The Department of Molecular, Cell and Cancer Biology (MCCB) at the University of Massachusetts Medical School was established in 2015, and is the product of a merger between the Program in Gene Function and Expression and the Department of Cancer Biology. This collection showcases the journal articles and other publications and presentations written by faculty and researchers of the Department of Molecular, Cell and Cancer Biology. See earlier collections for selected Gene Function and Expression and Cancer Biology publications published before the departmental merger.

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Publications from 2018

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RUNX1 Is an Oncogenic Transcription Factor that Regulates MYB and MYC Enhancer Activity in T-ALL, AHyun Choi

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ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, and Lihua Julie Zhu

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The Role of RIPK1 Kinase Activity in Regulating Inflammation and Necroptotic Death, Matija Zelic

Publications from 2017

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Understanding Multiple Independent Functions of the Tip60 Acetyltransferase in Embryonic Development, Diwash Acharya

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Cleaning House: Selective Autophagy of Organelles, Allyson L. Anding and Eric H. Baehrecke

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Development of Chimeric Cas9 Nucleases for Accurate and Flexible Genome Editing, Mehmet F. Bolukbasi

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A role for Tau protein in maintaining ribosomal DNA stability and cytidine deaminase-deficient cell survival, Elias Bou Samra, Geraldine Buhagiar-Labarchede, Christelle Machon, Jerome Guitton, Rosine Onclercq-Delic, Michael R. Green, Olivier Alibert, Claude Gazin, Xavier Veaute, and Mounira Amor-Gueret

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The alpha6beta4 integrin promotes resistance to ferroptosis, Caitlin W. Brown, John J. Amante, Hira Lal Goel, and Arthur M. Mercurio

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Molecular Basis and Targeted Inhibition of CBFbeta-SMMHC Acute Myeloid Leukemia, Lucio H. Castilla and John H. Bushweller

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RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia, AHyun Choi, Anuradha Illendula, John A. Pulikkan, Justine E. Roderick, Jessica M. Tesell, Jun Yu, Nicole M. Hermance, Lihua (Julie) Zhu, Lucio H. Castilla, John H. Bushweller, and Michelle A. Kelliher

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JAK/STAT pathway inhibition overcomes IL7-induced glucocorticoid resistance in a subset of human T-cell acute lymphoblastic leukemias, C. Delgado-Martin, L. K. Meyer, B. J. Huang, M. S. Zinter, J. V. Nguyen, G. A. Smith, J. Taunton, S. S. Winter, Justine R. Roderick, Michelle A. Kelliher, T. M. Horton, B. L. Wood, D. T. Teachey, and M. L. Hermiston

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Mitochondrial dysfunction in cancer: Potential roles of ATF5 and the mitochondrial UPR, Pan Deng and Cole M. Haynes

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Regulation of Pluripotency and Differentiation by Chromatin Remodeling Factors, Ly-Sha Ee

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Clinical application of a cancer genomic profiling assay to guide precision medicine decisions, Cheryl Eifert, Angeliki Pantazi, Ruobai Sun, Jia Xu, Pablo Cingolani, Joerg Heyer, Meaghan Russell, Maria Lvova, Jennifer Ring, Julie Y. Tse, Stephen Lyle, and Alexei Protopopov

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Integrating the UPRmt into the mitochondrial maintenance network, Christopher J. Fiorese and Cole M. Haynes

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Killers creating new life: caspases drive apoptosis-induced proliferation in tissue repair and disease, Caitlin E. Fogarty and Andreas Bergmann

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Molecular definitions of autophagy and related processes, Lorenzo Galluzzi, Eric H. Baehrecke, and Guido Kroemer

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Transcription factor Hlx controls a systematic switch from white to brown fat through Prdm16-mediated co-activation, Lei Huang, Dongning Pan, Qingbo Chen, Lihua (Julie) Zhu, Jianhong Ou, Martin Wabitsch, and Yong-Xu Wang

