Photo of Prof Francesco Falciani

Prof Francesco Falciani

Functional and Comparative Genomics

    Publications

    2019

    A novel panel of differentially-expressed microRNAs in breast cancer brain metastasis may predict patient survival (Journal article)

    Giannoudis, A., Clarke, K., Zakaria, R., Vareslija, D., Farahani, M., Rainbow, L., . . . Palmieri, C. (2019). A novel panel of differentially-expressed microRNAs in breast cancer brain metastasis may predict patient survival. SCIENTIFIC REPORTS, 9. doi:10.1038/s41598-019-55084-z

    DOI: 10.1038/s41598-019-55084-z

    Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment (Journal article)

    Rivetti, C., Allen, T. E. H., Brown, J. B., Butler, E., Carmichael, P. L., Colbourne, J. K., . . . Carnpos, B. (2020). Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment. TOXICOLOGY IN VITRO, 62. doi:10.1016/j.tiv.2019.104692

    DOI: 10.1016/j.tiv.2019.104692

    Computationally Predicted Gene Regulatory Networks in Molluscan Biomineralisation Identify Extracellular Matrix Production and Ion Transportation Pathways. (Journal article)

    Sleight, V. A., Antczak, P., Falciani, F., & Clark, M. S. (2019). Computationally Predicted Gene Regulatory Networks in Molluscan Biomineralisation Identify Extracellular Matrix Production and Ion Transportation Pathways.. Bioinformatics (Oxford, England). doi:10.1093/bioinformatics/btz754

    DOI: 10.1093/bioinformatics/btz754

    SAERMA: Stacked Autoencoder Rule Mining Algorithm for the Interpretation of Epistatic Interactions in GWAS for Extreme Obesity (Journal article)

    Montañez, C. A. C., Fergus, P., Chalmers, C., Malim, N. A. H., Abdulaimma, B., Reilly, D., & Falciani, F. (n.d.). SAERMA: Stacked Autoencoder Rule Mining Algorithm for the Interpretation of Epistatic Interactions in GWAS for Extreme Obesity. Retrieved from http://arxiv.org/abs/1908.10166v1

    Transcriptomic analysis reveals genes and miRNAs dysregulated in high risk primary uveal melanoma (Conference Paper)

    Aughton, K., Lake, S. L., Takeshita, L., Falciani, F., Kalirai, H., & Coupland, S. E. (2019). Transcriptomic analysis reveals genes and miRNAs dysregulated in high risk primary uveal melanoma. In INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE Vol. 60. Retrieved from http://gateway.webofknowledge.com/

    Deciphering the complex role of thrombospondin-1 in glioblastoma development (Journal article)

    Daubon, T., Leon, C., Clarke, K., Andrique, L., Salabert, L., Darbo, E., . . . Bikfalvi, A. (2019). Deciphering the complex role of thrombospondin-1 in glioblastoma development. NATURE COMMUNICATIONS, 10. doi:10.1038/s41467-019-08480-y

    DOI: 10.1038/s41467-019-08480-y

    Identification of microRNAs differentially expressed in brain metastasis secondary to breast cancer (Conference Paper)

    Giannoudis, A., Clarke, K., Zakaria, R., Vareslija, D., Farahani, M., Rainbow, L., . . . Palmieri, C. (2019). Identification of microRNAs differentially expressed in brain metastasis secondary to breast cancer. In CANCER RESEARCH Vol. 79. doi:10.1158/1538-7445.SABCS18-P6-05-02

    DOI: 10.1158/1538-7445.SABCS18-P6-05-02

    Systems biology reveals how altered TGF beta signalling with age reduces protection against pro-inflammatory stimuli (Journal article)

    Hodgson, D., Rowan, A. D., Falciani, F., & Proctor, C. J. (2019). Systems biology reveals how altered TGF beta signalling with age reduces protection against pro-inflammatory stimuli. PLOS COMPUTATIONAL BIOLOGY, 15(1). doi:10.1371/journal.pcbi.1006685

    DOI: 10.1371/journal.pcbi.1006685

    2018

    Structure-Based Networks for Drug Validation (Journal article)

    Cangea, C., Grauslys, A., Liò, P., & Falciani, F. (n.d.). Structure-Based Networks for Drug Validation. Retrieved from http://arxiv.org/abs/1811.09714v1

    Chemical Hazard Prediction and Hypothesis Testing Using Quantitative Adverse Outcome Pathways (Journal article)

