Consultations and Collaborations

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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
• 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. 

2024

• Yang Y, Jeong J, Su T, Lai S, Zhang P, Garcia-Milian R, Graham M, Liu X, McConnell MJ, Utsumi T, Pereira J, Iwakiri Y. Interleukin-7-based identification of liver lymphatic endothelial cells reveals their unique structural features, JHEP Reports, 2024, 101069, https://doi.org/10.1016/j.jhepr.2024.101069.

2023

• Martinez-Morilla S, Moutafi M, Fernandez AI, Jessel S, Divakar P, Wong PF, Garcia-Milian R, Schalper KA, Kluger HM, Rimm DL. Digital spatial profiling of melanoma shows CD95 expression in immune cells is associated with resistance to immunotherapy. Oncoimmunology. 2023 Sep 27;12(1):2260618. doi: 10.1080/2162402X.2023.2260618. PMID: 37781235; PMCID: PMC10540659
• Gallini S, Annusver K, Rahman NT, Gonzalez DG, Yun S, Matte-Martone C, Xin T, Lathrop E, Suozzi KC, Kasper M, Greco V. Injury prevents Ras mutant cell expansion in mosaic skin. Nature. 2023 Jul;619(7968):167-175. doi: 10.1038/s41586-023-06198-y. Epub 2023 Jun 21. PMID: 37344586
• Wang Y, Popovic Z, Charkoftaki G, Garcia-Milian R, Lam TT, Thompson DC, Chen Y, Vasiliou V. Multi-omics profiling reveals cellular pathways and functions regulated by ALDH1B1 in colon cancer cells. Chem Biol Interact. 2023 Sep 15;384:110714. doi: 10.1016/j.cbi.2023.110714. Epub ahead of print. PMID: 37716420.
• Chiorazzi M, Martinek J, Krasnick B, Zheng Y, Robbins KJ, Qu R, Kaufmann G, Skidmore Z, Juric M, Henze LA, Brösecke F, Adonyi A, Zhao J, Shan L, Sefik E, Mudd J, Bi Y, Goedegebuure SP, Griffith M, Griffith O, Oyedeji A, Fertuzinhos S, Garcia-Milian R, Boffa D, Detterbeck F, Dhanasopon A, Blasberg J, Judson B, Gettinger S, Politi K, Kluger Y, Palucka K, Fields RC, Flavell RA. Autologous humanized PDX modeling for immuno-oncology recapitulates features of the human tumor microenvironment. J Immunother Cancer. 2023 Jul;11(7):e006921. doi: 10.1136/jitc-2023-006921. PMID: 37487666.
• Lu L, Zhang Q, Shen X, Zhen P, Marin A, Garcia-Milian R, Roper J, Khan SA, Johnson CH. Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer. bioRxiv [Preprint]. 2023 May 5:2023.05.05.539577. doi: 10.1101/2023.05.05.539577. PMID: 37205388; PMCID: PMC10187315.
• Ganesh S, Lam TT, Garcia-Milian R, D'Souza D, Nairn AC, Elgert K, Eitan E, Ranganathan M. Peripheral signature of altered synaptic integrity in young onset Cannabis Use Disorder: A proteomic study of circulating extracellular vesicles. World J Biol Psychiatry. 2023 Mar 30:1-13. doi: 10.1080/15622975.2023.2197039
• Ren J, Qu R, Rahman NT, Lewis JM, King ALO, Liao X, Mirza FN, Carlson KR, Huang Y, Gigante S, Evans B, Rajendran BK, Xu S, Wang G, Foss FM, Damsky W, Kluger Y, Krishnaswamy S, Girardi M. Integrated transcriptome and trajectory analysis of cutaneous T-cell lymphoma identifies putative precancer populations. Blood Adv. 2023 Feb 14;7(3):445-457. doi: 10.1182/bloodadvances.2022008168. PMID: 35947128
• Luo X, Fang W, Ji J, Zhang Y, Garcia-Milian R, Wang Z, Tan Y, Wang S, Wang X, Guo X, Luo X. Association of lesion location with post-stroke depression in China: a systematic review and meta-analysis. EC Psychol Psychiatr. 2023 Mar;12(3):34-45. Epub 2023 Feb 22. PMID: 36913221; PMCID: PMC9997510
• Kabir I, Zhang X, Dave JM, Chakraborty R, Qu R, Chandran RR, Ntokou A, Gallardo-Vara E, Aryal B, Rotllan N, Garcia-Milian R, Hwa J, Kluger Y, Martin KA, Fernández-Hernando C, Greif DM. The age of bone marrow dictates the clonality of smooth muscle-derived cells in atherosclerotic plaques. Nat Aging. 2023 Jan;3(1):64-81. doi: 10.1038/s43587-022-00342-5

