Biochemistry Publications

 

Scientists in the Department of Biochemistry have expertise in genome dynamics, epigenetics, and gene expression; human genetics and clinical biochemistry; signal transduction and intracellular communication; macromolecular structure and dynamics; proteomics; and bioinformatics.

Visit the Department of Biochemistry Research website for additional information,

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Submissions from 2021

Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues., Seana L Hill, Peter K Rogan, Yi Xuan Wang, and Joan H M Knoll

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Improved radiation expression profiling in blood by sequential application of sensitive and specific gene signatures, Eliseos J. Mucaki, Ben C. Shirley, and Peter K. Rogan

Gene expression for biodosimetry and effect prediction purposes: promises, pitfalls and future directions - key session ConRad 2021., Patrick Ostheim, Sally A Amundson, Christophe Badie, Dimitry Bazyka, Angela C Evans, Shanaz A Ghandhi, Maria Gomolka, Milagrosa López Riego, Peter K Rogan, Robert Terbrueggen, Gayle E Woloschak, Frederic Zenhausern, Hanns L Kaatsch, Simone Schüle, Reinhard Ullmann, Matthias Port, and Michael Abend

Automated Cytogenetic Biodosimetry at Population-Scale., Peter Rogan, Eliseos J. Mucaki, Ben Shirley, Li Yanxin, Ruth Wilkins, Farrah Norton, Olga Sevriukova, Ngoc Duy Pham, Edward Waller, and Joan H.M. Knoll

Submissions from 2020

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Pathway-extended gene expression signatures integrate novel biomarkers that improve predictions of patient responses to kinase inhibitors, Ashis Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, and Peter Rogan

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A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections, Ashis J. Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, and Peter Rogan

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Pathway‐extended gene expression signatures integrate novel biomarkers that improve predictions of patient responses to kinase inhibitors, Ashis Bagchee‐Clark, Eliseos J. Mucaki, Tyson Whitehead, and Peter Rogan

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Pathway-extended gene expression signatures integrate novel biomarkers that improve predictions of patient responses to kinase inhibitors, Jem Bagchee-Clark, Eliseos J. Mucaki, Tyson Whitehead, and Peter Rogan

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Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices., Shruti Rao, Beth Pitel, Alex H Wagner, Simina M Boca, Matthew McCoy, Ian King, Samir Gupta, Ben Ho Park, Jeremy L Warner, James Chen, Peter Rogan, Debyani Chakravarty, Malachi Griffith, Obi L Griffith, and Subha Madhavan

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Estimating partial body ionizing radiation exposure by automated cytogenetic biodosimetry, Peter Rogan

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Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing, Peter Rogan

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Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling., Peter K Rogan, Eliseos J Mucaki, Ruipeng Lu, Ben C Shirley, Edward Waller, and Joan H M Knoll

Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling., Peter K Rogan, Eliseos J Mucaki, Ruipeng Lu, Ben C Shirley, Edward Waller, and Joan H M Knoll

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Estimating partial body ionizing radiation exposure by automated cytogenetic biodosimetry, Ben Shirley and Peter Rogan

Submissions from 2019

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Multigene signatures of responses to chemotherapy derived by biochemically-inspired machine learning., Peter K. Rogan

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RADIATION DOSE ESTIMATION BY COMPLETELY AUTOMATED INTERPRETATION OF THE DICENTRIC CHROMOSOME ASSAY, Peter Rogan, Yanxin Li, Ben Shirley, Ruth Wilkins, Farrah Norton, and Joan Knoll

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Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations., Peter Rogan and Ruipeng Lu

Submissions from 2018

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N6-Furfuryladenine is protective in Huntington’s disease models by signaling huntingtin phosphorylation, Laura E. Bowie, Tamara Maiuri, Melanie Alpaugh, Michelle Gabriel, Nicolas Arbez, Danny Galleguillos, Claudia L.K. Hung, Shreya Patel, Jianrun Xia, Nicholas T. Hertz, Christopher A. Ross, David W. Litchfield, Simonetta Sipione, and Ray Truant

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BRCA1 and BRCA2 5′ noncoding region variants identified in breast cancer patients alter promoter activity and protein binding, Leslie J. Burke, Jan Sevcik, Gaetana Gambino, Emma Tudini, Eliseos J. Mucaki, Ben C. Shirley, Phillip Whiley, Michael T. Parsons, Kim De Leeneer, Sara Gutiérrez-Enríquez, Marta Santamariña, Sandrine M. Caputo, Elizabeth Santana dos Santos, Jana Soukupova, Marketa Janatova, Petra Zemankova, Klara Lhotova, Lenka Stolarova, Mariana Borecka, Alejandro Moles-Fernández, Siranoush Manoukian, Bernardo Bonanni, Stacey L. Edwards, Marinus J. Blok, Thomas van Overeem Hansen, Maria Rossing, Orland Diez, Ana Vega, Kathleen B.M. Claes, David E. Goldgar, and Etienne Rouleau

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The clinical significance of occult gastrointestinal primary tumours in metastatic cancer: A population retrospective cohort study, Malek B. Hannouf, Eric Winquist, Salaheddin M. Mahmud, Muriel Brackstone, Sisira Sarma, George Rodrigues, Peter K. Rogan, Jeffrey S. Hoch, and Gregory S. Zaric

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In mammalian skeletal muscle, phosphorylation of TOMM22 by protein kinase CSNK2/CK2 controls mitophagy, Bojana Kravic, Angelika B. Harbauer, Vanina Romanello, Luca Simeone, F. Nora Vögtle, Tobias Kaiser, Marion Straubinger, Danyil Huraskin, Martin Böttcher, Cristina Cerqua, Eva Denise Martin, Daniel Poveda-Huertes, Andreas Buttgereit, Adam J. Rabalski, Dieter Heuss, Rüdiger Rudolf, Oliver Friedrich, David Litchfield, Michael Marber, Leonardo Salviati, Dimitrios Mougiakakos, Winfried Neuhuber, Marco Sandri, Chris Meisinger, and Said Hashemolhosseini

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Predicting Response to Platin Chemotherapy Agents with Biochemically-inspired Machine Learning, Peter Rogan, Eliseos J. Mucaki, and Dan Lizotte

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Pan-cancer repository of validated natural and cryptic mRNA splicing mutations, Peter Rogan, Eliseos J. Mucaki, and Ben C. Shirley

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Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning, Peter Rogan, Jonathan Z.L. Zhao, and Eliseos J. Mucaki

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Detection of Amyloid Beta (Aβ) Oligomeric Composition Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS)., Jasmine S-H Wang, Shawn N Whitehead, and Ken K-C Yeung