Advaita Bioinformatics Science
A leader in the interpretation of high-throughput biomedical data.
Advaita Bioinformatics: Science
Read the research behind our software solutions as well as the research that it has supported. For instance, iPathwayGuide is widely cited in high-impact publications such as: Cell Stem Cell, Cancer Research, Diabetes, and many more.
Please contact us if you know if studies that are missing from this list!
Paper
# of Citations
Identifying significantly impacted pathways: a comprehensive review and assessment.
Genome Biology, 20:203, October, 2019
Ontological analysis of gene expression data: current tools, limitations, and open problems.
Bioinformatics 21 (18), 3587-3595
A systems biology approach for pathway level analysis.
Genome Research, 2007, Vol. 17 (10), pages 1537-1545.
A novel signaling pathway impact analysis (SPIA).
Bioinformatics (2009), Vol. 25 (1), pages 75-82.
Global functional profiling of gene expression.
Genomics 81 (2), 98-104
Reliability and reproducibility issues in DNA microarray measurements.
TRENDS in Genetics 22 (2), 101-109
Data analysis tools for DNA microarrays.
(Book) CRC Press
Profiling gene expression using onto-express.
Genomics 79 (2), 266-270
Use and misuse of the gene ontology annotations.
Nature Reviews Genetics 9 (7), 509-515
Onto-tools, the toolkit of the modern biologist: onto-express, onto-compare, onto-design and onto-translate.
Nucleic acids research 31 (13), 3775-3781
Onto-Tools: New Additions and Improvements in 2006.
Nucleic Acids Research, Vol. 35, pages W206-W211, July 2007.
Statistics and data analysis for microarrays using R and bioconductor.
(Book) CRC Press
Analysis and correction of crosstalk effects in pathway analysis.
Genome Research, 2013, Vol. 23 (9).
A system biology approach for the steady-state analysis of gene signaling networks.
In Proceedings of the Congress on pattern recognition 12th Iberoamerican conference on Progress in pattern recognition, image analysis and applications (CIARP’07).
Comba, A., Motsch, S., Dunn, P.J., Hollon, T.C., Argento, A.E, Zamler, D.B., Kish, P.E., Kahana, A., Kleer, C.G., Castro, M.G., & Lowenstein, P.R. (2021). Spatiotemporal analysis of glioma heterogeneity reveals Col1A1 as an actionable 1 target to disrupt tumor mesenchymal differentiation, invasion and malignancy. bioRxiv
Duan, S., Nordmeier, S., Byrnes, A.E., & Buxton, I.L.O. (2021). Extracellular vesicle-mediated purinergic signaling contributes to host microenvironment plasticity and metastasis in triple negative breast cancer. International Journal of Molecular Sciences, 22(2), 597.
Helmer, R.A., Martinez-Zaguilan, R., Kaur, G., Smith, L.A., Dufour, J.M., & Chilton, B.S. (2021). Helicase-like transcription factor-deletion from the tumor microenvironment in a cell line-derived xenograft model of colorectal cancer reprogrammed the the human transcriptome-S-nitroso-proteome to promote inflammation and redirect metastasis. PLOS ONE 16(5): e0251132.
Jiagge, E.M., Ulintz, P.J., Wong, S., McDermott, S.P., Fossi, S.I., Suhan, T.K., Hoenerhoff, M.J., Bensenhaver, B.M., Salem, B., Dziubinski, M., Oppong, J.K., Aitpillah, F., Ishmael, K., Osei-Bonsu, E., Adjei, E., Baffour, A., Aldrich, J., Kurdoglu, A., Fernando, K., Draig, D.W., Trent, J.M., Li, J., Chitale, D., Newman, L.A., Carpten, J.D., Wicha, M.S., & Merajver, S.D. (2021). Multiethnic PDX models predict a possible immune signature associated with TNBC of African ancestry. Breast Cancer Research and Treatment, 186, 391-401.
Kishimoto, K., Kanazawa., K, Nomura, M., Tanaka, T., Shigemoto-Kuroda, T., Fukui, K., Kurosawa, K., Kawai, M., Kato, H., Terasaki, K., Sakamoto, Y., Yamashita, Y., Sato, I., Tanuma, N., Tamai, K., Kitabayashi, I., Matsuura, K., Watanabe, T., Yasuda, J., Tsuji, H., & Shima, H. (2021). Ppp6c deficiency accelerates K‐rasG12D‐induced tongue carcinogenesis. Cancer Medicine, 10(13), 4451-4464.
Krieg, C., Carloni, S., Weber, L.M., Fosso, B., Hardiman, G., Mileti, E., El Aidy, S., Marzano, M., Pesole, G., Asnicar, F., Segata, N., Robinson, M.D., & Guglietta, S. (2021). Loss of C3aR induces immune infiltration and inflammatory microbiota in a novel spontaneous model of colon cancer. bioRxiv.
Lidberg, K.A., Muthusamy, S., Adil, M., Patel, R.S., Wang, L., Bammler, T.K., Reichel, J., Yeung, C.K., Himmelfarb, J., Kelly, E.J., & Shreeram, A., (2021). Multi-omic Characterization of Human Tubular Epithelial Cell Response to Serum. bioRxiv.
Liu, J., Qiu, J., Zhang, Z., Zhou, L., Li, Y., Ding, D., Zhang, Y., Zou, D., Wang, D., Zhou, Q., & Lang, T. (2021). SOX4 maintains the stemness of cancer cells via transcriptionally enhancing HDAC1 revealed by comparative proteomics study. Cell Biosci, 11, 23.
Merritt, N., Garcia, K,. Rajendran, D., Lin, Z.Y., Zhang, X., Mitchell, K.A., Borcherding, N., Fullenkamp, C., & Chimenti, M.S. (2021). TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex. eLife, 10:e62857.
Tsuji, Y., Nonoguchi, N., Okuzaki, D., Wada, Y., Motooka, D., Hirota, Y., Toho, T., Yoshikawa, N., Furuse, M., Kawabata, S., Miyatai, S.I., Nakamura, H., Yamamoto, R., Nakamura, S., Kuroiwa, T., & Wanibuchi, M. (2021). The Up-Regulation of CXCL12-CXCR4 Axis By Radiotherapy Could Accelerate Glioma Progression., Research Square.
Weber, H., Ruoff, R., & Garabedian, M.J. (2021). MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen. PLOS Genetics, 17(1): e1008540.
Wesley, Y.Y., Hill, S.T., Chan, E.R., Pink, J.J., Cooper, K., Leachman, S., Lund, A.W., Kulkarni, R., & Bordeaux, J.S. (2021). Computational Drug Repositioning Identifies Statins as Modifiers of Prognostic Genetic Expression Signatures and Metastatic Behavior in Melanoma. Journal of Investigative Dermatology, 141(7), 1802-1809.
Wills, C.A., Liu, X., Chen, L., Zhao, Y., Dower, C.M., Sundstrom, J., & Wong, H.G. (2021). Chemotherapy-induced upregulation of small extracellular vesicle-associated PTX3 accelerates breast cancer metastasis. Cancer Research, 81(2), 452-463.
Argento, A.E., Kadiyala, P., Ventosa, M., Patel, P., Zamler, D.B., Nunez, F.J., Zhao, L., Castro, M.G., & Lowenstein, P.R. (2020). Fyn tyrosine kinase, a downstream target of receptor tyrosine kinases, modulates antiglioma immune responses. Neuro-Oncology, 22(6), 806-818.
Balogh, A., Reiniger, L., Hetey, S., Kiraly, P., Toth, E., Karaszi, K., Juhasz, K., Gelencser, Z., Zvara, A., Szilagyi, A., Puskas, L.G., Matko, J., Papp, Z., Kovalszky, I., Juhasz, C., & Than, N.G. (2020). Decreased Expression of ZNF554 in Gliomas is Associated with the Activation of Tumor Pathways and Shorter Patient Survival. International Journal of Molecular Sciences, 21(16):5762.
Caro, D., Rivera, D., Ocampo, Y., Müller, K., & Franco, L.A., (2020). A promising naphthoquinone [8-hydroxy-2-(2-thienylcarbonyl) naphtho [2, 3-b] thiophene-4, 9-dione] exerts anti-colorectal cancer activity through ferroptosis and inhibition of MAPK signaling pathway based on RNA sequencing. Open Chemistry, 18(1):1242-1255.
Fernández, G., Jose, M. (2020). In vitro antitumor activity of arachidonic and docosahexaenoic acids as both monoacylglycerols and free fatty acids on colorectal cancer cells., Tesis Universidad de Almeria [90].
Herkenne, S., Ek, O., Zamberlan, M., Pellattiero, A., Chergova, M., Chivite, I., Novotna, E., Rigoni, G., Fonseca, T.B., Samardzic, D., Agnellini, A., Bean, C., Beneditti, G.D., Tiso, N., Argenton, F., Viola, A., Soriano, M.E., Giacomello, M., Ziviani, E., Sales, G., Claret, M., Graupera, M., & Scorrano, L. (2020). Developmental and tumor angiogenesis requires the mitochondria-shaping protein Opa1. Cell Metabolism, 31(5), 987-1003.e8.
Mendez, F., Kadiyala, P., Nunez, F.J., Carney, S., Nunez, F.M., Gauss, J.C., Ravindran, R., Pawar, S., Edwards, M, Garcia-Fabiani, M.B., Haase, S., Lowenstein, P.R., & Castro, M.G. (2020). Therapeutic efficacy of immune stimulatory thymidine kinase and fms-like tyrosine kinase 3 ligand (TK/Flt3L) gene therapy in a mouse model of high-grade brainstem glioma. Clinical Cancer Research, 26(15), 4080-4092.
Nagesh, P.K.B., Chowdhury, P., Hatami, E., Jain, S., Dan, N., Kashyap, V.K., Chauhan, S.C., Jaggi, M., & Yallapu, M.M. (2020). Tannic acid inhibits lipid metabolism and induce ROS in prostate cancer cells. Sci Rep, 10, 980.