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Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells, Sunyoung Hwang, H. Tobias Gustafsson, Ciara O'Sullivan, Gianna Bisceglia, Xinhe Huang, Christian Klose, Andrej Schevchenko, Robert C. Dickson, Paola Cavaliere, Noah Dephoure, and Eduardo M. Torres

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Global increase in replication fork speed during a p57KIP2-regulated erythroid cell fate switch, Yung Hwang, Melinda Futran, Daniel Hidalgo, Ramona Pop, Divya Ramalingam Iyer, Ralph Scully, Nicholas R. Rhind, and Merav Socolovsky

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Actionable gene-based classification toward precision medicine in gastric cancer, Hiroshi Ichikawa, Stephen Lyle, and Toshifumi Wakai

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A synthetic biology approach to probing nucleosome symmetry, Yuichi Ichikawa, Caitlin M. Connolly, Hsin-Jung Chou, Yuanyuan Chen, Upasna Sharma, Hsuiyi V. Chen, Vineeta Bajaj, Daniel Na. Bolon, Oliver J. Rando, and Paul D. Kaufman

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MELK Promotes Melanoma Growth by Stimulating the NF-kappaB Pathway, Radoslav Janostiak, Navin Rauniyar, TuKiet T. Lam, Jianhong Ou, Lihua Julie Zhu, Michael R. Green, and Narendra Wajapeyee

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Myricetin improves endurance capacity and mitochondrial density by activating SIRT1 and PGC-1alpha, Hoe-Yune Jung, Namgyu Lee, and Kyong-Tai Kim

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Regulation of the Drosophila Initiator Caspase Dronc through Ubiquitylation, Hatem E. Kamber Kaya

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An inhibitory mono-ubiquitylation of the Drosophila initiator caspase Dronc functions in both apoptotic and non-apoptotic pathways, Hatem E. Kamber Kaya, Mark Ditzel, Pascal Meier, and Andreas Bergmann

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Mitochondrial Stress Restores the Heat Shock Response and Prevents Proteostasis Collapse during Aging, Johnathan Labbadia, Renee M. Brielmann, Mario F. Neto, Yi-Fan Lin, Cole M. Haynes, and Richard I. Morimoto

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Mitochondrial Sterol Oxidation Marks the Spot, Lilian Lamech and Cole M. Haynes

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The Dkk3 gene encodes a vital intracellular regulator of cell proliferation, Jack L. Leonard, Deborah Marie Leonard, Scot A. Wolfe, Jilin Liu, Jaime A. Rivera-Perez, Michelle Yang, Ryan T. Leonard, Jacob P. S. Johnson, Prashant Kumar, Kate L. Liebmann, Amanda A. Tutto, Zhongming Mou, and Karl J. Simin

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CK2 inhibitor CX-4945 destabilizes NOTCH1 and synergizes with JQ1 against human T-acute lymphoblastic leukemic cells, Haiwei Lian, Dun Li, Yun Zhou, Esther Landesman-Bollag, Guanglan Zhang, Nicole M. Anderson, Kevin Charles. Tang, Justine E. Roderick, Michelle A. Kelliher, David C. Seldin, Hui Fu, and Hui Feng

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Complement-Related Regulates Autophagy in Neighboring Cells, Lin Li, Frederico S. L. M. Rodrigues, Christina Kary, Alicia Contet, Mary Logan, Richard H. Baxter G, Will Wood, and Eric H. Baehrecke

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Complement-Related Regulates Autophagy in Neighboring Cells, Lin Lin

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A Graphene-Based Flexible Pressure Sensor with Applications to Plantar Pressure Measurement and Gait Analysis, Cunguang Lou, Shuo Wang, Tie Liang, Chenyao Pang, Lei Huang, Mingtao Run, and Xiuling Liu