    Perkins, E. J., Gayen, K., Shoemaker, J. E., Antczak, P., Burgoon, L., Falciani, F., . . . Garcia-Reyero, N. (2019). Chemical Hazard Prediction and Hypothesis Testing Using Quantitative Adverse Outcome Pathways. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 36(1), 91-102. doi:10.14573/altex.1808241

    DOI: 10.14573/altex.1808241

    Comparative toxicity of three phenolic compounds on the embryo of fathead minnow, Pimephales promelas (Journal article)

    Li, E., Bolser, D. G., Kroll, K. J., Brockmeier, E. K., Falciani, F., & Denslow, N. D. (2018). Comparative toxicity of three phenolic compounds on the embryo of fathead minnow, Pimephales promelas. AQUATIC TOXICOLOGY, 201, 66-72. doi:10.1016/j.aquatox.2018.05.024

    DOI: 10.1016/j.aquatox.2018.05.024

    In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass (Micropterus salmoides) (Journal article)

    Basili, D., Zhang, J. -L., Herbert, J., Krol, K., Denslow, N. D., Martyniuk, C. J., . . . Antczak, P. (2018). In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass (Micropterus salmoides). ENVIRONMENTAL SCIENCE & TECHNOLOGY, 52(13), 7553-7565. doi:10.1021/acs.est.8b02805

    DOI: 10.1021/acs.est.8b02805

    2017

    Linking genotype to clinical phenotype through proteomic analysis of CLL trial samples (Conference Paper)

    Eagle, G., Zhuang, J., Oates, M., Kitteringham, N., Herbert, J., Falciani, F., . . . Hillmen, P. (2017). Linking genotype to clinical phenotype through proteomic analysis of CLL trial samples. In LEUKEMIA & LYMPHOMA Vol. 58 (pp. 100-101). Retrieved from http://gateway.webofknowledge.com/

    The Role of Eif6 in Skeletal Muscle Homeostasis Revealed by Endurance Training Co-expression Networks (Journal article)

    Clarke, K., Ricciardi, S., Pearson, T., Bharudin, I., Davidsen, P. K., Bonomo, M., . . . Falciani, F. (2017). The Role of Eif6 in Skeletal Muscle Homeostasis Revealed by Endurance Training Co-expression Networks. CELL REPORTS, 21(6), 1507-1520. doi:10.1016/j.celrep.2017.10.040

    DOI: 10.1016/j.celrep.2017.10.040

    Kinome-wide transcriptional profiling of uveal melanoma reveals new vulnerabilities to targeted therapeutics (Journal article)

    Bailey, F. P., Clarke, K., Kalirai, H., Kenyani, J., Shahidipour, H., Falciani, F., . . . Eyers, P. A. (2018). Kinome-wide transcriptional profiling of uveal melanoma reveals new vulnerabilities to targeted therapeutics. PIGMENT CELL & MELANOMA RESEARCH, 31(2). doi:10.1111/pcmr.12650

    DOI: 10.1111/pcmr.12650

    The Role of Omics in the Application of Adverse Outcome Pathways for Chemical Risk Assessment (Journal article)

    Brockmeier, E. K., Hodges, G., Hutchinson, T. H., Butler, E., Hecker, M., Tollefsen, K. E., . . . Falciani, F. (2017). The Role of Omics in the Application of Adverse Outcome Pathways for Chemical Risk Assessment. TOXICOLOGICAL SCIENCES, 158(2), 252-262. doi:10.1093/toxsci/kfx097

    DOI: 10.1093/toxsci/kfx097

    NR4A orphan nuclear receptor family members, NR4A2 and NR4A3, regulate neutrophil number and survival (Journal article)

    Prince, L. R., Prosseda, S. D., Higgins, K., Carlring, J., Prestwich, E. C., Ogryzko, N. V., . . . Sabroe, I. (2017). NR4A orphan nuclear receptor family members, NR4A2 and NR4A3, regulate neutrophil number and survival. BLOOD, 130(8), 1014-1025. doi:10.1182/blood-2017-03-770164

    DOI: 10.1182/blood-2017-03-770164

    PATHOGEN-SPECIFIC TRADE-OFFS IN HOST TOLERANCE AND SUSCEPTIBILITY PHENOTYPES (Conference Paper)

