC is antagonized by a MEK5-ERK5 compensatory mechanism 
Angelina V. Vaseva, Devon R. Blake, Thomas S.K. Gilbert, Serina Ng, Galen Hostetter, Salma H. Azam, Dagliyan Ozkan, Irem, Prson Gautam, Kirsten L. Bryant, Kenneth H. Pearce, Laura E. Herring, Haiyong Han, Lee M. Graves, Agnieszka K. Witkiewicz, Erik S. Knudsen, Chad V. Pecot, Naim Rashid, Peter J. Houghton, Krister Wennerberg, Adrienne D. Cox and Channing J. Der 
2018 | Cancer Cell  

Leaky gut biomarkers in depression and suicidal behavior 
Lars Ohlsson, Anna Gustafsson, Eva Lavant, Klara Suneson, Lena Brundin, Åsa Westrin, Lennart Ljunggren and Daniel Lindqvist 
In press | Acta Psychiatrica Scandinavica 

Small nucleolar RNA score: an assay to detect formalin-overfixed tissue 
Wim Ammerlaan, Johanna Trouet, Michael C. Sachs, Ping Guan, Latarsha Carithers, Pauline Lambert, Sonia Frasquiho, Laurent Antunes, Olga Kofanova, Daniel Rohrer, Dana R. Valley, Alex Blanski, Scott Jewell, Helen Moore and Fay Betsou 
2018 | Biopreservation and Biobanking 

Functional analysis and fine mapping of the 9p22.2 ovarian cancer susceptibility locus 
Melissa A. Buckley, Nicholas T. Woods, Jonathan P. Tyrer, Gustavo Mendoza-Fandiño, Kate Lawrenson, Dennis J. Hazelett, Hamed S. Najafabadi, Anxhela Gjyshi, Renato S. Carvalho, Paulo C. Lyra, Jr., Simon G. Coetzee, Howard C. Shen, Ally W. Yang, Madalene A. Earp, Sean J. Yoder, Harvey Risch, Georgia Chenevix-Trench, Susan J. Ramus, Catherine M. Phelan, Gerhard A. Coetzee, Houtan Noushmehr, Timothy R. Hughes, Thomas A. Sellers, Ellen L. Goode, Paul D. Pharoah, Simon A. Gayther and Alvaro N.A. Montiero 
2018 | Cancer Research

Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states 
Yan Yan, X. Edward Zhou, Scott J. Novick, Simon J. Shaw, Yingwu Li, Joseph S. Brunzelle, Yasumichi Hitoshi, Patrick R. Griffin, H. Eric Xu and Karsten Melcher 
2018 | Journal of Biological Chemistry 

A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity 
Evan M. Cornett, Bradley M. Dickson, Krzysztof Krajewski, Nicholas Spellmon, Andrew Umstead, Robert M. Vaughan, Kevin M. Shaw, Philip P. Versluis, Martis W. Cowles, Joseph Brunzelle, Zhe Yang, Irving E. Vega, Zu-Wen Sun and Scott B. Rothbart 
2018 | Science Advances 

Deciphering protein glycosylation by computational integration of on-chip profiling, glycan-array data, and mass spectrometry 
Zachary Klamer, Peter Hsueh, David Ayala-Talavera and Brian Haab 
In press | Molecular & Cellular Proteomics 

Loss of myeloid-specific TGF-β signaling decreases CTHRC1 to downregulate bFGF and the development of H19930-induced osteolytic bone lesions 
Sourik S. Ganguly, Paul G. Daft, Jingchen Cao, Xiangqi Meng, Zhendong A. Zhong, Alexandra Vander Ark, Austin Meadows, Zach Madaj, Bart Williams and Xiaohong Li 
2018 | Cancers 

Metabolomic profiling of bile acids in an experimental model of prodromal Parkinson’s disease 
Stewart F. Graham, Nolwen L. Rey, Zafer Ugur, Ali Yilmaz, Eric Sherman, Michael Maddens, Ray O. Bahado-Singh, Katelyn Becker, Emily Schulz, Lindsay K. Meyerdirk, Jennifer A. Steiner, Jiyan Ma and Patrik Brundin 
2018 | Metabolites  

ATP hydrolysis-coupled peptide translocation mechanism of Mycobacterium tuberculosis ClpB 
Hongjun Yu, Tania J. Lupoli, Amanda Kovach, Xing Meng, Gongpu Zhao, Carl F. Nathan and Huilin Li 
2018 | Proceedings of the National Academy of Sciences U.S.A. 