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CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy, Leyuan Ma, Jeffrey I. Boucher, Janet L. Paulsen, Sebastian Matuszewski, Christopher A. Eide, Jianhong Ou, Garrett Eickelberg, Richard D. Press, Lihua (Julie) Zhu, Brian J. Druker, Susan Branford, Scot A. Wolfe, Jeffrey D. Jensen, Celia A. Schiffer, Michael R. Green, and Daniel N. Bolon

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CAF-1 p150 and Ki-67 Regulate Nuclear Structure Throughout the Human Cell Cycle, Timothy D. Matheson

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The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer, Timothy D. Matheson and Paul D. Kaufman

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Defining a therapeutic window for kinase inhibitors in leukemia to avoid neutropenia, Kate McArthur, Akshay A. D'Cruz, David Segal, Kurt Lackovic, Andrew F. Wilks, Joanne A. O'Donnell, Cameron J. Nowell, Motti Gerlic, David C. S. Huang, Christopher J. Burns, and Ben A. Croker

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Differential involvement of the microtubule cytoskeleton in insulin receptor substrate 1 (IRS-1) and IRS-2 signaling to AKT determines the response to microtubule disruption in breast carcinoma cells, Jose Mercado-Matos, Jennifer L. Clark, Andrew J. Piper, Jenny Janusis, and Leslie M. Shaw

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RUNX1 and breast cancer, Jose Mercado-Matos, Asia N. Matthew-Onabanjo, and Leslie M. Shaw

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A Mechanistic Investigation of Insulin Receptor Substrate 2 Function in Breast Cancer Progression, Jose R. Mercado-Matos

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Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis, Haiwei Mou, Jill Moore, Sunil K. Malonia, Yingxiang Li, Deniz M. Ozata, Soren Hough, Chun-Qing Song, Jordan L. Smith, Andrew H. Fischer, Zhiping Weng, Michael R. Green, and Wen Xue

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CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion, Haiwei Mou, Jordan L. Smith, Lingtao Peng, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Deniz M. Ozata, Yingxiang Li, Charles P. Emerson Jr., Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng, and Wen Xue

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RIPK1 mediates a disease-associated microglial response in Alzheimer's disease, Dimitry Ofengeim, Michelle A. Kelliher, and Junying Yuan

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DISC1 Modulates Neuronal Stress Responses by Gate-Keeping ER-Mitochondria Ca(2+) Transfer through the MAM, Sung Jin Park, Su Been Lee, Yeongjun Suh, Su-Jeong Kim, Namgyu Lee, Ji-Ho Hong, Cana Park, Youngsik Woo, Koko Ishizuka, Joung-Hun Kim, Per-Olof Berggren, Akira Sawa, and Sang Ki Park

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Tumor-promoting function of apoptotic caspases by an amplification loop involving ROS, macrophages and JNK in Drosophila, Ernesto Perez, Jillian L. Lindblad, and Andreas Bergmann

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MicroRNAs of the mir-17~92 cluster regulate multiple aspects of pancreatic tumor development and progression, Brian J. Quattrochi, Anushree Gulvady, David R. Driscoll, Makoto Sano, David S. Klimstra, Christopher E. Turner, and Brian C. Lewis

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The mitochondrial unfolded protein response: Signaling from the powerhouse, Mohammed A. Qureshi, Cole M. Haynes, and Mark W. Pellegrino

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Comprehensive genomic sequencing detects important genetic differences between right-sided and left-sided colorectal cancer, Yoshifumi Shimada, Stephen Lyle, Kazuaki Takabe, and Toshifumi Wakai

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Utility of comprehensive genomic sequencing for detecting HER2-positive colorectal cancer, Yoshifumi Shimada, Stephen Lyle, and Toshifumi Wakai

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The mitochondrial UPR: mechanisms, physiological functions and implications in ageing, Tomer Shpilka and Cole M. Haynes

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Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice, Chun-Qing Song, Yingxiang Li, Haiwei Mou, Jill Moore, Angela I. Park, Soren Hough, Zachary Kennedy, Andrew H. Fischer, Darryl Conte Jr., Zhiping Weng, and Wen Xue