    Antczak, P., Williams, D., Olohan, L., Kay, S., Fang, Y., Gregory, R., . . . Cossins, A. R. (2017). PATHOGEN-SPECIFIC TRADE-OFFS IN HOST TOLERANCE AND SUSCEPTIBILITY PHENOTYPES. In AQUACULTURE Vol. 472 (pp. 145-146). Retrieved from http://gateway.webofknowledge.com/

    HOW CONSISTENT ARE WE? INTERLABORATORY COMPARISON STUDY IN FATHEAD MINNOWS USING THE MODEL ESTROGEN 17 alpha-ETHINYLESTRADIOL TO DEVELOP RECOMMENDATIONS FOR ENVIRONMENTAL TRANSCRIPTOMICS (Journal article)

    Feswick, A., Isaacs, M., Biales, A., Flick, R. W., Bencic, D. C., Wang, R. -L., . . . Munkittrick, K. R. (2017). HOW CONSISTENT ARE WE? INTERLABORATORY COMPARISON STUDY IN FATHEAD MINNOWS USING THE MODEL ESTROGEN 17 alpha-ETHINYLESTRADIOL TO DEVELOP RECOMMENDATIONS FOR ENVIRONMENTAL TRANSCRIPTOMICS. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 36(10), 2614-2623. doi:10.1002/etc.3799

    DOI: 10.1002/etc.3799

    Transcriptional mechanism of vascular endothelial growth factor-induced expression of protein kinase C beta II in chronic lymphocytic leukaemia cells (Journal article)

    Al-Sanabra, O., Duckworth, A. D., Glenn, M. A., Brown, B. R. B., Angelillo, P., Lee, K., . . . Slupsky, J. R. (2017). Transcriptional mechanism of vascular endothelial growth factor-induced expression of protein kinase C beta II in chronic lymphocytic leukaemia cells. SCIENTIFIC REPORTS, 7. doi:10.1038/srep43228

    DOI: 10.1038/srep43228

    Assessment of gene expression profiles of peripheral blood mononuclear cells from patients with a history of carbamazepine hypersensitivity (Conference Paper)

    Yip, V., Zhang, E., Clarke, K., Francis, B., Rainbow, L., Falciani, F., . . . Pirmohamed, M. (2017). Assessment of gene expression profiles of peripheral blood mononuclear cells from patients with a history of carbamazepine hypersensitivity. In LANCET Vol. 389 (pp. 104). Retrieved from http://gateway.webofknowledge.com/

    Transcriptional responses to hyperplastic MRL signalling in Drosophila (Journal article)

    Jonchere, V., Alqadri, N., Herbert, J., Dodgson, L., Mason, D., Messina, G., . . . Bennett, D. (2017). Transcriptional responses to hyperplastic MRL signalling in Drosophila. OPEN BIOLOGY, 7(2). doi:10.1098/rsob.160306

    DOI: 10.1098/rsob.160306

    2016

    Accurate Admission Transcriptomic Signature of the Severity of Acute Pancreatitis (Other)

    Nunes, Q. M., Lane, B., Huang, W., Altaf, K., Rainbow, L., Armstrong, J., . . . Sutton, R. (2016). Accurate Admission Transcriptomic Signature of the Severity of Acute Pancreatitis. In PANCREAS (Vol. 45, Iss. 10, pp. 1530). Retrieved from http://gateway.webofknowledge.com/

    THROMBOSPONDIN-1 IS A MASTER REGULATOR OF GLIOBLASTOMA VASCULARIZATION AND INFILTRATION (Conference Paper)

    Daubon, T., Leon, C., Clarke, K., Falciani, F., Bikfalvi, A., & Bjerkvig, R. (2016). THROMBOSPONDIN-1 IS A MASTER REGULATOR OF GLIOBLASTOMA VASCULARIZATION AND INFILTRATION. In NEURO-ONCOLOGY Vol. 18 (pp. 29). Retrieved from http://gateway.webofknowledge.com/

    Thrombospondin-1 is a master regulator of glioblastoma vascularization and infiltration (Conference Paper)

    Daubon, T., Leon, C., Clarke, K., Poulet, M., Miletic, H., Falciani, F., . . . Bikfalvi, A. (2016). Thrombospondin-1 is a master regulator of glioblastoma vascularization and infiltration. In CANCER RESEARCH Vol. 76. doi:10.1158/1538-7445.AM2016-4413

    DOI: 10.1158/1538-7445.AM2016-4413

    A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells (Journal article)