The vermiform appendix impacts the risk of developing Parkinson’s disease 
Bryan A. Killinger*, Zachary Madaj*, Jacek W. Sikora, Nolwen Rey, Alec J. Haas, Yamini Vepa, Daniel Lindqvist, Honglei Chen, Paul M. Thomas, Patrik Brundin, Lena Brundin and Viviane Labrie 
2018 | Science Translational Medicine  

Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD 
Minge Du, Zuanning Yuan, Hongjun Yu, Nadine Henderson, Samema Sarowar, Gongpu Zhao, Glenn T. Werneburg, David G. Thanassi and Huilin Li 
2018 | Nature 

The chromatin accessibility landscape of primary human cancers 
M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago D. Silva, Clarice Groenveld, Christopher K. Wong, Seung Woo Cho, . . ., Peter W. Laird, Christina Curtis, The Cancer Genome Atlas Research Network, William J. Greenleaf and Howard Y. Chang 
2018 | Science 

Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium 
Yihe Huang, Paige A. Winkler, Weinan Sun, Wei Lü and Juan Du 
2018 | Nature 

α-Synuclein expression from a single copy transgene increases sensitivity to stress and accelerates neuronal loss in genetic models of Parkinson’s disease 
Jason F. Cooper, Katie K. Speielbauer, Megan M. Senchuk, Saravanapriah Nadarajan, Monica P. Colaiácovo and Jeremy M. Van Raamsdonk 
2018 | Experimental Neurology 

Effects of treatment with adalimumab on blood lipid levels and atherosclerosis in patients with rheumatoid arthritis 
Ulf Bergström, Stefan Jovinge, Jerker Persson, Lennart T.H. Jacobsson and Carl Turesson 
2018 | Current Therapeutic Research 

Conformational heterogeneity of the allosteric drug and metabolite (ADaM) site in AMP-activated protein kinase (AMPK) 
Xin Gu, Michael D. Bridges, Yan Yan, Parker W. de Waal, X. Edward Zhou, Kelly M. Suino-Powell, H. Eric Xu, Wayne L. Hubbell and Karsten Melcher 
2018 | Journal of Biological Chemistry 

A phase I trial of guadecitabine (SGI-110) and irinotecan in metastatic colorectal cancer patients previously exposed to irinotecan 
Valerie Lee, Judy S. Wang, Marianna L. Zahurak, Elske C. Gootjes, Henk M.W. Verheul, Rose M. Parkinson, Zachary Kerner, Anup Sharma, Gary L. Rosner, Ana De Jesus-Acosta, Daniel A. Laheru, Dung T. Le, Aram Oganesian, Ellen Lilly-Foreman, Thomas Brown, Peter A. Jones, Stephen B. Baylin, Nita Ahuja and Nilofer S. Azad 
2018 | Clinical Cancer Research 

NF1 deficiency correlates with estrogen receptor signaling and diminished survival in breast cancer 
Patrick S. Dischinger, Elizabeth A. Tovar, Curt J. Essenburg, Zachary B. Madaj, Eve E. Gardner, Megan E. Callaghan, Ashley N. Turner, Anil K. Challa, Tristan Kempston, Bryn Eagleson, Robert A. Kesterson, Roderick T. Bronson, Megan J. Bowman, Carrie R. Graveel and Matthew R. Steensma 
2018 | npj Breast Cancer 

Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1 
Robert M.Vaughan, Bradley M. Dickson, Matthew F. Whelihan, Andrea L. Johnstone, Evan M. Cornett, Marcus A. Cheek, Christine A. Ausherman, Martis W. Cowles, Zu-Wen Sun and Scott B. Rothbart 
2018 | Proceedings of the National Academy of Sciences U.S.A.  