Ocampo, Y., Caro, D., Rivera, D., Piermattey, J., Gaitan., R., & Franco, L.A. (2020). Transcriptome Changes in Colorectal Cancer Cells upon Treatment with Avicequinone B, Advanced Pharmaceutical Bulletin, 10(4), 638–647.
Sarmiento-Castro, A., Caamaño-Gutiérrez, E., Sims, A.H., Hull, N.J., James, M.I., Santiago-Gomez, A., Eyre, R., Clark, C., Brown, M.E., Brooks, M.D., Wicha, M.S., Howell, S.J., Clarke, R.B., Simoes, B.M. (2020). Increased expression of interleukin-1 receptor characterizes anti-estrogen-resistant ALDH+ breast cancer stem cells. Stem Cell Reports, 15(2), 307-316.
Ulm, M.A., Redfern, T.M., Wilson, B.R., Ponnusamy, S., Asemota, S., Blackburn, P.W., Wang, Y., ElNaggar, A.C., & Nararyanan, R. (2020). Integrin-Linked Kinase Is a Novel Therapeutic Target in Ovarian Cancer. Journal of Personalized Medicine, 10(4), 246.
Verma, S., Shankar, E., Chan, E.R., & Gupta, S. (2020). Metabolic Reprogramming and Predominance of Solute Carrier Genes during Acquired 
Resistance in Prostate Cancer. Cells, 9(12), 2535.
Yong, K.M.A., Ulintz, P.J., Caceres, S., Cheng, X., Bao, L., Wu, Z., Jiagge, E.M., & Merajver, S.D., (2020). Heterogeneity at the invasion front of triple negative breast cancer cells. Sci Rep, 10, 5781.
Liu, Y., Lang, T., Jin, B., Chen, F., Zhang, Y., Beuerman, R.W., Zhou, L. and Zhang, Z., 2017. Luteolin inhibits colorectal cancer cell epithelial-to-mesenchymal transition by suppressing CREB1 expression revealed by comparative proteomics study. Journal of proteomics 161, pp.1-10.
Han, K., Lang, T., Zhang, Z., Zhang, Y., Sun, Y., Shen, Z., Beuerman, R.W., Zhou, L. and Min, D., 2018. Luteolin attenuates Wnt signaling via upregulation of FZD6 to suppress prostate cancer stemness revealed by comparative proteomics. Scientific reports, 8(1), p.8537.
Ortea, I., González-Fernández, M. J., Ramos-Bueno, R. P., & Guil-Guerrero, J. L. (2018). Proteomics study reveals that docosahexaenoic and arachidonic acids exert different in vitro anticancer activities in colorectal cancer cells. Journal of agricultural and food chemistry, 66(24), 6003-6012.
Wagner, S., Ball, G. R., Pockley, A. G., & Miles, A. K. (2018). Application of omic technologies in cancer research. Translational Medicine Reports, 2(1).
Mrowczynski, O.D., Madhankumar, A.B., Sundstrom, J.M., Zhao, Y., Kawasawa, Y.I., Slagle-Webb, B., Mau, C., Payne, R.A., Rizk, E.B., Zacharia, B.E. and Connor, J.R., 2018. Exosomes impact survival to radiation exposure in cell line models of nervous system cancer. Oncotarget, 9(90), p.36083.
Zeinali, M., Murlidhar, V., Fouladdel, S., Shao, S., Zhao, L., Cameron, H., Bankhead III, A., Shi, J., Cuneo, K.C., Sahai, V. and Azizi, E., 2018. Profiling Heterogeneous Circulating Tumor Cells (CTC) Populations in Pancreatic Cancer Using a Serial Microfluidic CTC Carpet Chip. Advanced Biosystems, 2(12), p.1800228.
Rücker, F. G., Dolnik, A., Blätte, T. J., Teleanu, V., Ernst, A., Thol, F., … & Bullinger, L. (2018). Chromothripsis is linked to TP53 alteration, cell cycle impairment, and dismal outcome in acute myeloid leukemia with complex karyotype. haematologica, 103(1), e17-e20.
Araújo, T., Khayat, A., Quintana, L., Calcagno, D., Mourão, R., Modesto, A., Paiva, J., Lima, A., Moreira, F., Oliveira, E. and Souza, M., 2018. Piwi like RNA-mediated gene silencing 1 gene as a possible major player in gastric cancer. World journal of gastroenterology, 24(47), 5338.
Ock, S., Ahn, J., Lee, S.H., Kim, H.M., Kang, H., Kim, Y.K., Kook, H., Park, W.J., Kim, S., Kimura, S. and Jung, C.K., 2018. Thyrocyte‐specific deletion of insulin and IGF‐1 receptors induces papillary thyroid carcinoma‐like lesions through EGFR pathway activation. International Journal of Cancer, 143(10), pp.2458-2469.
Renz, B.W., Tanaka, T., Sunagawa, M., Takahashi, R., Jiang, Z., Macchini, M., Dantes, Z., Valenti, G., White, R.A., Middelhoff, M.A. and Ilmer, M., 2018. Cholinergic Signaling via Muscarinic Receptors Directly and Indirectly Suppresses Pancreatic Tumorigenesis and Cancer Stemness. Cancer discovery, 8(11), pp.1458-1473.
Luo, M., Shang, L., Brooks, M.D., Jiagge, E., Zhu, Y., Buschhaus, J.M., Conley, S., Fath, M.A., Davis, A., Gheordunescu, E. and Wang, Y., 2018. Targeting breast cancer stem cell state equilibrium through modulation of redox signaling. Cell metabolism, 28(1), pp.69-86.
Todorova, K., Metodiev, M.V., Metodieva, G., Mincheff, M., Fernández, N. and Hayrabedyan, S., 2016. Micro-RNA-204 Participates in TMPRSS2/ERG Regulation and Androgen Receptor Reprogramming in Prostate Cancer. Hormones and Cancer, pp.1-21.
Simonik, E.A., Cai, Y., Kimmelshue, K.N., Brantley-Sieders, D.M., Loomans, H.A., Andl, C.D., Westlake, G.M., Youngblood, V.M., Chen, J., Yarbrough, W.G. and Brown, B.T., 2016. LIM-Only Protein 4 (LMO4) and LIM Domain Binding Protein 1 (LDB1) Promote Growth and Metastasis of Human Head and Neck Cancer (LMO4 and LDB1 in Head and Neck Cancer). PloS one, 11(10), p.e0164804.
Klener, P., Fronkova, E., Berkova, A., Jaksa, R., Lhotska, H., Forsterova, K., Soukup, J., Kulvait, V., Vargova, J., Fiser, K. and Prukova, D., 2016. Mantle cell lymphoma‐variant Richter syndrome: Detailed molecular‐cytogenetic and backtracking analysis reveals slow evolution of a pre‐MCL clone in parallel with CLL over several years. International Journal of Cancer.
Colacino, J.A., McDermott, S.P., Sartor, M.A., Wicha, M.S. and Rozek, L.S., 2016. Transcriptomic profiling of curcumin-treated human breast stem cells identifies a role for stearoyl-coa desaturase in breast cancer prevention.Breast Cancer Research and Treatment, pp.1-13.
Kravchenko, D.S., Lezhnin, Y.N., Kravchenko, J.E., Chumakov, S.P. and Frolova, E.I., 2016. Study of Molecular Mechanisms of PDLIM4/RIL in Promotion of the Development of Breast Cancer. Biol Med (Aligarh), 8(2), p.2.
Na, Y., Kaul, S.C., Ryu, J., Lee, J.S., Ahn, H.M., Kaul, Z., Kalra, R.S., Li, L., Widodo, N., Yun, C.O. and Wadhwa, R., 2016. Stress chaperone mortalin contributes to epithelial-mesenchymal transition and cancer metastasis.Cancer research, pp.canres-2704.
Sanford, T., Welty, C., Meng, M. and Porten, S., 2015. MP68-18 MOLECULAR ANALYSIS OF UROTHELIAL TUMORS IN PATIENTS WITH AND WITHOUT METASTASIS STRATIFIED BY T STAGE. The Journal of Urology, 193(4), p.e865.
Hernandez, C., Huebener, P., Pradere, J. P., Antoine, D. J., Friedman, R. A., & Schwabe, R. F. (2018). HMGB1 links chronic liver injury to progenitor responses and hepatocarcinogenesis. The Journal of clinical investigation, 128(6).
Bacich, Dean, Wasim H. Chowdhury, Ronald Rodriguez, and Zhiping Wang. “Increased expression of TRIP13 drives the tumorigenesis of bladder cancer in association with the EGFR signaling pathway.”
Racioppi, L., Nelson, E.R., Huang, W., Mukherjee, D., Lawrence, S.A., Lento, W., Masci, A.M., Jiao, Y., Park, S., York, B. and Liu, Y., 2019. CaMKK2 in myeloid cells is a key regulator of the immune-suppressive microenvironment in breast cancer. Nature communications, 10(1), p.2450.
Cartwright, R., Franklin, L., Tikkinen, K.A.O., Kalliala, I., Miotla, P., Rechberger, T., Offiah, I., McMahon, S., O’Reilly, B., Lince, S., Kluivers, K., Post, W., Poelmans, G., Palmer, M.R., Wessels, H., Wong, A., Kuh, D., Kivimaki, M., Kumari, M., Mangino, M., Spector, T., Guggenheim, J.A., Lehne, B., De Silva, N.M.G., Evans, D.M., Lawlor, D., Karhunen, V., Mannikko, M., Marczak, M., Bennett, P.R., Khullar, V., Järvelin, M.R., &Walley, A. (2021). Genome wide association study identifies two novel loci associated with female stress and urgency urinary incontinence. Journal of Urology.
Cortes-Selva, D., Gibbs, L., Maschek, J.A., Nascimento, M., Van Ry, T., Cox, J.E., Amiel, E., & Fairfax, K.C. (2021). Metabolic reprogramming of the myeloid lineage by Schistosoma mansoni infection persists independently of antigen exposure. PLOS Pathogens, 17(1): e1009198.
