Advaita Bioinformatics Science2020-09-08T17:23:02-04:00

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 Team2019-10-11T13:47:14-04:00


# 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 iPathwayGuide2020-05-18T15:14:35-04:00


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.


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 Methamphetamine 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.

Liver and Kidney Disease

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.

Molecular and Cellular Biology

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.

Developmental Biology and Stem Cells

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.

Neurology and Neuroscience

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.

Diabetes and Metabolic Disorders

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,

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.


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).

Pharmaceuticals and Drugs

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.

Bone Growth and Morphogenesis

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.


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 Tamoxifen.” 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.


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.

Environmental Science

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.


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.

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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