    Trevino, V., Cassese, A., Nagy, Z., Zhuang, X., Herbert, J., Antzack, P., . . . Falciani, F. (2016). A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells. PLOS COMPUTATIONAL BIOLOGY, 12(4). doi:10.1371/journal.pcbi.1004884

    DOI: 10.1371/journal.pcbi.1004884

    Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective (Journal article)

    Davidsen, P. K., Turan, N., Egginton, S., & Falciani, F. (2016). Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective. JOURNAL OF APPLIED PHYSIOLOGY, 120(3), 297-309. doi:10.1152/japplphysiol.01110.2014

    DOI: 10.1152/japplphysiol.01110.2014

    ChainRank, a chain prioritisation method for contextualisation of biological networks (Journal article)

    Tenyi, A., de Atauri, P., Gomez-Cabrero, D., Cano, I., Clarke, K., Falciani, F., . . . Maier, D. (2016). ChainRank, a chain prioritisation method for contextualisation of biological networks. BMC BIOINFORMATICS, 17. doi:10.1186/s12859-015-0864-x

    DOI: 10.1186/s12859-015-0864-x

    2015

    Genomic and transcriptomic predictors of triglyceride response to regular exercise (Journal article)

    Sarzynski, M. A., Davidsen, P. K., Sung, Y. J., Hesselink, M. K. C., Schrauwen, P., Rice, T. K., . . . Bouchard, C. (2015). Genomic and transcriptomic predictors of triglyceride response to regular exercise. BRITISH JOURNAL OF SPORTS MEDICINE, 49(23), 1524-1531. doi:10.1136/bjsports-2015-095179

    DOI: 10.1136/bjsports-2015-095179

    Adverse Outcome Pathways for Regulatory Applications: Examination of Four Case Studies With Different Degrees of Completeness and Scientific Confidence (Journal article)

    Perkins, E. J., Antczak, P., Burgoon, L., Falciani, F., Garcia-Reyero, N., Gutsell, S., . . . Willett, C. (2015). Adverse Outcome Pathways for Regulatory Applications: Examination of Four Case Studies With Different Degrees of Completeness and Scientific Confidence. TOXICOLOGICAL SCIENCES, 148(1), 14-25. doi:10.1093/toxsci/kfv181

    DOI: 10.1093/toxsci/kfv181

    Eukaryotic translation initiation factor 6 is a novel regulator of reactive oxygen species-dependent megakaryocyte maturation (Journal article)

    Ricciardi, S., Miluzio, A., Brina, D., Clarke, K., Bonomo, M., Aiolfi, R., . . . Biffo, S. (2015). Eukaryotic translation initiation factor 6 is a novel regulator of reactive oxygen species-dependent megakaryocyte maturation. JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 13(11), 2108-2118. doi:10.1111/jth.13150

    DOI: 10.1111/jth.13150

    Systems Biology Approach Reveals a Calcium-Dependent Mechanism for Basal Toxicity in Daphnia magna (Journal article)

    Antczak, P., White, T. A., Giri, A., Michelangeli, F., Viant, M. R., Cronin, M. T. D., . . . Falciani, F. (2015). Systems Biology Approach Reveals a Calcium-Dependent Mechanism for Basal Toxicity in Daphnia magna. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 49(18), 11132-11140. doi:10.1021/acs.est.5b02707

    DOI: 10.1021/acs.est.5b02707

    A Bayesian Model for the Identification of Differentially Expressed Genes in Daphnia Magna Exposed to Munition Pollutants (Journal article)

    Cassese, A., Guindani, M., Antczak, P., Falciani, F., & Vannucci, M. (2015). A Bayesian Model for the Identification of Differentially Expressed Genes in Daphnia Magna Exposed to Munition Pollutants. BIOMETRICS, 71(3), 803-811. doi:10.1111/biom.12303

    DOI: 10.1111/biom.12303

    Freshwater Conservation and Biomonitoring of Structure and Function (Chapter)

    Gray, C., Bista, I., Creer, S., Demars, B. O. L., Falciani, F., Monteith, D. T., . . . Woodward, G. (2015). Freshwater Conservation and Biomonitoring of Structure and Function. In Aquatic Functional Biodiversity (pp. 241-271). Elsevier. doi:10.1016/b978-0-12-417015-5.00010-4

    DOI: 10.1016/b978-0-12-417015-5.00010-4

    Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer (Journal article)