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Ki-67 Regulates Cell Cycle Progression and Heterochromatin Organization, Xiaoming Sun

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Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs, Feng Wang, Kurtis N. McCannell, Ana Boskovic, Xiaochun Zhu, JongDae Shin, Jun Yu, Judith Gallant, Meg Byron, Jeanne B. Lawrence, Lihua Julie Zhu, Stephen N. Jones, Oliver J. Rando, Thomas G. Fazzio, and Ingolf Bach

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Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer, Yue Wang, Matthew H. Ung, Sharon B. Cantor, and Chao Cheng

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BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment, Georg E. Winter, Justine E. Roderick, Michelle A. Kelliher, and James E. Bradner

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(CCUG)n RNA toxicity in a Drosophila model of myotonic dystrophy type 2 (DM2) activates apoptosis, Vildan Betul Yenigun, Mario Sirito, Alla Amcheslavsky, Tomek Czernuszewicz, Jordi Colonques-Bellmunt, Irma Garcia-Alcover, Marzena Wojciechowska, Clare Bolduc, Zhihong Chen, Arturo Lopez Castel, Ralf Krahe, and Andreas Bergmann

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Critical role for arginase 2 in obesity-associated pancreatic cancer, Tamara Zaytouni, Pei-Yun Tsai, Daniel S. Hitchcock, Cory D. DuBois, Elizaveta Freinkman, Lin Lin, Vicente Morales-Oyarvide, Patrick J. Lenehan, Brian M. Wolpin, Mari Mino-Kenudson, Eduardo M. Torres, Nicholas Stylopoulos, Clary B. Clish, and Nada Y. Kalaany

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GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, and Scot A. Wolfe

Publications from 2016

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The TCA cycle transferase DLST is important for MYC-mediated leukemogenesis, N. M. Anderson, Michelle A. Kelliher, and H. Feng

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Insulin Receptor Substrate Adaptor Proteins Mediate Prognostic Gene Expression Profiles in Breast Cancer, Marc A. Becker, Yasir H. Ibrahim, Annabell S. Oh, Dedra H. Fagan, Sara A. Byron, Aaron L. Sarver, Adrian V. Lee, Leslie M. Shaw, Cheng Fan, Charles M. Perou, and Douglas Yee

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Mdm2 Phosphorylation Regulates Its Stability and Has Contrasting Effects on Oncogene and Radiation-Induced Tumorigenesis, Michael I. Carr, Justine E. Roderick, Hugh S. Gannon, Michelle A. Kelliher, and Stephen N. Jones (Cell reports)

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Requirement and Function of Hippo Pathway Signaling in the Mammalian Gastrointestinal Tract: A Dissertation, Jennifer L. Cotton

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The mitokine quest(ion), Pan Deng and Cole M. Haynes

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The beneficial role of extracellular reactive oxygen species in apoptosis-induced compensatory proliferation, Neha Diwanji and Andreas Bergmann

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Levels of YCG1 Limit Condensin Function during the Cell Cycle: A Dissertation, Tyler W. Doughty

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Levels of Ycg1 Limit Condensin Function during the Cell Cycle, Tyler W. Doughty, Heather E. Arsenault, and Jennifer A. Benanti

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The Impact of mTORC2 Signaling on the Initiation and Progression of KRAS-Driven Pancreatic Neoplasias: A Dissertation, David R. Driscoll

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Investigation of RNA Binding Protein Pumilio as a Genetic Modifier of Mutant CHMP2B in Frontotemporal Dementia (FTD): A Masters Thesis, Xing Du

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The Transcription Factor ATF5 Mediates a Mammalian Mitochondrial UPR, Christopher J. Fiorese, Anna M. Schulz, Yi-Fan Lin, Nadine Rosin, Mark W. Pellegrino, and Cole M. Haynes

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Extracellular Reactive Oxygen Species Drive Apoptosis-Induced Proliferation via Drosophila Macrophages, Caitlin E. Fogarty, Neha Diwanji, Jillian L. Lindblad, Meghana Tare, Alla Amcheslavsky, Kalpana Makhijani, Katja Bruckner, Yun Fan, and Andreas Bergmann

