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Consultations and Collaborations

Consultations

Consultation is available (free of charge) to individuals, groups, or teams to address bioinformatics-related research questions and needs. Consultation is mainly provided in-person or remotely over Zoom, but less complex questions may be addressed over email or by phone.

Examples of consultation topics include:

  • Identification of appropriate bioinformatics software or databases to answer specific research questions
  • Hands-on tutorials on bioinformatics software licensed by the Medical Library (should be the first example)
  • Analysis of bulk and single-cell ChIP-, ATAC-, RNA-seq, and microarray data using library-licensed bioinformatics tools
  • Discussion of analysis using command line tools and R/Python packages
  • Enrichment (pathway and network) analysis and visualization of differentially regulated molecules 
  • Finding, retrieving, and using public datasets for cross-referencing research results or hypothesis testing 
  • Development or narrowing hypothesis in silico by using existing public omics data and literature
 

Collaborations

We provide free support and instruction on OMICS data analysis for various kinds of biomedical research projects. By request, we provide letters of support for grants and also collaborate on analyzing the data. See examples of our recent collaborations below. 

visual of co-author collaboration network between medical library bioinformatics support and YSM/YSPH departments

 

2022

2021

2020

2019

  • Sahraei, M., Chaube, B., Liu, Y., Sun, J., Kaplan, A., Price, N. L., Ding, W., Oyaghire, S., García-Milian, R., Mehta, S., Reshetnyak, Y. K., Bahal, R., Fiorina, P., Glazer, P. M., Rimm, D. L., Fernández-Hernando, C., & Suárez, Y. (2019). Suppressing miR-21 activity in tumor-associated macrophages promotes an antitumor immune response. The Journal of clinical investigation, 129(12), 5518–5536. https://doi.org/10.1172/JCI127125
  • Chen, Y., Manna, S. K., Golla, S., Krausz, K. W., Cai, Y., Garcia-Milian, R., Chakraborty, T., Chakraborty, J., Chatterjee, R., Thompson, D. C., Gonzalez, F. J., & Vasiliou, V. (2019). Glutathione deficiency-elicited reprogramming of hepatic metabolism protects against alcohol-induced steatosis. Free radical biology & medicine, 143, 127–139. https://doi.org/10.1016/j.freeradbiomed.2019.07.025
  • Landau, S. I., Guo, X., Velazquez, H., Torres, R., Olson, E., Garcia-Milian, R., Moeckel, G. W., Desir, G. V., & Safirstein, R. (2019). Regulated necrosis and failed repair in cisplatin-induced chronic kidney disease. Kidney international, 95(4), 797–814. https://doi.org/10.1016/j.kint.2018.11.042
  • Charkoftaki G, Thompson DC, Golla JP, Garcia-Milian R, Lam TT, Engel J, Vasiliou V. Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells.Chem Biol Interact. 2019 Mar 6. pii: S0009-2797(18)31314-0. doi: 10.1016/j.cbi.2019.02.030
  • Chen Y, Golla S, Garcia-Milian R, Thompson D, Gonzalez FJ, Vasiliou V. Hepatic metabolic adaptation in a murine model of glutathione deficiency. Chemo-Biological Interactions (2019)

2018

  • Mis M, Yang Y, Tanaka B, Gomis-Perez C, Liu S, Dib-Hajj F, Adi T, Garcia-Milian R, Schulman B, Dib-Hajj D, Waxman S. Resilience to Pain: A Peripheral Component Identified using induced Pluripotent Stem Cells. The Journal of Neuroscience. (2018) doi: 10.1523/JNEUROSCI.2433-18. 
  • Perkins AN, Inayat-Hussain SH, Deziel NC, Johnson CH, Ferguson SS, Boyles AL, Garcia-Milian R, Thompson DC, Vasiliou V. Evaluation of Potential Carcinogenicity of Organic Chemicals in Synthetic Turf Crumb Rubber Environmental Research, Elsevier, October 2018 
  • Inayat-Hussain S, Aziz AM, Fukumura M, Chai MJ, Deziel N, Garcia-Milian R, Vasiliou V, Low WJ. Prioritization of Reproductive Toxicants in Unconventional Oil and Gas Operations Using a Multi-Country Regulatory Data-Driven Hazard Assessment. Environment International 117:348-358, 2018 doi: 10.1016/j.envint.2018.05.010 
  • Garcia-Milian R, Hersey D, Vukmirovic M, Duprilot F. (2018) Data challenges of biomedical researchers in the age of omics. PeerJ 6:e5553 
  • Pelekanou V, Anastasiou E, Bakogeorgou E, Notas G, Kampa M, Garcia-Milian R, Lavredaki K, Moustou E. Estrogen receptor-alpha isoforms are the main estrogen receptors expressed in Non-Small Cell Lung Carcinoma. Steroids (Elsevier) 2018 pii: S0039-128X(18)30016-3. doi: 10.1016/j.steroids.2018.01.008

2017

  • Guo X, Qiu W, Garcia-Milian R, Lin X,  Zhang Y, Cao Y, Tan Y, Wang Z, Shi J, Wang J,  Liu D, Song L, Xu Y, Wang X, Liu Na, Sun T, Zheng J, Luo J, Zhang H, Xu J, Kang L, Ma C, Wang K, Luo X. Genome-wide significant, replicated and functional risk variants for Alzheimer’s disease Journal of Neural Transmission p1-17, 2017 

2016

  • Zuo L, Garcia-Milian R, Guo X, Zhong C, Tan Y, Wang Z, Wang J, Chiang-Shan Li, Luo X. Replicable risk nicotinic cholinergic receptor genes for nicotine dependence. Genes 7(11), 95 doi:10.3390/genes7110095, 2016