Computational Sciences publications for year 2022.

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 Srivastava, A 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. LloydAnuj 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

12.  1: Abdelfattah N, Kumar P, Wang C, Leu JS, Flynn, WF, Gao R, Baskin DS, Pichumani K, Ijare OB, Wood SL, Powell SZ, Haviland DL, Parker Kerrigan BC, Lang FF, Prabhu SS, Huntoon KM, Jiang W, Kim BYS, George, J,Yun K.  Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target.  Nat Commun. 2022 Feb 9;13(1):767.  https://mouseion.jax.org/stfb2022/20/

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 XYSanderson 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 SrivastavaParveen 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

5.  15: Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C; GAGH Phenopacket Modeling Consortium, Haendel MA,.  The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. 2022 Jun;40(6):817-820.  https://mouseion.jax.org/stfb2022/127/

6. 24: Banda K, Kumar P, Straub R, Dobrolecki L, Rodriguez IV, Yost SE, Chandok H, Radke MR, Somlo G, Yuan Y, Lewis MT, Swisher EM,. Genomic and epigenomicBRCAalterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas.  Sci Transl Med. 2022 Jul 6;14(652):eabn1926.  https://mouseion.jax.org/stfb2022/113/

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)

3.  Ma W, Wang C, Li R, Han Z, Jiang Y, Zhang X, Divisi D, Capobianco E, Zhang L, Dong W. PTS is activated by ATF4 and promotes LUAD development via the Wnt pathway Transl Lung Cancer Res 2022; 11(9): 1912-1925. doi:10.21037/tlcr-22-593 https://tlcr.amegroups.com/article/view/68407/html

4. Alexander GM, Heiman-Patterson TD, Bearoff F, Sher RB, Hennessy L, Terek S, Caccavo N, Cox GA, Philip VM, Blankenhorn EA. Identification of quantitative trait loci for survival in the mutant dynactin p150Glued mouse model of motor neuron disease. PLoS One. 2022;17(9):e0274615. PubMed PMID: 36107978; PMCID: PMC9477371 https://libkey.io/libraries/3075/36107978

5. Brabec JL, Ouardouz M, Mahoney JM, Scott RC, Hernan AE. Differential regulation of gene expression pathways with dexamethasone and ACTH after early life seizures. Neurobiol Dis. 2022;174:105873. PubMed PMID: 36152945 https://libkey.io/libraries/3075/36152945

6. Brown LG, Haack AJ, Kennedy DS, Adams KN, Stolarczuk JE, Takezawa MG, Berthier E, Thongpang S, Lim FY, Chaussabel D, Garand M, Theberge AB. At-home blood collection and stabilization in high temperature climates using homeRNA. Front Digit Health. 2022;4:903153. PubMed PMID: 36033636; PMCID: PMC9405416 https://libkey.io/libraries/3075/36033636

7.  Martinek J, Wu TC, Sun L, Lin J, Kim KI, Marches F, Robson P, George J, Palucka K. Multiplex immunofluorescence-guided laser capture microdissection for spatial transcriptomics of metastatic melanoma tissues. STAR Protoc. 2022;3(4):101698. PubMed PMID: 36149794 https://doi.org/10.1016/j.xpro.2022.101698

8.  10: Chen M, Galante RJ, Han O, Lian Jm George J, Pack AI,.High-throughput visual assessment of sleep stages in mice using machine learning. Sleep. 2022 Feb 14;45(2):zsab260.  https://mouseion.jax.org/stfb2022/51/

  9.  15: Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, 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,Davis-Dusenbery B, Dean DA 2nd,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/

10. 29: Tang-Schomer MD, Chandok H, Wu WB, Lau CC, Bookland MJ, George J.  3D patient-derived tumor models to recapitulate pediatric brain tumors In Vitro.  Transl Oncol. 2022 Jun;20:101407.  https://mouseion.jax.org/stfb2022/47/

4Q-2022

1. Xu H, Bensalel J, Raju S, Capobianco E, Lu ML, Wei J. Characterization of huntingtin interactomes and their dynamic responses in living cells by proximity proteomics J. Neurochemistry. First published: 27 November 2022 https://doi.org/10.1111/jnc.15726.

2.  Chan LE, Casiraghi E, Laraway B,Coleman B,Blau H, Zaman A, Harris NL, Wilkins K, Antony B, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J. Metformin is associated with reduced COVID-19 severity in patients with prediabetes. Diabetes Res Clin Pract. 2022;194:110157. PubMed PMID: 36400170; PMCID: PMC9663381https://libkey.io/libraries/3075/36400170

3.  Rinchai D, Deola S, Zoppoli G, Kabeer BSA, Taleb S, Pavlovski I, Maacha S, Gentilcore G, Toufiq M, Mathew L, Liu L, Vempalli FR, Mubarak G, Lorenz S, Sivieri I, Cirmena G, Dentone C, Cuccarolo P, Giacobbe DR, Baldi F, Garbarino A, Cigolini B, Cremonesi P, Bedognetti M, Ballestrero A, Bassetti M, Hejblum BP, Augustine T, Van Panhuys N, Thiebaut R, Branco R, Chew T, Shojaei M, Short K, Feng CG, PREDICT-19 Consortium, Zughaier SM, De Maria A, Tang B, Ait Hssain A, Bedognetti D, Grivel JC,Chaussabel D. High-temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines. Sci Adv. 2022;8(45):eabp9961. PubMed PMID: 36367935; PMCID: PMC9651857https://libkey.io/libraries/3075/36367935.

4.  Song Y, Chen MZhang Y, Li J, Liu B, Li N, Chen M, Qiao M, Wang N, Cao Y, Lu S, Chen J, Sun W, Gao F, Wang H. Loss of circSRY reduces γH2AX level in germ cells and impairs mouse spermatogenesis. Life Sci Alliance. 2023;6(2). PubMed PMID: 36414375; PMCID: PMC9684031https://libkey.io/libraries/3075/36414375

5.  Woo XY, Srivastava A, Mack PC,Graber JH,Sanderson  BJ,Lloyd, MW,Chen MDomanskyi S, Gandour-Edwards R, Tsai RA,Keck J,Cheng M,Bundy M,Jocoy EL, Riess JW, Holland W, Grubb SCPeterson JGStafford GAPaisie C,Neuhauser SB, Karuturi RKMGeorge J,Simons AK,Chavaree M, Tepper CG, Goodwin N, Airhart SD, Lara PN, Openshaw TH,Liu ET, Gandara DR, Bult CJ. A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non-Small Cell Lung Cancer. Cancer Res. 2022;82(22):4126-38. PubMed PMID: 36069866; PMCID: PMC9664138https://libkey.io/libraries/3075/36069866.

6.    Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VMChen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell. 2022;185(24):4654-73.e28. PubMed PMID: 36334589https://libkey.io/libraries/3075/36334589

7.  Capobianco E. Overview of triple negative breast cancer prognostic signatures in the context of data science-driven clinico-genomics research.  Ann Transl Med 2022; 10(24): 1300. doi: 10.21037/atm-22-5477. https://atm.amegroups.com/article/view/107342/html