Gomez-Lopez, N., Romero, R., Varrey, A., Leng, Y., Miller, D., Done, B., Xu. Y., Bhatti, G., Motomura, K., Gershater, M., Pique-Regi, R., & Tarca, A.L. (2021). RNA sequencing reveals diverse functions of amniotic fluid neutrophils and monocytes/macrophages in intra-amniotic infection. Journal of Innate Immunity, 13, 63-82.
Motomura, K., Romero, R., Galaz, J., Tarca, A.L., Done, B., Xu, Y., Leng, Y., Garcia-Flores, V., Arenas-Hernandez, M., Theis, K.R., Gershater, M., Jung, E., Hsu, C.D., & Gomez-Lopez, N. (2021). RNA sequencing reveals distinct immune responses in the chorioamniotic membranes of women with preterm labor and microbial or sterile intra-amniotic inflammation. Infection and Immunity, 89(5): e00819-20.
Stein, M.M., Conery, M., Magnaye, K.M., Clay, S.M., Billstrand, C., Nicolae, R., Naughton, K., Ober, C., & Thompson, E.E. (2021). Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes. Scientific Reports, 11, 1107.
Wang, Z., Chimenti, M.S., Strouse, C., & Weiner, G.J. (2021). T cells, particularly activated CD4+ cells, maintain anti-CD20-mediated NK cell viability and antibody dependent cellular cytotoxicity. Cancer Immunology, Immunotherapy.
Motomura, K., Romero, R., Tarca, A.L., Galaz, J., Bhatti, G., Done, B., Arenas-Hernandez, M., Chaur, D., & Gomez-Lopez, N. (2020). Pregnancy-specific transcriptional changes upon endotoxin exposure in mice. Journal of Perinatal Medicine, 48(7), 700-722.
Rahman, A.A., Soto-Avellaneda, A., Jin, H.Y., Stojkovska, I., Lai, N.K., Albright, J.E., Webb, A.R., Oe, E., Valarde, J.P., Oxford, A.E., Urquhart, P.E., Wagner, B., Brown, C., Amado, I., Vasquez, P., Lehning, N., Grozdanov, V., Pu, X., Danzer, K.M., & Morrison, B.E. (2020). Enhanced Hyaluronan Signaling and Autophagy Dysfunction by VPS35 D620N. Neuroscience, 441, 33-45.
Schlievert, P.M., Gourronc, F.A., Leung, D.Y.M., & Klingelhutz, A.J. (2020). Human Keratinocyte Response to Superantigens. mSphere, 5(5): e00803-20.
Tchessalova, D., & Tronson, N.C. (2020). Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge. Neuroscience, 428, 76-89.
Van Den Broek, B., Pintelon, I., Hamad, I., Kessels, S., Haidar, M., Hellings, N., Hendriks, J.J.A., Kleinewietfeld, M., Brone, B., Timmerman, V., Timmermans, J.P., Somers, V., Michiels, L., & Irobi, J. (2020). Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis. Journal of Extracellular Vesicles, 10(1).
Wu, Q., Mills, E.A., Wang, Q., Dowling, C.A., Fisher, C., Kirch, B., Lundy, S.K., Fox, D.A., & Mao-Draayer, Y. (2020). Siponimod enriches regulatory T and B lymphocytes in secondary progressive multiple sclerosis. JCI Insight, 5(3): e134251.
Fuentes-González, A.M., Muñoz-Bello, J.O., Manzo-Merino, J., Contreras-Paredes, A., Pedroza-Torres, A., Fernández-Retana, J., Pérez-Plasencia, C. and Lizano, M., 2019. Intratype variants of the E2 protein from human papillomavirus type 18 induce different gene expression profiles associated with apoptosis and cell proliferation. Archives of virology, pp.1-14.
Chakraborty, P., Kuo, R., Vervelde, L., Dutia, B. M., Kaiser, P., & Smith, J. (2019). Macrophages from Susceptible and Resistant Chicken Lines have Different Transcriptomes following Marek’s Disease Virus Infection. Genes, 10(2), 74.
Cortes-Selva, D., Elvington, A. F., Ready, A., Rajwa, B., Pearce, E. J., Randolph, G. J., & Fairfax, K. C. (2018). Schistosoma mansoni infection-induced transcriptional changes in hepatic macrophage metabolism correlate with an athero-protective phenotype. Frontiers in Immunology, 9.
Tjitro, R., Campbell, L. A., Basova, L., Johnson, J., Najera, J. A., Lindsey, A., & Marcondes, M. C. G. (2018). Modeling the Function of TATA Box Binding Protein in Transcriptional Changes Induced by HIV-1 Tat in Innate Immune Cells and the Effect of 
Exposure. Frontiers in immunology, 9.
Jouan, Y., Patin, E. C., Hassane, M., Si-Tahar, M., Baranek, T., & Paget, C. (2018). Thymic program directing the functional development of γδT17 cells. Frontiers in immunology, 9.
Lin, C.K.E., Kaptein, J.S. and Sheikh, J., 2017. Differential expression of microRNAs and their possible roles in patients with chronic idiopathic urticaria and active hives. Allergy & Rhinology, 8(2), pp.e67-e80.
Wang, S., Campos, J., Gallotta, M., Gong, M., Crain, C., Naik, E., Coffman, R.L. and Guiducci, C., 2016. Intratumoral injection of a CpG oligonucleotide reverts resistance to PD-1 blockade by expanding multifunctional CD8+ T cells. Proceedings of the National Academy of Sciences, p.201608555.
Eddens, T., Campfield, B.T., Serody, K., Manni, M.L., Horne, W., Elsegeiny, W., McHugh, K.J., Pociask, D., Chen, K., Zheng, M. and Alcorn, J.F., 2016. A Novel CD4+ T-cell Dependent Murine Model of Pneumocystis Driven Asthma-like Pathology. American Journal of Respiratory And Critical Care Medicine, (ja).
Andres-Terre, M., McGuire, H.M., Pouliot, Y., Bongen, E., Sweeney, T.E., Tato, C.M. and Khatri, P., 2015. Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses. Immunity, 43(6), pp.1199-1211.
Kaur, G., Helmer, R. A., Smith, L. A., Martinez-Zaguilan, R., Dufour, J. M., & Chilton, B. S. (2018). Alternative splicing of helicase-like transcription factor (Hltf): Intron retention-dependent activation of immune tolerance at the feto-maternal interface. PloS one, 13(7), e0200211.
Jiang, J., Shihan, M. H., Wang, Y., & Duncan, M. K. (2018). Lens Epithelial Cells Initiate an Inflammatory Response Following Cataract Surgery. Investigative ophthalmology & visual science, 59(12), 4986-4997.
Lidberg, K.A., Muthusamy, S., Adil, M., Patel, R.S., Wang, L., Bammler, T.K., Reichel, J., Yeung, C.K., Himmelfarb, J., Kelly, E.J., & Akilesh, S. (2021). Multi-omic Characterization of Human Tubular Epithelial Cell Response to Serum. bioRxiv.
Fierro-Fernandez, M., Miguel, V., Marquez-Exposito, L., Nuevo-Tapioles, C., Herrero, J.I., Blanco-Ruiz, E., Tituaña, J., Castillo, C., Cannata, P., Monsalve, M., Ruiz-Ortega, M., Ramos, R., & Lamas, S. (2020). MiR‐9‐5p protects from kidney fibrosis by metabolic reprogramming. The FASEB Journal, 34(1), 410-431.
Hammad, S.M., Twal, W.O., Arif, E., Semler, A.J., Klein, R.L., & Nihalani, D. (2020). Transcriptomics Reveal Altered Metabolic and Signaling Pathways in Podocytes Exposed to C16 Ceramide-Enriched Lipoproteins. Genes, 11(2), 178.
Nistala, R., Ren, J., An, J., Strawn, T., Rawat, S., Patel, P., & Whaley-Connell, A. (2020). Abstract P024: Proximal Tubule Specific Dpp4 Deletion Slows Kidney Disease Progression In Western Diet-fed Obese Mice. Hypertension, 76:AP024.
Parafati, M., Bae, S.H., Kirby, R.J., Fitzek, M., Iyer, P., Engkvist, O., Smith, D.M., & Malany, S. (2020). Pluripotent Stem Cell-Derived Hepatocytes Phenotypic Screening Reveals Small Molecules Targeting the CDK2/4-C/EBPα/DGAT2 Pathway Preventing ER-Stress Induced Lipid Accumulation. Int. J. Mol. Sci., 21(24), 9557.
Parafati, M., Kirby, R. J., Khorasanizadeh, S., Rastinejad, F., & Malany, S. (2018). A nonalcoholic fatty liver disease model in human induced pluripotent stem cell-derived hepatocytes, created by endoplasmic reticulum stress-induced steatosis. Disease models & mechanisms, 11(9), dmm033530.
Lamontagne, J., Mell, J.C. and Bouchard, M.J., 2016. Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression. PLoS Pathog, 12(2), p.e1005438.
Hariharan, K., Stachelscheid, H., Rossbach, B., Oh, S.J., Mah, N., Schmidt-Ott, K., Kurtz, A. and Reinke, P., 2019. Parallel generation of easily selectable multiple nephronal cell types from human pluripotent stem cells. Cellular and Molecular Life Sciences, 76(1), pp.179-192.
Menon, R., Otto, E.A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y.C., Troyanskaya, O., Spence, J.R., Kretzler, M. and Cebrian, C., 2018. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development, 145(16), p.dev164038.
Fortier, S.M., Penke, L.R., King, D., Pham, T.X., Ligresti, G., & Peters-Golden, M. (2021). Myofibroblast dedifferentiation proceeds via distinct transcriptomic and phenotypic transitions. JCI Insight, 6(6): e144799.
Germain, A., Levine, S.M., & Hanson, M.R. (2021). In-Depth Analysis of the Plasma Proteome in ME/CFS Exposes Disrupted Ephrin-Eph and Immune System Signaling. Proteomes, 9(1):6.
Mori, H., Dugan, C.E., Nishii, A., Benchamana, A., Li, Z., Cadenhead IV, T.S., Das, A.K., Evans, C.R., Overmyer, K.A., Romanelli, S.M., Peterson, S.K., Bagchi, D.P., Corsa, C.A., & MacDougald, O.A. (2021). The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures. PLOS Biology, 19(5): e3000988.