Dual inhibition of DNA and histone methyltransferases increases viral mimicry in ovarian cancer cells 
Minmin Liu, Stacey L. Thomas, Ashley K. DeWitt, Wanding Zhou, Zachary B. Madaj, Hitoshi Ohtani, Stephen B. Baylin, Gangning Liang and Peter A. Jones 
2018 | Cancer Research 

Biobanks and the moral concerns of donors: a democratic deliberation 
Raymond G. De Vries, Kerry A. Ryan, Linda Gordon, Chris D. Krenz, Tom Tomlinson, Scott Jewell and Scott Y.H. Kim 
2018 | Qualitative Health Research 

Bone loss from Wnt inhibition mitigated by concurrent alendronate therapy 
Babita Madan, Mitchell J. McDonald, Gabrielle E. Foxa, Cassandra R. Diegel, Bart O. Williams and David M. Virshup 
2018 | Bone Research 

Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses 
Hitoshi Ohtani, Minmin Liu, Wanding Zhou, Gangning Liang and Peter A. Jones 
2018 | Genome Research 

SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions 
Wanding Zhou, Timothy J. Triche, Jr., Peter W. Laird and Hui Shen 
2018 | Nucleic Acids Research

14-3-3 proteins reduce cell-to-cell transfer and propagation of pathogenic alpha-synuclein 
Bing Wang, Rachel Underwood, Anjali Kamath, Colleen Britain, Michael B. McFerrin, Pamela J. McLean, Laura A. Volpicelli-Daley, Robert H. Whitaker, William J. Placzek, Katelyn Becker, Jiyan Ma and Talene A. Yacoubian 
2018 | Journal of Neuroscience 

Novel common genetic susceptibility loci for colorectal cancer 
Stephanie L. Schmitt, Christopher K. Edlund, Frederick R. Schumacher, Jian Gong, Tabitha A. Harrison, Jeroen R. Huyghe, Chenxu Qu, Marilena Melas, David J. Van Den Berg, Hansong Wang, Stephanie Tring, . . ., Gerhard A. Coetzee, Michelle Cotterchio, . . ., Li Hsu, David V. Conti and Stephen B. Gruber 
2018 | Journal of the National Cancer Institute

Molecular mechanism of GPCR-mediated arrestin activation 
Naomi R. Latorraca, Jason K. Wang, Brian Bauer, Raphael J.L. Townshend, Scott A. Hollingsworth, Julie E. Olivieri, H. Eric Xu, Martha E. Sommer and Ron O. Dror 
2018 | Nature

Nuclear PTEN localization contributes to DNA damage repair in endometrial cancer and could have a diagnostic benefit for therapeutic management of the disease 
Ananda Mukherjee, Amanda L. Patterson, Jitu W. George, Tyler J. Carpenter, Zachary B. Madaj, Galen Hostetter, John I. Risinger and Jose M. Teixeira 
2018 | Molecular Cancer Therapeutics

Global deletion of tetraspanin CD82 attenuates bone growth and enhances bone marrow adipogenesis 
Alexis Bergsma, Sourik S. Ganguly, Daniel Dick, Bart O. Williams and Cindy K. Miranti 
2018 | Bone

Integrated molecular characterization of testicular germ cell tumors
Hui Shen, Juliann Shih, Daniel P. Hollern, Linghua Wang, Reanne Bowlby, Satish K. Tickoo, Vésteinn Thorsson, Andrew J. Mungall, Yulia Newton, Apurva M. Hegde, Joshua Armenia, . . ., The Cancer Genome Atlas Research Network, Rehan Akbani, David A. Wheeler, Peter W. Laird, Katherine L. Nathanson, Victoria K. Cortessis, and Katherine A. Hoadley 
2018 | Cell Reports

