Computational Sciences Publications

2022 Publications

1Q - 2022

1. Westermann-Clark E, Soundararajan R, Fukumoto J, Patil SS, Stearns TM, Saji S, Czachor A, Hernandez-Cuervo H, Breitzig M, Krishnamurthy S, Lockey RF, and N Kolliputi (2022) Matrix Metalloproteinase 7 Expression and Apical Epithelial Defects in Atp8b1 Mutant Mouse Model of Pulmonary Fibrosis. Biomolecules. https://pubmed.ncbi.nlm.nih.gov/35204783/.

2. Vida Ravanmehr, Hannah Blau, Luca Cappelletti, Tommaso Fontana, Leigh Carmody, Ben Coleman, Joshy George, Justin Reese, Marcin Joachimiak, Giovanni Bocci, Peter Hansen, Carol Bult, Jens Rueter, Elena Casiraghi, Giorgio Valentini, Christopher Mungall, Tudor I Oprea, Peter N Robinson, Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer, NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab113, https://doi.org/10.1093/nargab/lqab113.

3. Abdelfattah, N., Kumar, P., Wang, C. et al. Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target. Nat Commun 13, 767 (2022). https://doi.org/10.1038/s41467-022-28372-y.

4. Anuj SrivastavaA Genomically and Clinically Annotated Patient Derived Xenograft (PDX) Resource for Preclinical Research in Non-Small Cell Lung Cancer https://www.biorxiv.org/content/10.1101/2022.03.06.483171v1

5. CSBC/PS-ON Image Analysis Working Group, Juan Carlos Vizcarra, Erik A Burlingame, Clemens B Hug, Yury Goltsev, Brian S White, Darren R Tyson, Artem Sokolov. (2022) A community-based approach to image analysis of cells, tissues and tumors. Comput Med Imaging Graph. https://pubmed.ncbi.nlm.nih.gov/34864359/

6. Roger P Alexander, Robert R Kitchen, Juan Pablo Tosar, Matthew Roth, Pieter Mestdagh, Klaas E A Max, Joel Rozowsky, Karolina Elżbieta Kaczor-Urbanowicz, Justin Chang, Leonora Balaj, Bojan Losic, Eric L Van Nostrand, Emily LaPlante, Bogdan Mateescu, Brian S White, Rongshan Yu, Aleksander Milosavljevic, Gustavo Stolovitzky, Ryan M Spengler. (2022) Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop. Front Genet. https://pubmed.ncbi.nlm.nih.gov/35047007/.

7. Lichao Wang, Binsheng Wang, Nathan S Gasek, Yueying Zhou, Rachel L Cohn, Dominique E Martin, Wulin Zuo, William F Flynn, Chun Guo, Evan R Jellison, Taewan Kim, Larissa G P Langhi Prata, Allyson K Palmer, Ming Li, Christina L Inman, Lauren S Barber, Iman M A Al-Naggar, Yanjiao Zhou, Wenqiang Du, Kshitiz, George A Kuchel, Alexander Meves, Tamar Tchkonia, James L Kirkland, Paul Robson, Ming Xu. (2022) Targeting p21Cip1 highly expressing cells in adipose tissue alleviates insulin resistance in obesity. Cell Metab. https://pubmed.ncbi.nlm.nih.gov/34813734/.

8. 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.

9. Jared R. Bagley, Lauren S. Bailey, Leona H. Gagnon, Hao He, Vivek M. Philip, Laura G. Reinholdt, Lisa M. Tarantino, Elissa J. Chesler, James D. JentschReversal Learning Phenotypes are Linked with Novel Genetic Loci in Diversity Outbred Mice. bioRxiv(2022) https://www.biorxiv.org/content/10.1101/2022.01.29.478259v1.

10. SA Schoenrock, L Gagnon, A Olson, M Leonardo, VM Phillip, H He, JD Jentsch, EJ Chesler, LM Tarantino, The Collaborative Cross strains and their founders vary widely in cocaine-induced behavioral sensitization bioRxiv(2022) https://www.biorxiv.org/content/10.1101/2022.02.01.478694v1

11. Xingyi Woo, Guillen, K.P., Fujita, M., Butterfield, A.J. et al. A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nat Cancer 3, 232–250 (2022). https://doi.org/10.1038/s43018-022-00337-6