Tigano, M., Vargas, D.C., Tremblay-Belzile, S., Fu, Y., & Sfeir, A. (2021). Nuclear sensing of breaks in mitochondrial DNA enhances immune surveillance. Nature, 591, 477-481.
ALZAHRANI, H. (2020). Protein Expression of Human Brain Microvascular Endothelial Cells in Response to Meningitic C. Sakazakii: in Vitro and in Silico Analyses. pjmhsonline.com.
Ávila-Mendoza, J., Subramani, A., Sifuentes, C.J., & Denver, R.J. (2020). Molecular mechanisms for Krüppel-like factor 13 actions in hippocampal neurons. Molecular Neurobiology, 57, 3785-3802.
Duran‐Ortiz, S., Young, J.A., Jara, A., Jense, E.A., Basu, R., List, E.O., Qian, Y., Kopchick, J.J., & Berryman, D.E. (2020). Differential gene signature in adipose tissue depots of growth hormone transgenic mice. Journal of Neuroendocrinology, 32(11), e12893.
Fischhuber, K., Matzinger, M., & Heiss, E.H. (2020). AMPK enhances transcription of selected Nrf2 target genes via negative regulation of Bach1. Front. Cell Dev. Biol., 8:628.
Nascimento, P.M.D., Medeiros, I.G., Falcao, R.M., Stransky, B., & de Souza, J.E.S. (2020). A decision tree to improve identification of pathogenic mutations in clinical practice. BMC Medical Informatics and Decision Making, 20(52).
van Gastel, J., Janssens, J., Etienne, H., Azmi, A., & Maudsley, S. (2020). The Investigation of the GIT2-RXFP3 Synergistic System and Its Potential Role in Aging and Age-related Disorders. Front. Aging Neurosci. Conference Abstract: 6th Belgian Brain Congress.
Avolio, R., Järvelin, A.I., Mohammed, S., Agliarulo, I., Condelli, V., Zoppoli, P., Calice, G., Sarnataro, D., Bechara, E., Tartaglia, G.G. and Landriscina, M., 2018. Protein Syndesmos is a novel RNA-binding protein that regulates primary cilia formation. Nucleic acids research, 46(22), pp.12067-12086.
Kowtharapu, B., Prakasam, R., Murín, R., Koczan, D., Stahnke, T., Wree, A., Jünemann, A. and Stachs, O., 2018. Role of Bone Morphogenetic Protein 7 (BMP7) in the Modulation of Corneal Stromal and Epithelial Cell Functions. International journal of molecular sciences, 19(5), p.1415.
Renaud, L., da Silveira, W.A., Glen, J., William, B., Hazard, E.S. and Hardiman, G., 2018. Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio). Current genomics, 19(7), pp.615-629.
Sharp-Tawfik, Arielle E., Alexis M. Coiner, Catherine B. MarElia, Melissa Kazantsis, Clare Zhang, and Brant R. Burkhardt. “Compositional analysis and biological characterization of Cornus officinalis on human 1.1 B4 pancreatic β cells.” Molecular and Cellular Endocrinology (2019): 110491.
Kusuhara, A., Babayev, E., Zhou, L.T., Singh, V.P., Gerton, J.L., & Duncan, F.E. (2021). Immature Follicular Origins and Disrupted Oocyte Growth Pathways Contribute to Decreased Gamete Quality During Reproductive Juvenescence in Mice. Front. Cell Dev. Biol., 9: 693742.
Massaro, A.N., Bammler, T.K., MacDonald, J.W., Perez, K.M., Comstock, B., & Juul, S.E. (2021). Whole genome methylation and transcriptome analyses to identify risk for cerebral palsy (CP) in extremely low gestational age neonates (ELGAN). Scientific Reports, 11, 5305.
Motomura, K., Romero, R., Galaz, J., Miller, D., Done, B., Arenas-Hernandez, M., Garcia-Flores, V., Tao, L., Tarca, A.L., & Gomez-Lopez, N. (2021). Human Chorionic 
Modulates the Transcriptome of the Myometrium and Cervix in Late Gestation. Reproductive Sciences, 28, 2246-2260.
Vilen, Z., Joeh, E., Critcher, M., Parker, C.G., & Huang, M.L. (2021). Proximity Tagging Identifies the Glycan-Mediated Glycoprotein Interactors of Galectin-1 in Muscle Stem Cells. ACS Chemical Biology.
Wang, J., Luo, X., Pan, J., Dong, X., Tian, X., Tu, Z., Ju, W., Zhang, M., Zhong, M., De Chen, C., Flory, M., Wang, Y., Brown, W.T., & Zhong, N. (2021). (Epi) genetic variants of the sarcomere-desmosome are associated with premature utero-contraction in spontaneous preterm labor. Environment International, 148: 106382.
Ávila-Mendoza, J., Subramani, A., & Denver, R.J. (2020). Krüppel-like factors 9 and 13 block axon growth by transcriptional repression of key components of the cAMP signaling pathway. Front Mol. Neurosci., 13: 602638.
Chehin, M.B., Fraietta, R., Lorenzon, A.R., Bonetti, T.C.S., & Motta, E.L.A. (2020). The insulin signaling pathway is dysregulated in cumulus cells from obese, infertile women with polycystic ovarian syndrome with an absence of clinical insulin resistance. Therapeutic Advances in Reproductive Health, 14.
Cramer, A.A.W., Prasad, V., Eftestøl, E., Song, T., Hansson, K.A., Dugdale, H.F., Sadayappan, S., Ochala, J., Gunersen, K., & Millay, D.P. (2020). Nuclear numbers in syncytial muscle fibers promote size but limit the development of larger myonuclear domains. Nature Communications, 11, 6287.
Gelencser, Z., Romero, R., Xu, Y., Kiraly, P., Demeter, A., Palhalmi, J., Gyorffy, B.A, Juhasz, K., Hupuczi, P., Kekesi, K.A., Meinhardt, G., Papp, Z., Draghich, S., Erez, O., Tarca, A.L., Knofler, M., & Than, N.G. (2020). Placenta-specific genes, their regulation during villous trophoblast differentiation and dysregulation in preterm preeclampsia. International Journal of Molecular Sciences, 21(2).
Keel, B.N., Lindholm-Perry, A.K., Oliver, W.T., Wells, J.E., Jones, S.A., & Rempel, L.A. (2020). Characterization and Comparative Analysis of Transcriptional Profiles of Porcine Colostrum and Mature Milk Across Multiple Parities. BMC Genomics.
Thomas, P.A., Schafler, E.D., Ruff, S.E., Voisin, M., Ha, S., & Logan, S.K. (2020). UXT in Sertoli cells is required for blood–testis barrier integrity. Biology of Reproduction, 103(4), 880-891.
Zhu, Z., Mesci, P., Bernatchez, J.A., Gimple, R.C., Wang, X., Schafer, S.T., Wettersten, H.I., Beck, S., Clark, A.E., Wu, Q., Prager, B.C., Kim, L.J.Y., Dhanwani, R., Sharma, S., Garancher, A., et al. (2020). Zika virus targets glioblastoma stem cells through a SOX2-integrin αvβ5 axis. Cell Stem Cell, 26(2), 187-204.e10.
Schubert, M. F., Noah, A. C., Bedi, A., Gumucio, J. P., & Mendias, C. L. (2019). Reduced Myogenic and Increased Adipogenic Differentiation Capacity of Rotator Cuff Muscle Stem Cells. JBJS, 101(3), 228-238.
Basu, A., Munir, S., Mulaw, M.A., Singh, K., Herold, B., Crisan, D., Sindrilaru, A., Treiber, N., Wlaschek, M., Huber-Lang, M. and Gebhard, F., 2018. A novel S100A8/A9 induced fingerprint of mesenchymal stem cells associated with enhanced wound healing. Scientific reports, 8(1), p.6205.
Colacino, J.A., Azizi, E., Brooks, M.D., Harouaka, R., Fouladdel, S., McDermott, S.P., Lee, M., Hill, D., Madden, J., Boerner, J. and Cote, M.L., 2018. Heterogeneity of human breast stem and progenitor cells as revealed by transcriptional profiling. Stem cell reports, 10(5), pp.1596-1609.
Dekker, S.E., Biesterveld, B.E., Bambakidis, T., Williams, A.M., Tagett, R., Johnson, C.N., Silleses, M., Liu, B., Li, Y., & Alam, H.B. (2021). Modulation of brain transcriptome by combined histone deacetylase inhibition and plasma treatment following traumatic brain injury and hemorrhagic shock. Shock, 55(1), 110-120.
Fries, G., Quevedo, J., Walss-Bass, C., & Soares, J. (2021). Epigenetic Alterations in the Hippocampus of Patients With Bipolar Disorder. Biological Psychiatry, 89(9),: S12-S13.
Garrick, J.M., Cole, T.B., Bammler, T.K., MacDonald, J.W., Marsillach, J., Furlong, C.E., & Costa, L.G. (2021). Paraoxonase 2 deficiency in mice alters motor behavior and causes region-specific transcript changes in the brain. Neurotoxicology and Teratology, 87: 107010.
Herron, J.M., Tomita, H., White, C.C., Kavanagh, T.J., & Xu, L. (2021). Benzalkonium Chloride Disinfectants Induce Apoptosis, Inhibit Proliferation, and Activate the Integrated Stress Response in a 3-D in Vitro Model of Neurodevelopment. Chemical Research in Toxicology, 34(5), 1265-1274.
Pauža, A.G., Mecawi, A.S., Paterson, A., Hindmarch, C.C.T., Greenwood, M., Murphy, D., & Greenwood, M.P. (2021). Osmoregulation of the transcriptome of the hypothalamic supraoptic nucleus: a resource for the community. Journal of Neuroendocrinology, e13007.
Willour, V. (2021). Transcriptomic Changes Induced by Lithium. Biological Psychiatry, 89(9).