2022

• Wang Y, Chen Y, Garcia-Milian R, Golla JP, Charkoftaki G, Lam TT, Thompson DC, Vasiliou V. Proteomic profiling reveals an association between ALDH and oxidative phosphorylation and DNA damage repair pathways in human colon adenocarcinoma stem cells. Chem Biol Interact. 2022 Sep 23:110175. doi: 10.1016/j.cbi.2022.110175. Epub ahead of print. PMID: 36162455.
• Asch RH, Pothula S, Toyonaga T, Fowles K, Groman SM, Garcia-Milian R, DiLeone RJ, Taylor JR, Esterlis I. Examining sex differences in responses to footshock stress and the role of the metabotropic glutamate receptor 5: an [18F]FPEB and positron emission tomography study in rats. Neuropsychopharmacology. 2022 Sep 13. doi: 10.1038/s41386-022-01441-y. Epub ahead of print. PMID: 36100654.
• Hinchcliff M, Garcia-Milian R, Di Donato S, Dill K, Bundschuh E, Galdo FD. Cellular and molecular diversity in rheumatic autoimmune diseases. Semin Immunol. 2022 Aug 5:101648. doi: 10.1016/j.smim.2022.101648. Epub ahead of print. PMID: 35940960
• Farhadian SF, Lindenbaum O, Zhao J, Corley MJ, Im Y, Walsh H, Vecchio A, Garcia-Milian R, Chiarella J, Chintanaphol M, Calvi R, Wang G, Ndhlovu LC, Yoon J, Trotta D, Ma S, Kluger Y, Spudich S. HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART. JCI Insight. 2022 Jul 8;7(13):e160267. doi: 10.1172/jci.insight.160267. PMID: 35801589.
• Charkoftaki G, Tan WY, Berrios-Carcamo P, Orlicky DJ, Golla JP, Garcia-Milian R, Aalizadeh R, Thomaidis NS, Thompson DC, Vasiliou V. Liver metabolomics identifies bile acid profile changes at early stages of alcoholic liver disease in mice. Chem Biol Interact. 2022 Jun 1;360:109931. doi: 10.1016/j.cbi.2022.109931. Epub 2022 Apr 14. PMID: 35429548.

2021

• Chandran RR, Xie Y, Gallardo-Vara E, Adams T, Garcia-Milian R, Kabir I, Sheikh AQ, Kaminski N, Martin KA, Herzog EL, Greif DM. Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis. Nat Commun. 2021 Dec 10;12(1):7179. doi: 10.1038/s41467-021-27499-8. PMID: 34893592; PMCID: PMC8664937.
• Zhang X, McDonald JG, Aryal B, Canfrán-Duque A, Goldberg EL, Araldi E, Ding W, Fan Y, Thompson BM, Singh AK, Li Q, Tellides G, Ordovás-Montanes J, Garcia-Milian R, Dixit VD, Ikonen E, Suárez Y, Fernández-Hernando C. Desmosterol suppresses macrophage inflammasome activation and protects against vascular inflammation and atherosclerosis. Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2107682118. doi: 10.1073/pnas.2107682118. PMID: 34782454; PMCID: PMC8617522.
• Thompson B, Chen Y, Davidson EA, Garcia-Milian R, Golla JP, Apostolopoulos N, Orlicky DJ, Schey K, Thompson DC, Vasiliou V. Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function. Ocul Surf. 2021 Aug 20:S1542-0124(21)00092-6. doi: 10.1016/j.jtos.2021.08.010. Epub ahead of print. PMID: 34425299
• Tiegs AW, Titus S, Mehta S, Garcia-Milian R, Seli E, Scott RT Jr. Cumulus cells of euploid versus whole chromosome 21 aneuploid embryos reveals differentially expressed genes. Reprod Biomed Online. 2021 Jun 26:S1472-6483(21)00299-6. doi: 10.1016/j.rbmo.2021.06.015. Epub ahead of print. PMID: 34417138
• Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. Cell Rep Med. 2021 May 18;2(5):100288. doi: 10.1016/j.xcrm.2021.100288. Epub 2021 May 3. PMID: 33969321; PMCID: PMC8091032.
• Furnary T, Garcia-Milian R, Liew Z, Whirledge S, Vasiliou V. In Silico Exploration of the Potential Role of Acetaminophen and Pesticides in the Etiology of Autism Spectrum Disorder. Toxics. 2021 Apr 27;9(5):97. doi: 10.3390/toxics9050097. PMID: 33925648; PMCID: PMC8146009.
• Charkoftaki G, Golla JP, Santos-Neto A, Orlicky DJ, Garcia-Milian R, Chen Y, Rattray NJW, Cai Y, Wang Y, Shern CT, Mironova V, Wang Y, Johnson CH, Thompson DC, Vasiliou V. Identification of dose-dependent DNA damage and repair responses from subchronic exposure to 1,4-dioxane in mice using a systems analysis approach. Toxicol Sci. 2021 Mar 10:kfab030. doi: 10.1093/toxsci/kfab030. Epub ahead of print. PMID: 33693819. 
• Titus S, Szymanska KJ, Musul B, Turan V, Taylan E, Garcia-Milian R, Mehta S, Oktay K (2021) Individual-oocyte transcriptomic analysis shows that genotoxic chemotherapy depletes human primordial follicle reserve in vivo by triggering proapoptotic pathways without growth activation. Scitific Reports. Jan 11;11(1):407. doi: 10.1038/s41598-020-79643-x. PMID: 33431979; PMCID: PMC7801500.