    Clarke, K., Daubon, T., Turan, N., Soulet, F., Zahari, M. M., Ryan, K. R., . . . Falciani, F. (2015). Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer. PLOS GENETICS, 11(7). doi:10.1371/journal.pgen.1005325

    DOI: 10.1371/journal.pgen.1005325

    Gene Transcription, Metabolite and Lipid Profiling in Eco-Indicator Daphnia magna Indicate Diverse Mechanisms of Toxicity by Legacy and Emerging Flame-Retardants (Journal article)

    Scanlan, L. D., Loguinov, A. V., Teng, Q., Antczak, P., Dailey, K. P., Nowinski, D. T., . . . Vulpe, C. D. (2015). Gene Transcription, Metabolite and Lipid Profiling in Eco-Indicator Daphnia magna Indicate Diverse Mechanisms of Toxicity by Legacy and Emerging Flame-Retardants. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 49(12), 7400-7410. doi:10.1021/acs.est.5b00977

    DOI: 10.1021/acs.est.5b00977

    Future water quality monitoring - Adapting tools to deal with mixtures of pollutants in water resource management (Journal article)

    Altenburger, R., Ait-Aissa, S., Antczak, P., Backhaus, T., Barcelo, D., Seiler, T. -B., . . . Brack, W. (2015). Future water quality monitoring - Adapting tools to deal with mixtures of pollutants in water resource management. SCIENCE OF THE TOTAL ENVIRONMENT, 512, 540-551. doi:10.1016/j.scitotenv.2014.12.057

    DOI: 10.1016/j.scitotenv.2014.12.057

    Stromal Transcriptional Profiles Reveal Hierarchies of Anatomical Site, Serum Response and Disease and Identify Disease Specific Pathways (Journal article)

    Filer, A., Antczak, P., Parsonage, G. N., Legault, H. M., O'Toole, M., Pearson, M. J., . . . Falciani, F. (2015). Stromal Transcriptional Profiles Reveal Hierarchies of Anatomical Site, Serum Response and Disease and Identify Disease Specific Pathways. PLOS ONE, 10(3). doi:10.1371/journal.pone.0120917

    DOI: 10.1371/journal.pone.0120917

    The SOLUTIONS project: Challenges and responses for present and future emerging pollutants in land and water resources management (Journal article)

    Brack, W., Altenburger, R., Schueuermann, G., Krauss, M., Herraez, D. L., van Gils, J., . . . Umbuzeiro, G. D. A. (2015). The SOLUTIONS project: Challenges and responses for present and future emerging pollutants in land and water resources management. SCIENCE OF THE TOTAL ENVIRONMENT, 503, 22-31. doi:10.1016/j.scitotenv.2014.05.143

    DOI: 10.1016/j.scitotenv.2014.05.143

    eIF6 coordinates insulin sensitivity and lipid metabolism by coupling translation to transcription (Journal article)

    Brina, D., Miluzio, A., Ricciardi, S., Clarke, K., Davidsen, P. K., Viero, G., . . . Biffo, S. (2015). eIF6 coordinates insulin sensitivity and lipid metabolism by coupling translation to transcription. NATURE COMMUNICATIONS, 6. doi:10.1038/ncomms9261

    DOI: 10.1038/ncomms9261

    2014

    Chronic Obstructive Pulmonary Disease heterogeneity: challenges for health risk assessment, stratification and management (Journal article)

    Roca, J., Vargas, C., Cano, I., Selivanov, V., Barreiro, E., Maier, D., . . . Consortium, S. -C. (2014). Chronic Obstructive Pulmonary Disease heterogeneity: challenges for health risk assessment, stratification and management. JOURNAL OF TRANSLATIONAL MEDICINE, 12. doi:10.1186/1479-5876-12-S2-S3

    DOI: 10.1186/1479-5876-12-S2-S3

    Systems Medicine: from molecular features and models to the clinic in COPD (Journal article)

    Gomez-Cabrero, D., Menche, J., Cano, I., Abugessaisa, I., Huertas-Miguelanez, M., Tenyi, A., . . . Tegner, J. (2014). Systems Medicine: from molecular features and models to the clinic in COPD. JOURNAL OF TRANSLATIONAL MEDICINE, 12. doi:10.1186/1479-5876-12-S2-S4

    DOI: 10.1186/1479-5876-12-S2-S4

    The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research (Journal article)

    Cano, I., Tenyi, A., Schueller, C., Wolff, M., Huertas Miguelanez, M. M., Gomez-Cabrero, D., . . . Maier, D. (2014). The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. JOURNAL OF TRANSLATIONAL MEDICINE, 12. doi:10.1186/1479-5876-12-S2-S6