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P-Rex1 Promotes Resistance to VEGF/VEGFR-Targeted Therapy in Prostate Cancer, Hira Lal Goel, Bryan M. Pursell, Leonard D. Shultz, Dale L. Greiner, Rolf A. Brekken, Craig W. Vander Kooi, and Arthur M. Mercurio

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Septate Junction Proteins Play Essential Roles in Morphogenesis Throughout Embryonic Development in Drosophila, Sonia Hall and Robert E. Ward 4th

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Small Molecule Inhibitor of CBFbeta-RUNX Binding for RUNX Transcription Factor Driven Cancers, Anuradha Illendula, John A. Pulikkan, Lucio H. Castilla, and John H. Bushweller

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RIPK1 mediates axonal degeneration by promoting inflammation and necroptosis in ALS, Yasushi Ito, Michelle A. Kelliher, and Junying Yuan

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Cancer Metabolism: Fueling More than Just Growth, Namgyu Lee and Dohoon Kim

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The initiator caspase Dronc is subject of enhanced autophagy upon proteasome impairment in Drosophila, T. V. Lee, H. E. Kamber Kaya, Rachel T. Simin, Eric H. Baehrecke, and Andreas Bergmann

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CYLD Proteolysis Protects Macrophages from TNF-Mediated Auto-necroptosis Induced by LPS and Licensed by Type I IFN, Diana Legarda, Scott J. Justus, Rosalind L. Ang, Nimisha Rikhi, Wenjing Li, Thomas M. Moran, Jianke Zhang, Emiko Mizoguchi, Matija Zelic, Michelle A. Kelliher, J. Magarian Blander, and Adrian T. Ting

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Autophagy-independent function of Atg1 for apoptosis-induced compensatory proliferation, Mingli Li, Jillian L. Lindblad, Ernesto Perez, Andreas Bergmann, and Yun Fan

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Tead and AP1 Coordinate Transcription and Motility, Xiangfan Liu, Huapeng Li, Mihir S. Rajurkar, Qi Li, Jennifer L. Cotton, Jianhong Ou, Lihua J. Zhu, Hira L. Goel, Arthur M. Mercurio, Joo-Seop Park, Roger J. Davis, and Junhao Mao

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High-Throughput Screening of Tyrosine Kinase Inhibitor Resistant Genes in CML, Leyuan Ma, Justine E. Roderick, Michelle A. Kelliher, and Michael R. Green

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Global Cysteine-Reactivity Profiling during Impaired Insulin/IGF-1 Signaling in C. elegans Identifies Uncharacterized Mediators of Longevity, Julianne Martell, Yonghak Seo, Daniel W. Bak, Samuel F. Kingsley, Heidi A. Tissenbaum, and Eranthie Weerapana

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Radial glia regulate vascular patterning around the developing spinal cord, Ryota L. Matsuoka, Michele Marass, Avdesh Avdesh, Christian S.M. Helker, Hans-Martin Maischein, Ann S. Grosse, Harmandeep Kaur, Nathan D. Lawson, Wiebke Herzog, and Didier Y.R. Stainier

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Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine, Masayuki Nagahashi, Toshifumi Wakai, and Stephen R. Lyle

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Clinical expression of facioscapulohumeral muscular dystrophy in carriers of 1-3 D4Z4 reduced alleles: experience of the FSHD Italian National Registry, Ana Nikolic and Rossella Tupler

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Prenatal Maternal Physical Activity and Stem Cells in Umbilical Cord Blood, Sagano Onoyama, Linghua Qiu, Hoi Pang Low, Chien-I Chang, William C. Strohsnitter, Errol R. Norwitz, Mary Lopresti, Kathryn Edmiston, I-Min Lee, Dimitrios Trichopoulos, Pagona Lagiou, and Chung-Cheng Hsieh