Xu, H., Fame, R.M., Sadegh, C., Sutin, J., Naranjo, C., Syau, D., Cui, J., Shipley, F.B., Vernon, A., Gao, F., Zhang, Y., Holtzman, M.J., Heiman, M., Warf, B.C., Lin, P.Y., & Lehtinen, M.K. (2021). Choroid plexus NKCC1 mediates cerebrospinal fluid clearance during mouse early postnatal development. Nature Communications, 12(447).
Ahlström, F.H.G., Mätlik, K., Viisanen, H., Blomkvist, K.B., Liu, X., Lilius, T., Sidorova, Y., Kalso, E.A., & Rauhala, P.V. (2020). Spared nerve injury causes sexually dimorphic mechanical allodynia and differential gene expression in spinal cords and dorsal root ganglia in rats. Research Square.
Donegan, J.J., Boley, A.M., Glenn, J.P., Carless, M.A., & Lodge, D.J. (2020). Developmental alterations in the transcriptome of three distinct rodent models of schizophrenia. Plos ONE, 15(6): e0232200.
Gokuladhas, S., Schierding, W., Cameron-Smith, D., Wake, M., Scotter, E.L., & O’Sullivan, J. (2020). Shared regulatory pathways reveal novel genetic correlations between grip strength and neuromuscular disorders. Frontiers in Genetics, 11:393.
Golovina, E., Vickers, M.H., Erb, C.D., & O’Sullivan, J.M. (2020). GWAS SNPs Impact Shared Regulatory Pathways Amongst Multimorbid Psychiatric Disorders and Cognitive Functioning. Frontiers in Psychiatry, 11: 560751.
Gramlich, O.W., Brown, A.J., Godwin, C.R., Chimenti, M.S., Boland, L.K., Ankrum, J.A., & Kardon, R.H. (2020). Systemic mesenchymal stem cell treatment mitigates structural and functional retinal ganglion cell degeneration in a mouse model of multiple sclerosis. Translational Vision Science & Technology, 9(16).
Lents, C.A., Nonneman, D.J., & Keel, B.N. (2020). SUN-242 Transcriptome of the Amygdala in Normal Cyclic and Acyclic Gilts. Journal of the Endocrine Society, 4(1).
Marui, S., Irigoitia, B., Lenczuk, A., Rocha, N.H., Brito, L.P, & Watanabe, T. (2020). SAT-410 Long Term Evaluation of TSH Receptor Antibodies and Thyroid Stimulating Immunoglobulin After Radioiodine Therapy for Thyrotoxicosis. Journal of the Endocrine Society, 4(S1).
Razmara, E., Azimi, H., Bitaraf, A., Daneshmand, M.A., Galehdari, M., Dokhanchi, M., Esmaeilzadeh-Gharehdaghi, E., & Garshasbi, M. (2020). Whole‐exome sequencing identified a novel variant in an Iranian patient affected by pycnodysostosis. Molecular genetics & Genomic Medicine, 8(3), e1118.
Sharma, K.D., Schaal, D., Kore, R.A., Hamzah, R.N., Pandanaboina, S.C., Hayar, A., Griffin, R.J., Srivatsan, M., Reyna, N.S., & Xie, J.Y. (2020). Glioma-derived exosomes drive the differentiation of neural stem cells to astrocytes. Plos ONE, 15(7): e0234614.
Xu, H., Fame, R.M., Sadegh, C., Sutin, J., Naranjo, C., Syau, D., et al. (2020). Non-canonical, potassium-driven cerebrospinal fluid clearance., CalTechAuthors.
Zhou, X., He, C., Ren, J., Dai, C., Stevens, S.R., Wang, Q., Zamler, D., Shingu, T., Yuan, L., Chandregowda, C.R., Wang, Y., Ravikumar, V., Rao, A.U.K., Zhou, F., Zheng, H., Rasband, M.N., Chen, Y., Lan, F., Heimberger, A.B., Segal, B.M., & Hu, J. (2020). Mature myelin maintenance requires Qki to coactivate PPARβ-RXRα–mediated lipid metabolism. The Journal of Clinical Investigation, 130(5), 2220-2236.
Bountali, A., Tonge, D. P., & Mourtada-Maarabouni, M. (2019). RNA sequencing reveals a key role for the long non-coding RNA MIAT in regulating neuroblastoma and glioblastoma cell fate. International journal of biological macromolecules.
Haenfler, J. M., Skariah, G., Rodriguez, C. M., Monteiro da Rocha, A., Parent, J. M., Smith, G. D., & Todd, P. K. (2018). Targeted reactivation of fmr1 transcription in fragile x syndrome embryonic stem cells. Frontiers in molecular neuroscience, 11, 282.
Flores, B. N., Li, X., Malik, A. M., Martinez, J., Beg, A. A., & Barmada, S. J. (2019). An Intramolecular Salt Bridge Linking TDP43 RNA Binding, Protein Stability, and TDP43-Dependent Neurodegeneration. Cell Reports, 27(4), 1133-1150.
Tang, Q., Zhang, C., Wu, X., Duan, W., Weng, W., Feng, J., Mao, Q., Chen, S., Jiang, J. and Gao, G., 2018. Comprehensive proteomic profiling of patients’ tears identifies potential biomarkers for the traumatic vegetative state. Neuroscience bulletin, 34(4), pp.626-638.
Zhao, X., Liao, Y., Morgan, S., Mathur, R., Feustel, P., Mazurkiewicz, J., Qian, J., Chang, J., Mathern, G.W., Adamo, M.A. and Ritaccio, A.L., 2018. Noninflammatory changes of microglia are sufficient to cause epilepsy. Cell reports, 22(8), pp.2080-2093.
Jokinen, V., Sidorova, Y., Viisanen, H., Suleymanova, I., Tiilikainen, H., Li, Z., Lilius, T.O., Mätlik, K., Anttila, J.E., Airavaara, M. and Tian, L., 2018. Differential Spinal and supraspinal activation of glia in a rat model of morphine tolerance. Neuroscience, 375, pp.10-24.
Burger, L. L., Vanacker, C., Phumsatitpong, C., Wagenmaker, E. R., Wang, L., Olson, D. P., & Moenter, S. M. (2018). Identification of genes enriched in GnRH neurons by translating ribosome affinity purification and RNAseq in mice. Endocrinology, 159(4), 1922-1940.
Diéguez-Hurtado, R., Kato, K., Giaimo, B.D., Nieminen-Kelhä, M., Arf, H., Ferrante, F., Bartkuhn, M., Zimmermann, T., Bixel, M.G., Eilken, H.M. and Adams, S., 2019. Loss of the transcription factor RBPJ induces disease-promoting properties in brain pericytes. Nature Communications, 10(1), p.2817.
Srivastava, A., Ritesh, K.C., Tsan, Y.C., Liao, R., Su, F., Cao, X., Hannibal, M.C., Keegan, C.E., Chinnaiyan, A.M., Martin, D.M. and Bielas, S.L., 2015. De novo Dominant ASXL3 Mutations Alter H2A Deubiquitination and Transcription in Bainbridge-Ropers Syndrome. Human molecular genetics, p.ddv499.
Allred, M.G., Chimenti, M.S., Ciecko, A.E., Chen, Y.G., & Lieberman, S.M. (2021). Characterization of Type I Interferon-Associated Chemokines and Cytokines in Lacrimal Glands of Nonobese Diabetic Mice. International Journal of Molecular Sciences, 22(7), 3767.
Kleinstein, S.E., McCorrison, J., Ahmed, A., Hasturk, H., Van Dyke, T.E., & Freire, M. (2021). Transcriptomics of type 2 diabetic and healthy human neutrophils. BMC Immunology, 22(37).
Rise, K., Tessem, M.B., Drabløs, F., & Rye, M.B. (2021). FunHoP-Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks. Genomics, Proteomics & Bioinformatics.
Wang, Z., Mohan, R., Chen, X., Matson, K., Waugh, J., Mao, Y., Zhang, S., Li, W., Tang, X., Satin, L.S., & Tang, X. (2021). microRNA-483 Protects Pancreatic β-Cells by Targeting ALDH1A3. Endocrinology, 162(5).
Zhu, H., & Leung, S. (2021). MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses. Plos ONE, 16(4): e0247556.
Bagchi, D.P., Nishii, A., Li, Z., DelProposto, J.B., Corsa, C.A., Mori, H., Hardij, J., Learman, B.S., Lumeng, C.N., & MacDougald, O.A. (2020). Wnt/β-catenin signaling regulates adipose tissue lipogenesis and adipocyte-specific loss is rigorously defended by neighboring stromal-vascular cells. Molecular Metabolism, 42:101078.
Cortes-Selva, D., Gibbs, L., Maschek, J.A., Van Ry, T., Rajwa, B., Cox, J.E., Amiel, E. & Fairfax, K.C. (2020). Schistosoma mansoni infection reprograms the metabolic potential of the myeloid lineage in a mouse model of metabolic syndrome. bioRxiv.
Debreceni, I.L., Chimenti, M.S., Serreze, D.V., Geurts, A.M., Chen, Y., & Lieberman, S.M. (2020). Toll-Like Receptor 7 Is Required for Lacrimal Gland Autoimmunity and Type 1 Diabetes Development in Male Nonobese Diabetic Mice. International Journal of Molecular Sciences, 21(24), 9478.
Russo, L., Muir, L., Geletka, L., Delproposto, J., Baker, N., Flesher, C., O’Rourke, R., & Lumeng, C.N. (2020). Cholesterol 25-hydroxylase (CH25H) as a promoter of adipose tissue inflammation in obesity and diabetes. Molecular Metabolism, 39:100983.
Ogura, Kohei, Kayo Okumura, Yukiko Shimizu, Teruo Kirikae, and Tohru Miyoshi-Akiyama. “Pathogenicity induced by invasive infection of Streptococcus dysgalactiae subsp. equisimilis in a mouse model of diabetes.” Frontiers in microbiology, 9 (2018).
Takeda, K., Sriram, S., Chan, X.H.D., Ong, W.K., Yeo, C.R., Tan, B., Lee, S.A., Kong, K.V., Hoon, S., Jiang, H. and Yuen, J.J., 2016. Retinoic Acid Mediates Visceral-specific Adipogenic Defects of Human Adipose-derived Stem Cells. Diabetes, p.db151315.
