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 Commun13, 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

2Q - 2022

1. Parker CC, Philip VM, Gatti DM, Kasparek S, Kreuzman AM, Kuffler L, Mansky B, Masneuf S, Sharif K, Sluys E, Taterra D, Taylor WM, Thomas M, Polesskaya O, Palmer AA, Holmes A, Chesler EJ. Alcohol Clin Exp Res. 2022 Apr 5. PMID: 35383961 https://pubmed.ncbi.nlm.nih.gov/35383961/.

2.  Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H; PDXNet Consortium, Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal- Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH.  PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery.  NAR Cancer. 2022 Apr 22;4(2):zcac014.  https://mouseion.jax.org/stfb2022/62/

3.  Uthaya Kumar,D.B.,Motakis,E.Yurieva,M.Kohar, V. et al. Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. Am J Physiol Lung Cell Mol Physiol. 322(6):L822-L841 (2022). https://doi.org/10.1152/ajplung.00254.2021. People might also be interested in the uploaded data (part of the UCSC Cell Browser project): https://cells.ucsc.edu/?ds=bronc-epi-in-vitro

4. Joshy George, Yaohui Chen, Nourhan Abdelfattah, Keiko Yamamoto, Thomas D. Gallup, Scott I. Adamson, Brad Rybinski, Anuj Srivastava, Parveen Kumar, et al. Cancer Stem Cells, not Bulk Tumor Cells, Determine Mechanisms of Resistance to SMO Inhibitors. Cancer Research Communications (2022) 2 (6): 402–416. https://doi.org/10.1158/2767-9764.CRC-22-0124

3Q-2022

1. Dwyer, Jennifer R; Racine, Jeremy; Chapman, Harold D; Quinlan, Anna; Presa, Maximiliano; Stafford, Grace A; Schmitz, Ingo; and Serreze, David V., "Nfkbid Overexpression in Nonobese Diabetic Mice Elicits Complete Type 1 Diabetes Resistance in Part Associated with Enhanced Thymic Deletion of Pathogenic CD8 T Cells and Increased Numbers and Activity of Regulatory T Cells." (2022). Faculty Research Ahead of Print. 327. https://mouseion.jax.org/stfbaop/327

2.  Guerri L, Dobbs LK, da Silva e Silva DA, Meyers A, Ge A, Lecaj L, Djakuduel C, Islek D, Hipolito D,  Badillo-Martinez A, Shen P-H, Marietta CA, Garamszegi SP, Capobianco E, Jiang Z, Schwandt M, Mash DC, Alvarez VA, Goldman D. Low dopamine D2 receptor expression drives gene networks related to GABA, cAMP, growth and neuroinflammation in striatal indirect pathway neurons, Biological Psychiatry Global Open Sciencehttps://doi.org/10.1016/j.bpsgos.2022.08.010(https://www.sciencedirect.com/science/article/pii/S2667174322001033)