Hot Papers

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

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