Cryo-EM structure of human rhodopsin bound to an inhibitory G protein 
Yanyong Kang, Oleg Kuybeda, Parker W. De Waal, Somnath Mukherjee, Ned Van Eps, Przemyslaw Dutka, X. Edward Zhou, Alberto Bartesaghi, Satchal Erramilli, Takefumi Morizumi, Xin Gu, Yanting Yin, Ping Liu, Yi Jiang, Xing Meng, Gongpu Zhao, Karsten Melcher, Oliver P. Ernst, Anthony A. Kossiakoff, Sriram Subramanian, and H. Eric Xu 
2018 | Nature

Parkin mediates the ubiquitination of VPS35 and modulates retromer-dependent endosomal sorting
Erin T. Williams, Liliane Glauser, Elpida Tsika, Haisong Jiang, Shariful Islam, and Darren J. Moore 
2018 | Human Molecular Genetics

Targeting energy metabolism via the mitochondrial pyruvate carrier as a novel approach to attenuate neurodegeneration 
Emmanuel Quansah, Wouter Peelaerts, J. William Langston, David K. Simon, Jerry Colca, and Patrik Brundin 
2018 | Molecular Neurodegeneration

Structure of the human lipid-gated cation channel TRPC3 
Chen Fan, Wooyoung Choi, Weinan Sun, Juan Du and Wei Lu 
2018 | eLife

Biochemical profiling of the brain and blood metabolome in a mouse model of prodromal Parkinson’s disease reveals distinct metabolic profiles 
Stewart F. Graham, Nolwen L. Rey, Ali Yilmaz, Preveen Kumar, Zachary Madaj, Michael Maddens, Ray O. Bahado-Singh, Katelyn Becker, Emily Schulz, Lindsay K. Meyerdirk, Jennifer A. Steiner, Jiyan Ma and Patrik Brundin 
2018 | Journal of Proteome Research

Structure of an ancient respiratory system 
Hongjun Yu, Chang-Hao Wu, Gerrit J. Schut, Dominik K. Haja, Gongpu Zhao, John W. Peters, Michael W.W. Adams and Huilin Li 
2018 | Cell

LRP1 suppresses bone resorption in mice by inhibiting the RANKL-stimulated NFκB and p38 pathways during osteoclastogenesis 
Di Lu, Jianshuang Li, Huadie Liu, Gabrielle E. Foxa, Kevin Weaver, Jie Li, Bart O. William and Tao Yang 
2018 | Journal of Bone and Mineral Research

Defining driver DNA methylation changes in human cancer 
Gerd P. Pfeifer 
2018 | International Journal of Molecular Sciences

DNA methylation loss in late-replicating domains is linked to mitotic cell division 
Wanding Zhou, Huy Q. Dinh, Zachary Ramjan, Daniel J. Weisenberger, Charles M. Nicolet, Hui Shen, Peter W. Laird and Benjamin P. Berman 
2018 | Nature Genetics

Genomic status of MET potentiates sensitivity to MET and MEK inhibition in NF1-related peripheral nerve sheath tumors
Jacqueline D. Peacock, Matthew G. Pridgeon, Elizabeth A. Tover, Curt J. Essenburg, Megan J. Bowman, Zachary B. Madaj, Julie Koeman, Elissa A. Boguslawski, Jamie Grit, Rebecca D. Dodd, Vadim Khachaturov, Diana M. Cardona, Mark Chen, David G. Kirsch, Flavio Maina, Rosanna Dono, Mary E. Winn, Carrie R. Graveel and Matthew R. Steensma 
2018 | Cancer Research

Prion infectivity is encoded exclusively within the structure of proteinase K–resistant fragments of synthetically generated recombinant PrPSc
Fei Wang, Xinhe Wang, Romany Abskharon and Jiyan Ma 
2018 | Acta Neuropathologica Communications

The atomic structure of a eukaryotic oligosaccharyltransferase complex 
Lin Bai, Tong Wang, Gongpu Zhao, Amanda Kovach and Huilin Li 
2018 | Nature

Detecting alpha synuclein seeding activity in formaldehyde-fixed MSA patient tissue by PMCA 
Katelyn Becker, Xinhe Wang, Kayla Vander Stel, Yaping Chu, Jeffrey Kordower and Jiyan Ma 
2018 | Molecular Neurobiology