2021 Computational Sciences Publications

1Q - 2021

  1. L. Urbanski, B. Angarola, M. Brugiolo, M. Yurieva, S. Park, O. Anczukow Myc regulates alternative splicing through a network of RNA binding proteins in breast cancerAACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD15-07 http://doi.org/10.1158/1538-7445.SABCS20-PD15-07
  2. Genetic variation regulates opioid-induced respiratory depression in mice. Sci Rep.2020 Sep 11;10(1):14970. DOI:10.1038/s41598-020-71804-2, Jason A Bubier,Hao He,Vivek M Philip,Tyler Roy,Christian Monroy Hernandez,Rebecca Bernat,Kevin D Donohue,Bruce F O'Hara,Elissa J Chesler.
  3. Singh K, Lin J, Lecomte N, Mohan P, Gokce A, Sanghvi VR, Jiang M, Grbovic-Huezo O, Burčul A, Stark SG, Romesser PB, Chang Q, Melchor JP, Beyer RK, Duggan M, Fukase Y, Yang G, Ouerfelli O, Viale A, de Stanchina E, Stamford AW, Meinke PT, Rätsch G, Leach SD, Ouyang Z, Wendel HG. (2021) Targeting eIF4A Dependent Translation of KRAS Signaling Molecules. Cancer Research, doi: 10.1158/0008-5472.CAN-20-2929 https://cancerres.aacrjournals.org/content/early/2021/02/24/0008-5472.CAN-20-2929
  4. Woo, X. Y., Giordano, J., Srivastava, A., Zhao, Z.-M., Lloyd, M. W., …, Bult, C. J., Medico, E., Chuang, J. H., PDXNET Consortium; EurOPDX Consortium (2021). Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nature Genetics, 53(1), 86-99. https://doi.org/10.1038/s41588-020-00750-6
  5. Köhler S, Gargano M.A., Matentzoglu N, Carmody L. C., Lewis-Smith D., Vasilevsky N. A., Danis D, . . . Robinson P. N., The Human Phenotype Ontology in 2021,Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D1207–D1217,https://doi.org/10.1093/nar/gkaa1043
  6. Danis D., Jacobsen J. O. B., Carmody L. C.,Gargano M. A., McMurry J. A., Hegde A., Haendel M. A., Valentini G., Smedley D., Robinson P. N. Interpretable prioritization of splice variants in diagnostic next-generation sequencing bioRxiv 2021.01.28.428499; doi: https://doi.org/10.1101/2021.01.28.428499

2Q - 2021

  1. Brian Q Geuther, Asaf Peer, Hao He, Gautam Sabnis, Vivek M Philip, Vivek Kumar (2021). Action detection using a neural network elucidates the genetics of mouse grooming behavior. eLife.https://elifesciences.org/articles/63207

  2. M Dey, B Ayan, M Yurieva, D Unutmaz, IT Ozbolat (2021) Studying Tumor Angiogenesis and Cancer Invasion in a Three‐Dimensional Vascularized Breast Cancer Micro‐Environment Advanced Biology https://onlinelibrary.wiley.com/doi/abs/10.1002/adbi.202100090

  3. Brabec, J.L., Lara, M.K., Tyler, A.L., & Mahoney, J.M. (2021) System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. Frontiers Genetics.

  4. Yi Li, Annat Haber, Christoph Preuss , Cai John, Asli Uyar, Hongtian Stanley Yang, Benjamin A Logsdon,Vivek Philip, R.  Krishna Murthy Karuturi, Gregory W. Carter. (2021) “TransferLearning-trained convolutional neural networks identify novel MRI biomarkers of Alzheimer’s disease progression”. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring.  http://doi.org/10.1002/dad2.12140

  5. Kira Young, Elizabeth Eudy, Rebecca Bell, Matthew A Loberg, Tim Stearns, Devyani Sharma, Lars Velten, Simon Haas, Marie-Dominique Filippi, Jennifer J Trowbridge. (2021). Decline in IGF1 in the bone marrow microenvironment initiates hematopoietic stem cell aging. Cell Stem Cell. https://pubmed.ncbi.nlm.nih.gov/33848471/