Aldiss, Peter, Michael E. Symonds, Jo E. Lewis, David J. Boocock, Amanda K. Miles, Ian Bloor, Francis JP Ebling, and Helen Budge. “Interscapular and Perivascular Brown Adipose Tissue Respond Differently to a Short-Term High-Fat Diet.” Nutrients 11, no. 5 (2019): 1065.
Manigrasso, M. B., Friedman, R. A., Ramasamy, R., D’Agati, V., & Schmidt, A. M. (2018). Deletion of the formin Diaph1 protects from structural and functional abnormalities in the murine diabetic kidney. American Journal of Physiology-Renal Physiology, 315(6), F1601-F1612.
Li, J., Wang, X., Ackerman, W., Batty, A., Kirk, S., White, W., Wang, X., Anastasakis, D., Samavati, L., Buhimschi, I. and Nelin, L., 2018. Dysregulation of Lipid Metabolism in Mkp-1 Deficient Mice during Gram-Negative Sepsis. International journal of molecular sciences, 19(12), p.3904.
Fierro-Fernández, M., Miguel, V., Márquez-Expósito, L., Nuevo-Tapioles, C., Herrero, J.I., Blanco-Ruiz, E., Tituaña, J., Castillo, C., Cannata, P., Monsalve, M. and Ruiz-Ortega, M., 2019. MiR-9-5p protects from kidney fibrosis by metabolic reprogramming. bioRxiv, p.667972.
Schatton, D., Pla-Martin, D., Marx, M.C., Hansen, H., Mourier, A., Nemazanyy, I., Pessia, A., Zentis, P., Corona, T., Kondylis, V. and Barth, E., 2017. CLUH regulates mitochondrial metabolism by controlling translation and decay of target mRNAs. J Cell Biol, pp.jcb-201607019.
Vomhof-DeKrey, Emilie E., Jun Lee, Jack Lansing, Chris Brown, Diane Darland, and Marc D. Basson. “Schlafen 3 knockout mice display gender-specific differences in weight gain, food efficiency, and expression of markers of intestinal epithelial differentiation, metabolism, and immune cell function.” PloS one 14, no. 7 (2019): e0219267.
Westphalen, C.B., Takemoto, Y., Tanaka, T., Macchini, M., Jiang, Z., Renz, B.W., Chen, X., Ormanns, S., Nagar, K., Tailor, Y. and May, R., 2016. Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis. Cell Stem Cell, 18(4), pp.441-455.
Aldiss, Peter, Jo E. Lewis, Irene Lupini, David J. Boocock, Amanda K. Miles, Francis JP Ebling, Helen Budge, and Michael E. Symonds. “Exercise does not induce browning of WAT at thermoneutrality and induces an oxidative, myogenic signature in BAT.” bioRxiv (2019): 649061.
Gangwar, R.S., Vinayachandran, V., Rengasamy, P., CHan, R., Park, B., Diamond-Zaluski, R., Ann Cara, E., Cha, A., Das, L., Asase, C., Maiseyeu, A., Deiuliis, J., Zhong, J., Mitzner, W., Biswal, S., & Rajagopalan, S. (2020). Differential contribution of bone marrow-derived infiltrating monocytes and resident macrophages to persistent lung inflammation in chronic air pollution exposure. Scientific Reports, 10(14348).
Helling, B.A., Sobreira, D.R., Hansen, G.T., Sakabe, N.J., Luo, K., Billstrand, C., Laxman, B., Nicolae, R.I., Bochkov, D.L., Gern, J.E., Nobrega, M.A., White, S.R., & Ober, C. (2020). Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma. Communications Biology, 3(678).
Mendonça, D.B., Nguyen, J.T., Haidar, F., Fox, A.L., Ray, C., Amatullah, H., Liu, F., Kim, J.K., & Krebsbach, P.H. (2020). MicroRNA-1911-3p targets mEAK-7 to suppress mTOR signaling in human lung cancer cells. Heliyon, 6(12): e05734.
Morin, A., McKennan, C.G., Pedersen, C.E.T., Stokholm, J., Chawes, B.L., Schoos, A.M., Naughton, K.A., Thorsen, J., Mortensen, M.S., Vercelli, D., Trivedi, U., Sorensen, S.J., Bisgaard, H., Nicolae, D.L., Bonnelykke, K., & Ober, C. (2020). Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. Journal of Allergy and Clinical Immunology, 146(6), 1358-1366.
Pokhilenko, V. (2020). How the Lung Microbiome Fights Bacterial and Viral Infection., interactive-plus.ru.
Renaud, L., da Silveira, W.A., Takamura, N., Hardiman, G., & Feghali-Bostwick, C. (2020). Prominence of IL6, IGF, TLR, and bioenergetics pathway perturbation in lung tissues of scleroderma patients with pulmonary fibrosis. Frontiers in Immunology, 11:383.
Talreja, J., Bauerfeld, C., Sendler, E., Pique-Regi, R., Luca, F., & Samavati, L. (2020). Derangement of metabolic and lysosomal gene profiles in response to 
treatment in sarcoidosis. Frontiers in Immunology, 11:779.
Thompson, E.E., Dang, Q., Mitchell-Handley, B., Rajendran, K., Ram-Mohan, S., Solway, J., Ober, C., & Krishnan, R. (2020). Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma. Genome Medicine, 12(64).
Mitt, M., Altraja, A. and Altraja, S., 2016. Altered Gene Expression Profiles In Human Bronchial Epithelial Cells Exposed To E-Cigarette Liquid: Results From A Genome-Wide Monitoring. In B58. BIG AND BIGGER (DATA): OMICS AND BIOMARKERS OF COPD AND OTHER CHRONIC LUNG DISEASES (pp. A4053-A4053). American Thoracic Society.
Gallotta, M., Assi, H., Degagné, É., Kannan, S. K., Coffman, R. L., & Guiducci, C. (2018). Inhaled TLR9 Agonist Renders Lung Tumors Permissive to PD-1 Blockade by Promoting Optimal CD4+ and CD8+ T-cell Interplay. Cancer research, 78(17), 4943-4956.
Iosef, C., Liu, M., Ying, L., Rao, S.P., Concepcion, K.R., Chan, W.K., Oman, A. and Alvira, C.M., 2018. Distinct roles for IκB kinases alpha and beta in regulating pulmonary endothelial angiogenic function during late lung development. Journal of cellular and molecular medicine, 22(9), pp.4410-4422.
Zhou, H., Manthey, J., Lioutikova, E., Yang, W., Yoshigoe, K., Yang, M.Q. and Wang, H., 2016. The up-regulation of Myb may help mediate EGCG inhibition effect on mouse lung adenocarcinoma. Human Genomics, 10(2), p.103.
Riemondy, K.A., Jansing, N.L., Jiang, P., Redente, E.F., Gillen, A.E., Fu, R., Miller, A.J., Spence, J.R., Gerber, A.N., Hesselberth, J.R. and Zemans, R.L., 2019. Single cell RNA sequencing identifies TGFβ as a key regenerative cue following LPS-induced lung injury. JCI insight.
Ortea, I., Rodríguez-Ariza, A., Chicano-Gálvez, E., Vacas, M.A. and Gámez, B.J., 2016. Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction. Journal of Proteomics. 2016 Feb 18.
Zhou, H., Manthey, J., Lioutikova, E., Yang, M.Q., Yang, W., Yoshigoe, K. and Wang, H., 2015, November. The upregulation of Myb and Peg3 may mediate EGCG inhibition effect on mouse lung adenocarcinoma. In Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on (pp. 1532-1535). IEEE.
Kumar, A., Bicer, E.M., Pfeffer, P., Monopoli, M.P., Dawson, K.A., Eriksson, J., Edwards, K., Lynham, S., Arno, M., Behndig, A.F. and Blomberg, A., 2017. Differences in the coronal proteome acquired by particles depositing in the lungs of asthmatic versus healthy humans. Nanomedicine: Nanotechnology, Biology and Medicine.
Lee, J., Arisi, I., Puxeddu, E., Mramba, L.K., Amicosante, M., Swaisgood, C.M., Pallante, M., Brantly, M.L., Sköld, C.M. and Saltini, C., 2018. Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro-inflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation. PloS one, 13(4), p.e0194803.
Jaya, Talreja, Talwar Harvinder, Christian Bauerfeld, Lawrence I. Grossman, Zhang Kezhong, Paul Tranchida, and Samavati Lobelia. “HIF-1α regulates IL-1β and IL-17 in sarcoidosis.” eLife 8 (2019).
Bhatti, U.F., Remmer, H., Williams, A.M., Biesterveld, B.E., Russo, R., Wakam, G., Kemp, M., Tagett, R., Liu, B., Li, Y., & Alam, H.B. (2021). Assessment of the Cytoprotective Effects of High-Dose 
Compared to a Clinically Used Lower Dose. Journal of Surgical Research, 266, 125-141.
Biesterveld, B.E., O’Connell, R., Kemp, M.T., Wakam, G.K., Williams, A.M., Pail, M.P., & Alam, H.B. (2021). Validation of intraosseous delivery of 
in a swine model of polytrauma. Trauma Surgery and Acute Care Open, 6:e000683.
Biesterveld, B.E., Siddiqui, A.Z., O’Connell, R.L., Remmer, H., Williams, A.M., Shamshad, A., Smith, W.M., Kemp, M.T., Wakam, G.K., & Alam, H.B. (2021). Protects Against Acute Kidney Injury in Hemorrhage and Trauma. Journal of Surgical Research, 266, 222-229.
Chantzichristos, D., Svensson, P.A., Garner, T., Glad, C.A.M., Walker, B.R., Bergthorsdottir, R., Ragnarsson, O., Trimpou, P., Stimson, R.H., Borresen, S.W., Feldt-Rasmussen, U., Jansson, P.A., Skrtic, S., Stevens, A., & Johannsson, G. (2021). Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial. Elife, 10:e62236.
