Advaita Bioinformatics Science2024-04-11T15:27:11-04:00

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!

Publications by Advaita Bioinformatics Team2022-03-02T13:42:47-05:00


# of Citations

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

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).

Select Publications Citing iPathwayGuide2022-09-09T15:35:17-04:00

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.

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The Science of Impact Analysis2018-10-13T11:16:39-04:00

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 ( 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.

Poster Download – Using Pathway Analysis to Predict Drug Response2018-10-13T11:17:57-04:00
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