    DOI: 10.1186/1479-5876-12-S2-S6

    eIF6-deficient mice exhibit thrombocytopenia due to a defect in polyploidization and maturation of megakaryocytes (Conference Paper)

    Ricciardi, S., Miluzio, A., Costa, L., Bonomo, M., Aiolfi, R., Brina, D., . . . Biffo, S. (2014). eIF6-deficient mice exhibit thrombocytopenia due to a defect in polyploidization and maturation of megakaryocytes. In FEBS JOURNAL Vol. 281 (pp. 283). Retrieved from http://gateway.webofknowledge.com/

    A HIERARCHICAL BAYESIAN MODEL FOR INFERENCE OF COPY NUMBER VARIANTS AND THEIR ASSOCIATION TO GENE EXPRESSION (Journal article)

    Cassese, A., Guindani, M., Tadesse, M. G., Falciani, F., & Vannucci, M. (2014). A HIERARCHICAL BAYESIAN MODEL FOR INFERENCE OF COPY NUMBER VARIANTS AND THEIR ASSOCIATION TO GENE EXPRESSION. ANNALS OF APPLIED STATISTICS, 8(1), 148-175. doi:10.1214/13-AOAS705

    DOI: 10.1214/13-AOAS705

    A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD (Journal article)

    Davidsen, P. K., Herbert, J. M., Antczak, P., Clarke, K., Ferrer, E., Peinado, V. I., . . . Falciani, F. (2014). A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD. GENOME MEDICINE, 6. doi:10.1186/s13073-014-0059-5

    DOI: 10.1186/s13073-014-0059-5

    2013

    Silver Nanowire Exposure Results in Internalization and Toxicity to Daphnia magna (Journal article)

    Scanlan, L. D., Reed, R. B., Loguinov, A. V., Antczak, P., Tagmount, A., Aloni, S., . . . Gilbert, B. (2013). Silver Nanowire Exposure Results in Internalization and Toxicity to Daphnia magna. ACS NANO, 7(12), 10681-10694. doi:10.1021/nn4034103

    DOI: 10.1021/nn4034103

    Molecular Toxicity Identification Evaluation (mTIE) Approach Predicts Chemical Exposure in Daphnia magna (Journal article)

    Antczak, P., Jo, H. J., Woo, S., Scanlan, L., Poynton, H., Loguinov, A., . . . Vulpe, C. (2013). Molecular Toxicity Identification Evaluation (mTIE) Approach Predicts Chemical Exposure in Daphnia magna. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 47(20), 11747-11756. doi:10.1021/es402819c

    DOI: 10.1021/es402819c

    Gene Expression Networks Underlying Ovarian Development in Wild Largemouth Bass (Micropterus salmoides) (Journal article)

    Martyniuk, C. J., Prucha, M. S., Doperalski, N. J., Antczak, P., Kroll, K. J., Falciani, F., . . . Denslow, N. D. (2013). Gene Expression Networks Underlying Ovarian Development in Wild Largemouth Bass (Micropterus salmoides). PLOS ONE, 8(3). doi:10.1371/journal.pone.0059093

    DOI: 10.1371/journal.pone.0059093

    Germinal center B cells govern their own fate via antibody feedback (Journal article)

    Zhang, Y., Meyer-Hermann, M., George, L. A., Figge, M. T., Khan, M., Goodall, M., . . . Toellner, K. -M. (2013). Germinal center B cells govern their own fate via antibody feedback. The Journal of Experimental Medicine, 210(3), 457-464. doi:10.1084/jem.20120150

    DOI: 10.1084/jem.20120150

    The experimental renal cell carcinoma model in the chick embryo (Journal article)

    Fergelot, P., Bernhard, J. -C., Soulet, F., Kilarski, W. W., Leon, C., Courtois, N., . . . Bikfalvi, A. (2013). The experimental renal cell carcinoma model in the chick embryo. ANGIOGENESIS, 16(1), 181-194. doi:10.1007/s10456-012-9311-z

    DOI: 10.1007/s10456-012-9311-z

    2012

    Identification and Pathway Mapping of Furan Target Proteins Reveal Mitochondrial Energy Production and Redox Regulation as Critical Targets of Furan Toxicity (Journal article)