Hadwen, J., Schock, S., Farooq, F., MacKenzie, A., & Plaza-Diaz, J. (2021). Separating the Wheat from the Chaff: The Use of Upstream Regulator Analysis to Identify True Differential Expression of Single Genes within Transcriptomic Datasets. International Journal of Molecular Sciences, 11(12), 6295.
Marie-Claire, C., Lejeune, F.X., Bellivier, F., & Etain, B. (2021). A Dna Methylation Signature Discriminates Between Excellent and Non-Response to Lithium in Patients With Bipolar Disorder Type 1. Biological Psychiatry, 89(9), S13-14.
Biesterveld, B.E., Pumiglia, L., Iancu, A., Shamshad, A.A., Remmer, H.A., Siddiqui, A.Z., O’Connell, R.L., Wakam, G.K., Temp, M.K., Williams, A.M., Pai, M.P., & Alam, H.B. (2020). 
treatment rescues injured tissues after traumatic brain injury. Journal of Trauma and Acute Care Surgery, 89(6), 1156-1165.
Parry, C.M., & Hawcutt, D. (2020). Fifteen-minute consultation: Pharmacogenomics: a guide for busy clinicians. Archives of Disease in Childhood-Education and Practice, 105, 107-110.
Zhang, C., Chery, S., Lazerson, A., Altman, N.H., Jackson, R., Holt, G., Campos, M., Schally, A.V., & Mirsaeidi, M. (2020). Anti-inflammatory effects of α-MSH through p-CREB expression in sarcoidosis like granuloma model. Scientific Reports, 10, 7277.
Kumar, A., Terakosolphan, W., Hassoun, M., Vandera, K.K., Novicky, A., Harvey, R., Royall, P.G., Bicer, E.M., Eriksson, J., Edwards, K. and Valkenborg, D., 2017. A Biocompatible Synthetic Lung Fluid Based on Human Respiratory Tract Lining Fluid Composition. Pharmaceutical Research, pp.1-12.
Shi, J., Wang, X., Lyu, L., Jiang, H., & Zhu, H. J. (2018). Comparison of protein expression between human livers and the hepatic cell lines HepG2, Hep3B, and Huh7 using SWATH and MRM-HR proteomics: Focusing on drug-metabolizing enzymes. Drug metabolism and pharmacokinetics, 33(2), 133-140.
Worthington, R., Ball, E., Wolf, B. and Takacs, G., 2017. Method to Identify Silent Codon Mutations That May Alter Peptide Elongation Kinetics and Co-translational Protein Folding. In Proteomics for Drug Discovery (pp. 237-243). Humana Press, New York, NY.
Wadhwa, R., Nigam, N., Bhargava, P., Dhanjal, J.K., Goyal, S., Grover, A., Sundar, D., Ishida, Y., Terao, K. and Kaul, S.C., 2016. Molecular Characterization and Enhancement of Anticancer Activity of Caffeic Acid Phenethyl Ester by γ Cyclodextrin. Journal of Cancer, 7(13), pp.1755-1771.
Bober, P., Tomková, Z., Alexovič, M., Ropovik, I., & Sabo, J. (2019). The unfolded protein response controls endoplasmic reticulum stress-induced apoptosis of MCF-7 cells via a high dose of vitamin C treatment. Molecular biology reports, 1-10.
Matsushita, Y., Chu, A.K.Y., Ono, W., Welch, J.D., & Ono, N. (2021). Intercellular interactions of an adipogenic CXCL12‐expressing stromal cell subset in murine bone marrow. Journal of Bone and Mineral Research, 36(6), 1145-1158.
Arias, C., Saavedra, N., Leal, K., Vásquez, B., Abdalla, D.S.P., & Salazar, L.A. (2020). Histological evaluation and gene expression profiling of autophagy-related genes for cartilage of young and senescent rats. International Journal of Molecular Sciences, 21(22), 8607.
Dudakovic, A., Nam, H.K., van Wijnen, A.J., & Hatch, N.E. (2020). Genetic background dependent modifiers of craniosynostosis severity. Journal of Structural Biology, 212(3), 107629.
Edwards, N.J., Hobson, E., Dey, D., Rhodes, A., Overmann, A., Hoyt, B., Walsh, S.A., Pagani, C.A., Strong, A.L., Hespe, G.E., Padmanabhan, K.R., Huber, A., Deng, C., Davis, T.A., & Levi, B. (2021). High Frequency Spectral Ultrasound Imaging Detects Early Heterotopic Ossification in Rodents. Stem Cells and Development, 30(9), 473-484.
Gohel, N., Senos, R., Goldstein, S.A., Hankenson, K.D., Hake, M.E., & Alford, A.I. (2020). Evaluation of global gene expression in regenerate tissues during Masquelet treatment. Journal of Orthopaedic Research, 38(10), 2120-2130.
Matsushita, Y., Nagata, M., Welch, J.D., Wong, S.Y., Ono, W., & Ono, N. (2020). Notch effector Hes1 marks an early perichondrial population of skeletal progenitor cells at the onset of endochondral bone development. bioRxiv.
Mathis, N. J., Adaniya, E. N., Smith, L. M., Robling, A. G., Jepsen, K. J., & Schlecht, S. H. (2019). Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth. PloS one, 14(4), e0214520.
Vishnoi, M., Boral, D., Liu, H., Sprouse, M.L., Yin, W., Goswami-Sewell, D., Tetzlaff, M.T., Davies, M.A., Oliva, I.C.G. and Marchetti, D., 2018. Targeting USP7 Identifies a Metastasis-Competent State within Bone Marrow–Resident Melanoma CTCs. Cancer research, 78(18), pp.5349-5362.
Bradford, S. T., Ranghini, E. J., Grimley, E., Lee, P. H., & Dressler, G. R. (2019). High-throughput screens for agonists of bone morphogenetic protein (BMP) signaling identify potent benzoxazole compounds. Journal of Biological Chemistry, 294(9), 3125-3136.
Mathis, N. J., Adaniya, E. N., Smith, L. M., Robling, A. G., Jepsen, K. J., & Schlecht, S. H. (2019). Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth. PloS one, 14(4), e0214520.
Pirog, Katarzyna A., Ella P. Dennis, Claire L. Hartley, Robert M. Jackson, Jamie Soul, Jean-Marc Schwartz, John F. Bateman, Raymond P. Boot-Handford, and Michael D. Briggs. “XBP1 signalling is essential for alleviating mutant protein aggregation in ER-stress related skeletal disease.” PLoS genetics 15, no. 7 (2019): e1008215.
Cardoso, T.F., Quintanilla, R., Tibau, J., Gil, M., Mármol-Sánchez, E., González-Rodríguez, O., González-Prendes, R. and Amills, M., 2017. Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle. BMC genomics, 18(1), p.603.
Hwang, H.T.V., Sandeep, N., Nair, R.V., Hu, D.Q., Zhao, M., Lan, I.S., Fajardo, G., Matkovich, S.J., Bernstein, D., & Reddy, S. (2021). Transcriptomic and Functional Analyses of Mitochondrial Dysfunction in Pressure Overload‐Induced Right Ventricular Failure. Journal of the American Heart Association, 10:e017835.
Yegorova, S., Yegorov, O., & Ferreira, L.F. (2021). RNA-sequencing reveals transcriptional signature of pathological remodeling in the diaphragm of rats after myocardial infarction. Gene, 770, 145356.
Guo, N.L., Bello, D., Ye, Q., Tagett, R., Chanetsa, L., Singh, D., Poh, T.Y., Setyawati, MI, Chotirmall, SH, Ng, KW, & Demokritou, P. (2020). Pilot deep RNA sequencing of worker blood samples from Singapore printing industry for occupational risk assessment. NanoImpact, 19, 100248.
Ordoño, J., Pérez-Amodio, S., Ball, K., Aguirre, A., & Engel, E. (2020). Lactate promotes cardiomyocyte dedifferentiation through metabolic reprogramming. bioRxiv.
Richards, D.J., Li, Y., Kerr, C.M., Yao, J., Beeson, G.C., Coyle, R.C., Chen, X., Jia, J., Damon, B., Wilson, R., Hazard, E.S., Hardiman, G., Menick, D.R., Beeson, C.C., Yao, H., Ye, T., & Mei, Y. (2020). Human cardiac organoids for the modelling of myocardial infarction and drug cardiotoxicity. Nature Biomedical Engineering, 4, 446-462.
Tharmalingam, S., Khurana, S., Murray, A., Lamothe, J., & Tai, T.C. (2020). Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents. Scientific Reports, 10, 18755.
Alkhanjaf, Abdulrab Ahmed M., Roberto Raggiaschi, Mark Crawford, Gabriella Pinto, and Jasminka Godovac Zimmermann. “Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF‐7 Breast Cancer Cells to 
PROTEOMICS–Clinical Applications (2019): 1900029.
Argenziano, Mariana A., Michael Xavier Doss, Megan Tabler, Agapios Sachinidis, and Charles Antzelevitch. “Transcriptional changes associated with advancing stages of heart failure underlie atrial and ventricular arrhythmogenesis.” PloS one 14, no. 5 (2019): e0216928.
Fu, X., Khalil, H., Kanisicak, O., Boyer, J.G., Vagnozzi, R.J., Maliken, B.D., Sargent, M.A., Prasad, V., Valiente-Alandi, I., Blaxall, B.C. and Molkentin, J.D., 2018. Specialized fibroblast differentiated states underlie scar formation in the infarcted mouse heart. The Journal of clinical investigation, 128(5).
Correll, R. N., Grimes, K. M., Prasad, V., Lynch, J. M., Khalil, H., & Molkentin, J. D. (2019). Overlapping and differential functions of ATF6α versus ATF6β in the mouse heart. Scientific reports, 9(1), 2059.
Phillips, E. H., Lorch, A. H., Durkes, A. C., & Goergen, C. J. (2018). Early pathological characterization of murine dissecting abdominal aortic aneurysms. APL Bioengineering, 2(4), 046106.
Faranda, A.P., Shihan, M.H., Wang, Y., & Duncan, M.K. (2021). The effect of sex on the mouse lens transcriptome. Experimental Eye Research, 209, 108676.