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The unconventional myosin CRINKLED and its mammalian orthologue MYO7A regulate caspases in their signalling roles, Mariam H. Orme, Meghana Tare, Andreas Bergmann, and Pascal Meier

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The unconventional myosin CRINKLED and its mammalian orthologue MYO7A regulate caspases in their signalling roles, Mariam H. Orme, Meghana Tare, Andreas Bergmann, and Pascal Meier

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The histone H3K9 demethylase KDM3A promotes anoikis by transcriptionally activating pro-apoptotic genes BNIP3 and BNIP3L, Victoria E. Pedanou, Stephane Gobeil, Sebastien Tabaries, Tessa M. Simone, Lihua Julie Zhu, Peter M. Siegel, and Michael R. Green

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RUNX1 and FOXP3 interplay regulates expression of breast cancer related genes, Maria Sol Recouvreux, Esteban Nicolas Grasso, Pablo Christian Echeverria, Luciana Rocha-Viegas, Lucio H. Castilla, Carolina Schere-Levy, Johanna Melisa Tocci, Edith Claudia Kordon, and Natalia Rubinstein

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A novel clinical tool to classify facioscapulohumeral muscular dystrophy phenotypes, Giulia Ricci and Rossella Ginevra Tupler

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An autophagy-independent function for Beclin 1 in cancer, Rasika Rohatgi and Leslie M. Shaw

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Activation of WNT/beta-Catenin Signaling Enhances Pancreatic Cancer Development and the Malignant Potential Via Up-regulation of Cyr61, Makoto Sano, David R. Driscoll, Wilfredo E. De Jesus-Monge, Brian J. Quattrochi, Victoria A. Appleman, Jianhong Ou, Lihua (Julie) Zhu, and Brian C. Lewis

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Function of the β4 Integrin in Cancer Stem Cells and Tumor Formation in Breast Cancer: A Masters Thesis, Huayan Sun

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No current evidence for widespread dosage compensation in S. cerevisiae, Eduardo M. Torres, Michael Springer, and Angelika Amon

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The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice, Elizabeth C. Townsend, Michelle A. Kelliher, Justine E. Roderick, and David M. Weinstock

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NEMO Prevents RIP Kinase 1-Mediated Epithelial Cell Death and Chronic Intestinal Inflammation by NF-kappaB-Dependent and -Independent Functions, Katerina Vlantis, Andy Wullaert, Apostolos Polykratis, Vangelis Kondylis, Marius Dannappel, Robin Schwarzer, Patrick Welz, Teresa Corona, Henning Walczak, Falk Weih, Ulf Klein, Michelle Kelliher, and Manolis Pasparakis

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Genetic characterization of two gain-of-function alleles of the effector caspase DrICE in Drosophila, Y. Wu, Jillian L. Lindblad, J. Garnett, H. E. Kamber Kaya, D. Xu, Y. Zhao, E. R. Flores, J. Hardy, and Andreas Bergmann

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Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo, Hao Yin, Chun-Qing Song, Joseph R. Dorkin, Lihua Julie Zhu, Yingxiang Li, Qiongqiong Wu, Angela I. Park, Junghoon Yang, Sneha Suresh, Aizhan Bizhanova, Ankit Gupta, Mehmet Fatih Bolukbasi, Stephen Walsh, Roman L. Bogorad, Guangping Gao, Zhiping Weng, Yizhou Dong, Victor Koteliansky, Scot A. Wolfe, Robert Langer, Wen Xue, and Daniel G. Anderson

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Biochemical and biomechanical drivers of cancer cell metastasis, drug response and nanomedicine, Tatsuyuki Yoshii, Yingying Geng, Shelly Peyton, Arthur M. Mercurio, and Vincent M. Rotello

Publications from 2015

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The p53R172H Mutant Does Not Enhance Hepatocellular Carcinoma Development and Progression, Leanne G. Ahronian, David R. Driscoll, David S. Klimstra, and Brian C. Lewis