Principal Investigators2020-09-14T10:54:02-04:00

Powering Extraordinary Scientists

Let’s Be Extraordinary Together

Principal Investigators wear many hats. They conceive of the research vision, write grants, write papers, speak on their research, and coordinate a team of collaborators, which may include postdocs, grad students, undergrads, and researchers at other institutions. This is on top of other duties such as teaching and committee work.

Our PIs hunger to make big breakthroughs that will contribute to saving lives. And they need to do this as efficiently as possible with their time. Yet, many life scientists have the sense that they need to master bioinformatics, or worse, learn to code, to get the most out of their data. Not true.

Advaita software empowers life scientists to interpret your own results, freeing you to use your expertise rather than start at the beginning of a new (to you) discipline just to get the most from your research.

Rest easy, let Advaita software take care of the bioinformatics so you can focus on the biology.


Multi-Omics Pathway Analysis

From bulk RNA-seq to single cell, from proteomics to epigenetics, our platform delivers powerful insights. Biologists depend on our state-of-the art pathway analysis, gene ontology analysis, upstream regulator predictions, and meta-analysis.

Learn more about iPathwayGuide

Identify & Prioritize Causal Mutations

Annotate and filter VCFs to identify rare, causal, clinically significant variants. Predict effects, impacted pathways and gene ontology terms. Allow customers to explore by sharing the browsable analysis.

Learn more about iVariantGuide

Search Several Databases, All At Once

Find related genes, microRNAs, pathways, biological processes, drugs, diseases, and references. We’ve created google for scientists bringing >108 biological relationships to your fingertips for free.

Learn more about iBioGuide

Extraordinary Customer Experiences

We have earned the trust of principal investigators worldwide. Let them tell you why they use Advaita Bioinformatics software.


Learn from The Barbara Ann Karmanos Cancer Center

Wei Chen works in the Biostatistics and Bioinformatics Core of the Karmanos Cancer Institute, which is also affiliated with Wayne State University. Located in midtown Detroit, it is the only National Cancer Institute (NCI)-designated comprehensive cancer center in metro Detroit and one of just 51 centers of its kind in the United States.


Learn from NIH – Perinatology Research Branch

The Perinatology Research Branch is the only Clinical Branch in the Division of Intramural Research of the National Institutes of Health to focus its research on human pregnancy and unborn children. Using a multidisciplinary approach to study pregnancy complications, the Branch is publishing an average of over 100 peer-reviewed papers per year.


Learn from Columbia University

Richard Friedman is an associate research scientist at the Herbert Irving Comprehensive Cancer Center at Columbia University. His bioinformatics analysis activities support about 25 principal investigators (PIs) in any one year. He has been using Advaita’s iPathwayGuide and its predecessor tools for over 15 years.


Learn from University of Delaware

Dr. Melinda Duncan is a tenured full professor in the University of Delaware Biological Sciences Department. She performs research in the areas of lens and eye development, cataract surgery and wound healing, and innate immunity. Her research group includes 12 people and uses Advaita software platform to understand and interpret their experimental data.


Learn from Morgan State University

Douglas Dluzen, Ph.D., is an Assistant Professor at Morgan State University, a historically black university in downtown Baltimore, Maryland. This public university has added a strong research focus to its long history of educating local and international students. Morgan State is an R2 research university and the premiere public urban research institute in Maryland.


Learn from Queen’s University, Belfast

Gary Hardiman is a Professor, School of Biological Science at Queen's University Belfast. Gary began using Advaita’s iPathwayGuide at the Medical University of South Carolina (MUSC). He knew of Advaita from array work that was done a while back and was impressed with the founder and the company. When he moved back to Ireland, he decided to bring iPathwayGuide with him.


Learn from SkinAxis

SkinAxis is a biotech company that provides advanced testing technology for skin research. The company focuses on testing, measuring, and monitoring active ingredients for, among other things, antiaging, spot removal and hydration. Pathway analysis is essential to the services it provides to its customers in the cosmetics, biotech, pharmaceutical, chemical, and diagnostics industries.

Analyze Now

  1. Register to explore demo data
  2. Subscribe to analyze your ‘omics data
  3. Review and interact with pathways impacted in your experiment
  4. Share your results with collaborators for interpretation and analysis iteration
  5. Create publication-ready figures simply and easily

What You Can Expect

  • Better Insights
  • Higher Quality
  • Superior Convenience
  • Unmatched Usability
  • Unparalleled Reproducibility
Register to Explore Advaita’s Platform with Demo Data

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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.


Since we acquired iPathwayGuide, it has become my main analysis tool for signaling pathways. It is both most powerful and among the easiest-to-use software for pathway analysis of gene list obtained from microarray experiments of which I am aware.

Richard Friedman, Columbia University
We tend to use open source tools where we can use them. But the open source tools are not evenly supported, their feature set is sometimes unevenly implemented. And, the licensing model of iPathwayGuide works so much better for the way we work with researchers than any of the commercial competitors in this space. So, it beats both freewar and other commercial products.
Bioinformatics Core Director, R1 Research University

I love using iPathwayGuide for my RNA-seq data analysis. Its extensive knowledge base provides me with accurate results, very quickly. I find the figures to be clear and appealing.

Ian Chu, UT Southwestern

Advaita is far superior to anything else I’ve seen. Your data gets uploaded, gets analyzed up on the cloud, and then you can share the results of that with anyone anywhere on the planet. And that’s very, very nice because it means you’re not hunched over one physical computer in a defined location or you’re not doing it with complex licensing so that other people can see the analysis. For me, that was key.

About Advaita Bioinformatics

Our software tools help principal investigators, core facilities, and enterprise bioinformatics teams analyze gene expression data (e.g. RNA-Seq or microarray) and variant data (e.g. DNA-Seq) to find biomarkers, identify impacted pathways, and pinpoint putative mechanisms. Currently, this frustrating process is slow, unreliable, expensive, and often requires multiple disjointed tools, which then provide irrelevant or incorrect results. While other solutions drop a haystack of results on you, we lead you straight to the needle.

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.

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