Faranda, A.P., Shihan, M.H., Wang, Y., & Duncan, M.K. (2021). The aging mouse lens transcriptome. Experimental Eye Research, 209, 108663.
Shihan, M.H., Kanwar, M., Wang, Y., Jackson, E.E., Faranda, A.P., & Duncan, M.K. (2020). Fibronectin has multifunctional roles in posterior capsular opacification (PCO). Matrix Biology, 90, 79-108.
Kadzielawa, K., Mathew, B., Stelman, C. R., Lei, A. Z., Torres, L., & Roth, S. (2018). Gene expression in retinal ischemic post-conditioning. Graefe’s Archive for Clinical and Experimental Ophthalmology, 256(5), 935-949.
Shan, S.W., Tse, D.Y.Y., Zuo, B., To, C.H., Liu, Q., McFadden, S.A., Chun, R.K.M., Bian, J., Li, K.K. and Lam, T.C., 2018. Integrated SWATH-based and targeted-based proteomics provide insights into the retinal emmetropization process in guinea pig. Journal of proteomics, 181, pp.1-15.
Cahill, T., da Silveira, W.A., Renaud, L., Williamson, T., Wang, H., Chung, D., Overton, I., Chan, S.S.L., & Hardiman, G. (2021). Induced Torpor as a Countermeasure for Low Dose Radiation Exposure in a Zebrafish Model. Cells, 10(4), 906.
Arnold, N.S., Hooten, N.N., Zhang, Y., Lehrmann, E., Wood III, W., Nunez, W.C., Thorpe Jr., R.J., Evans, M.K., & Dluzen D.F. (2020). The association between poverty and gene expression within peripheral blood mononuclear cells in a diverse Baltimore City cohort. PloS ONE, 15(9),: e0239654.
Mitra, T., Mahanty, A., Ganguly, S., & Mohanty, B.P. (2020). Transcriptomic responses to pollution in natural riverine environment in Rita rita. Environmental Research, 186, 109508.
Renaud, L., Agarwal, N., Richards, D.J., Falcinelli, S., Hazard, E.S., Carnevali, O., Hyde, J. and Hardiman, G., 2019. Transcriptomic analysis of short-term 17α-ethynylestradiol exposure in two Californian sentinel fish species sardine (Sardinops sagax) and mackerel (Scomber japonicus). Environmental pollution, 244, pp.926-937.
Williams, K.E., Lemieux, G.A., Hassis, M.E., Olshen, A.B., Fisher, S.J. and Werb, Z., 2016. Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals.Proceedings of the National Academy of Sciences, p.201600645.
Aldiss, P., Lewis, J.E., Lupini, I., Bloor, I., Chavoshinejad, R., Boocock, D.J., Miles, A.K., Ebling, F.J.P., Budge, H., & Symonds, M.E. (2021). Cold exposure drives weight gain and adiposity following chronic suppression of brown adipose tissue. bioRxiv.
Aldiss, P., Lewis, J.E., Lupini, I., Bloor, I., Chavoshinejad, R., Boocock, D.J., Miles, A.K., Ebling, F.J.P., Budge, H., & Symonds, M.E. (2020). Exercise training in obese rats does not induce browning at thermoneutrality and induces a muscle-like signature in brown adipose tissue. Frontiers in Endocrinology, 11:97.
Magri, K., Eftedal, I., Magri, V.P., Matity, L., Azzopardi, C.P., Muscat, S., & Pace, N.P. (2021). Acute effects on the human peripheral blood transcriptome of decompression sickness secondary to scuba diving. Frontiers in Physiology, 12:660402.
Mori, H., Dugan, C.E., Nishii, A., Benchamana, A., Li, Z., Cadenhead IV, T.S., Das, A.K., Evans, C.R., Overmyer, K.A., Romanelli, S.M., Peterson, S.K., Bagchi, D.P., Corsa, C.A., Hardij, J., Learman, B.S., El Azzouny, M., Coon, J.J., Inoki, K., & MacDougald, O.A. (2021). The molecular and metabolic program for adaptation of white adipocytes to cool physiologic temperatures. Plos Biology, 19(5): e3000988.
Jia, J, Jeon, EJ, Li, M, Richards, DJ, Lee, S, & … (2020). Evolutionarily conserved sequence motif analysis guides development of chemically defined hydrogels for therapeutic vascularization. Science Advances, 6(28).
Kalil, B., Pestana-Oliveira, N., Santos, I.R., Carolino, R.O.G., & Anselmo-Franci, J.A. (2020). MON-017 Effect of Estradiol Therapy on Depressive like Behavior in an Ovarian Intact Rat Model of Perimenopause. Journal of the Endocrine Society, 4(S1).
Mahjoubi, F., Ghadir, M., Samanian, S., Heydari, I., & Honardoost, M. (2020). Hyperphosphatemic familial tumoral calcinosis caused by a novel variant in the GALNT3 gene. Journal of Endocrinological Investigation, 43, 1125-1130.
Mohanty, B.P., Mahanty, A., Mitra, T., Mohanty, S., Naik, A.K., & Parija, S.C. (2020). Proteomic and transcriptomic changes in rat liver following oral feeding of formaldehyde. Chemosphere, 245, 1225599.
Ulintz, P.J., Larouche, J., Mohiuddin, M., Macias, J.C., Kurpiers, S.J., Liu, W., Choi, J.J., Brown, L.A., Markworth, J.F., de Silva, K., Levi, B.D., Merajver, S.D., Chakkalakal, J.V., Jang, Y.C., Brooks, S.V., & Aguilar, C.A. (2020). Single Cell Deconstruction of Muscle Stem Cell Heterogeneity During Aging Reveals Sensitivity to the Neuromuscular Junction. bioRxiv.
Tarca, A.L., Romero, R., Benshalom-Tirosh, N., Than, N.G., Gudicha, D.W., Done, B., Pacora, P., Chaiworapongsa, T., Panaitescu, B., Tirosh, D. and Gomez-Lopez, N., 2019. The prediction of early preeclampsia: Results from a longitudinal proteomics study. PloS one, 14(6), p.e0217273.
Creeth, H.D., McNamara, G.I., Tunster, S.J., Boque-Sastre, R., Allen, B., Sumption, L., Eddy, J.B., Isles, A.R. and John, R.M., 2018. Maternal care boosted by paternal imprinting in mammals. PLoS biology, 16(7), p.e2006599.
Foote, A.P., Keel, B.N., Zarek, C.M. and Lindholm-Perry, A.K., 2017. Beef steers with average dry matter intake and divergent average daily gain have altered gene expression in the jejunum. Journal of Animal Science.
Lee, S.E., Son, G.W., Park, H.R., Jin, Y.H., Park, C.S. and Park, Y.S., 2015. Integrative analysis of miRNA and mRNA profiles in response to myricetin in human endothelial cells. BioChip Journal, 9(3), pp.239-246.
Huang, Q., Sun, M. A., & Yan, P. (2018). Pathway and Network Analysis of Differentially Expressed Genes in Transcriptomes. In Transcriptome Data Analysis (pp. 35-55). Humana Press, New York, NY.
Valianou, M., Filippidou, N., Johnson, D.L., Vogel, P., Zhang, E.Y., Liu, X., Lu, Y., Jane, J.Y., Bissler, J.J. and Astrinidis, A., 2019. Rapalog resistance is associated with mesenchymal-type changes in Tsc2-null cells. Scientific reports, 9(1), p.3015.
Maxwell, A.J., Ding, J., You, Y., Dong, Z., Chehade, H., Alvero, A., Mor, Y., Draghici, S., & Mor, G. (2021). Identification of key signaling pathways induced by SARS‐CoV2 that underlie thrombosis and vascular injury in COVID‐19 patients. Journal of Leukocyte Biology, 109(1), 35-47.
Pushparaj, P.N., Damiati, L.A., Denetiu, L., Bakhashab, S., Asif, M., Hussain, A., Ahmed, S., Hamdard, M.H., & Rasool, M. (2021). Deciphering Novel SARS CoV-2 specific Disease Pathways from RNA Sequencing Data of COVID-19 Infected A549 Cells and Potential Therapeutics using Next Generation Knowledge Discovery Platforms. Research Square.
Bock, J.O. & Ortea, I. (2020). Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response. Aging (Albany NY), 12(12), 11277-11286.
Ionescu, M.I. (2020). An overview of the crystallized structures of the SARS-CoV-2. The Protein Journal, 39, 600-618.
Reyes, F.R., & Pérez, G.G. (2020). Pandemia SARS-CoV-2/COVID-19, perspectivas y desafíos. Revista del Centro de Investigacion de la Universidad La Salle, 14(54).
Most existing pathway analysis methods focus on either the number of differentially expressed genes observed in a given pathway (enrichment analysis methods), or on the correlation between the pathway genes and the class of the samples (functional class scoring methods). Both approaches treat pathways as simple sets of genes, disregarding the complex gene interactions that these pathways are built to describe.
More recently, biological annotations have started to include descriptions of gene interactions in the form of gene signaling networks, such as KEGG (Ogata et al., 1999), BioCarta (www.biocarta.com) and Reactome (Joshi-Tope et al., 2005). This richer type of annotations have opened the possibility of an automatic analysis aimed to identify the gene signaling networks that are relevant in a given condition, and perhaps even the specific signals or signal perturbations involved. This approach is not well suited for a systems biology approach that aims to account for system-level dependencies and interactions, as well as identify perturbations and modifications at the pathway or organism level (Stelling, 2004).
Advaita’s products are based on Impact Analysis method that leverages the information about type, function, position and interaction between genes in a given pathway. Impact Analysis combines the evidence obtained from the classical enrichment analysis with a novel type of evidence, which measures the actual perturbation on a given pathway under a given condition. We illustrate the capabilities of the novel method on four real datasets. The results obtained on these data show that Impact Analysis has better specificity and more sensitivity than several widely used pathway analysis methods.
Get Started!
Get in touch with Advaita to learn how our software will improve quality and efficiency for your Core Facility, Enterprise Bioinformatics team, or Research Lab.