  6. David E Harrison, Randy Strong, Peter Reifsnyder, Navasuja Kumar, Elizabeth Fernandez, Kevin Flurkey, Martin A Javors, Marisa Lopez-Cruzan, Francesca Macchiarini, James F Nelson, Alessandro Bitto, Amy L Sindler, Gino Cortopassi, Kylie Kavanagh, Lin Leng, Richard Bucala, Nadia Rosenthal, Adam Salmon, Timothy M Stearns, Molly Bogue , Richard A Miller. (2021). 17-a-estradiol late in life extends lifespan in aging UM-HET3 male mice; nicotinamide riboside and three other drugs do not affect lifespan in either sex. Aging Cell. https://pubmed.ncbi.nlm.nih.gov/33788371/

  7. Olivier B Poirion, Zheng Jing, Kumardeep Chaudhary, Sijia Huang, Lana X Garmire , DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data, Genome med. DOI: 10.1186/s13073-021-00930-x

  8. David E Harrison, Randy Strong, Peter Reifsnyder, Navasuja Kumar, Elizabeth Fernandez, Kevin Flurkey, Martin A Javors, Marisa Lopez-Cruzan, Francesca Macchiarini, James F Nelson, Alessandro Bitto, Amy L Sindler, Gino Cortopassi, Kylie Kavanagh, Lin Leng, Richard Bucala, Nadia Rosenthal, Adam Salmon, Timothy M Stearns, Molly Bogue , Richard A Miller. (2021). 17-a-estradiol late in life extends lifespan in aging UM-HET3 male mice; nicotinamide riboside and three other drugs do not affect lifespan in either sex. Aging Cell. https://pubmed.ncbi.nlm.nih.gov/33788371/

  9. Brian S. White, Suleiman A. Khan, Mike J. Mason, Muhammad Ammad-ud-din, Swapnil Potdar, Disha Malani, Heikki Kuusanmäki, Brian J. Druker, Caroline Heckman, Olli Kallioniemi, Stephen E. Kurtz, Kimmo Porkka, Cristina E. Tognon, Jeffrey W. Tyner, Tero Aittokallio, Krister Wennerberg, and Justin Guinney (2021). Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia. npj Precision Oncology. https://pubmed.ncbi.nlm.nih.gov/34302041/

3Q - 2021

1.  Mahboubeh R. Rostami, Michelle G. LeBlanc, Yael Strulovici-Barel, Wulin Zuo, Jason G. Mezey, Sarah L. O’Beirne, Robert J. Kaner, Philip L. Leopold and Ronald G. Crystal (2021). Smoking shifts human small airway epithelium club cells toward a lesser differentiated population. npj Genomic Medicine. https://pubmed.ncbi.nlm.nih.gov/34497273/2.

2. Young K, Eudy E, Bell R, Loberg MA, Stearns T, Sharma D, Velten L, Haas S, Filippi MD, Trowbridge JJ (2021). Decline in IGF1 in the bone marrow microenvironment initiates hematopoietic stem cell aging. Cell Stem Cell. https://pubmed.ncbi.nlm.nih.gov/33848471/

3. Ayyala, Deepak Nag, Jianan Lin, and Zhengqing Ouyang. "Differential RNA methylation using multivariate statistical methods." Briefings in bioinformatics (2021). https://pubmed.ncbi.nlm.nih.gov/34586372/

4Q - 2021

1. Byers, C., Spruce, C., Fortin, H. J., Hartig, E. I., Czchanski, A., Munger, S. C., Reinholdt, L. G., Skelly, D. A., Baker, C. L. Genetic control of the pluripotency epigenome determines differentiation bias in mouse embryonic stem cells. EMBO J 2021 doi:10.15252/embj.2021109445

2.  Soner Koc, Michael W. Lloyd, …, Anuj Srivastava, Xing Yi Woo, Brian J. Sanderson, Brian White, …, Peter N. Robinson, Carol J. Bult, Brandi Davis-Dusenbery, Dennis A. Dean II, Jeffrey H. Chuang. “PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery”. bioRxiv (2021) https://www.biorxiv.org/content/10.1101/2021.10.15.464537v1.full.pdf

3. Sepaniac LA, Martin W, Dionne LA, Stearns TM, Reinholdt LG, and J Stumpff (2021) Micronuclei in Kif18a mutant mice form stable micronuclear envelopes and do not promote tumorigenesis. J Cell Biol. https://pubmed.ncbi.nlm.nih.gov/34515734/