2020

• Wang A, Rahman N-T, McGeary MK, Murphy M, McHenry A, Peterson D, Bosenberg M, Flavell RA, King B, Damsky W. (2020) Treatment of granuloma annulare and suppression of proinflammatory cytokine activity with tofacitinib, Journal of Allergy and Clinical Immunology, https://doi.org/10.1016/j.jaci.2020.10.012
• Burman A, Garcia-Milian R, Wood M, DeWitt NA, Vasiliou V, Guller S, Abrahams VM, Whirledge S. (2020) Acetaminophen Attenuates Invasion and Alters the Expression of Extracellular Matrix Enzymes and Vascular Factors in Human First Trimester Trophoblast Cells, Placenta, https://doi.org/10.1016/j.placenta.2020.12.002
• Ahsan MK, Figueroa-Hall L, Baratta V, Garcia-Milian R, Lam TT, Hoque K, Salas PJ, Ameen NA (2020) Glucocorticoids and serum- and glucocorticoid-inducible kinase 1 are potent regulators of CFTR in the native intestine: implications for stress-induced diarrhea. Am J Physiol Gastrointest Liver Physiol. Aug 1;319(2):G121-G132. doi: 10.1152/ajpgi.00076.2020. Epub 2020 Jun 22. PMID: 32567324; PMCID: PMC7500270
• Burman, A., Garcia-Milian, R., & Whirledge, S. (2020). Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals. Human genomics, 14(1), 19. https://doi.org/10.1186/s40246-020-00269-1
• Kandel-Kfir, M., Garcia-Milian, R., Gueta, I., Lubitz, I., Ben-Zvi, I., Shaish, A., Shir, L., Harats, D., Mahajan, M., Canaan, A., & Kamari, Y. (2020). IFNγ potentiates TNFα/TNFR1 signaling to induce FAT10 expression in macrophages. Molecular immunology, 117, 101–109. https://doi.org/10.1016/j.molimm.2019.11.004
• Luo, X., Guo, X., Tan, Y., Zhang, Y., Garcia-Milian, R., Wang, Z., Shi, J., Yu, T., Ji, J., Wang, X., Xu, J., Zhang, H., Zuo, L., Lu, L., Wang, K., & Li, C. R. (2020). KTN1 variants and risk for attention deficit hyperactivity disorder. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 183(4), 234–244. https://doi.org/10.1002/ajmg.b.32782
• Sun, Y., Mironova, V., Chen, Y., Lundh, E., Zhang, Q., Cai, Y., Vasiliou, V., Zhang, Y., Garcia-Milian, R., Khan, S. A., & Johnson, C. H. (2020). Molecular Pathway Analysis Indicates a Distinct Metabolic Phenotype in Women With Right-Sided Colon Cancer. Translational oncology, 13(1), 42–56. https://doi.org/10.1016/j.tranon.2019.09.004

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