    Moro, S., Chipman, J. K., Antczak, P., Turan, N., Dekant, W., Falciani, F., & Mally, A. (2012). Identification and Pathway Mapping of Furan Target Proteins Reveal Mitochondrial Energy Production and Redox Regulation as Critical Targets of Furan Toxicity. TOXICOLOGICAL SCIENCES, 126(2), 336-352. doi:10.1093/toxsci/kfs005

    DOI: 10.1093/toxsci/kfs005

    Identification and angiogenic role of the novel tumor endothelial marker CLEC14A (Journal article)

    Mura, M., Swain, R. K., Zhuang, X., Vorschmitt, H., Reynolds, G., Durant, S., . . . Bicknell, R. (2012). Identification and angiogenic role of the novel tumor endothelial marker CLEC14A. ONCOGENE, 31(3), 293-305. doi:10.1038/onc.2011.233

    DOI: 10.1038/onc.2011.233

    2011

    Analysis of Normal-Tumour Tissue Interaction in Tumours: Prediction of Prostate Cancer Features from the Molecular Profile of Adjacent Normal Cells (Journal article)

    Trevino, V., Tadesse, M. G., Vannucci, M., Al-Shahrour, F., Antczak, P., Durant, S., . . . Falciani, F. (2011). Analysis of Normal-Tumour Tissue Interaction in Tumours: Prediction of Prostate Cancer Features from the Molecular Profile of Adjacent Normal Cells. PLOS ONE, 6(3). doi:10.1371/journal.pone.0016492

    DOI: 10.1371/journal.pone.0016492

    A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease (Journal article)

    Turan, N., Kalko, S., Stincone, A., Clarke, K., Sabah, A., Howlett, K., . . . Falciani, F. (n.d.). A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease. PLoS Computational Biology, 7(9), e1002129. doi:10.1371/journal.pcbi.1002129

    DOI: 10.1371/journal.pcbi.1002129

    A computational framework for gene regulatory network inference that combines multiple methods and datasets (Journal article)

    Gupta, R., Stincone, A., Antczak, P., Durant, S., Bicknell, R., Bikfalvi, A., & Falciani, F. (2011). A computational framework for gene regulatory network inference that combines multiple methods and datasets. BMC SYSTEMS BIOLOGY, 5. doi:10.1186/1752-0509-5-52

    DOI: 10.1186/1752-0509-5-52

    A systems biology approach sheds new light on Escherichia coli acid resistance (Journal article)

    Stincone, A., Daudi, N., Rahman, A. S., Antczak, P., Henderson, I., Cole, J., . . . Falciani, F. (2011). A systems biology approach sheds new light on Escherichia coli acid resistance. NUCLEIC ACIDS RESEARCH, 39(17), 7512-7528. doi:10.1093/nar/gkr338

    DOI: 10.1093/nar/gkr338

    REVERSE ENGINEERING ADVERSE OUTCOME PATHWAYS (Journal article)

    Perkins, E. J., Chipman, J. K., Edwards, S., Habib, T., Falciani, F., Taylor, R., . . . Loguinov, A. (2011). REVERSE ENGINEERING ADVERSE OUTCOME PATHWAYS. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 30(1), 22-38. doi:10.1002/etc.374

    DOI: 10.1002/etc.374

    Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis (Journal article)

    Lin, H., Halsall, J. A., Antczak, P., O'Neill, L. P., Falciani, F., & Turner, B. M. (2011). Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis. NATURE GENETICS, 43(12), 1169-1170. Retrieved from http://gateway.webofknowledge.com/

    Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach (Journal article)

    Williams, T. D., Turan, N., Diab, A. M., Wu, H., Mackenzie, C., Bartie, K. L., . . . Falciani, F. (n.d.). Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach. PLoS Computational Biology, 7(8), e1002126. doi:10.1371/journal.pcbi.1002126

    DOI: 10.1371/journal.pcbi.1002126

    2010

    Mapping Drug Physico-Chemical Features to Pathway Activity Reveals Molecular Networks Linked to Toxicity Outcome (Journal article)

    Antczak, P., Ortega, F., Chipman, J. K., & Falciani, F. (2010). Mapping Drug Physico-Chemical Features to Pathway Activity Reveals Molecular Networks Linked to Toxicity Outcome. PLOS ONE, 5(8). doi:10.1371/journal.pone.0012385

    DOI: 10.1371/journal.pone.0012385

    Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model (Journal article)

    Soulet, F., Kilarski, W. W., Antczak, P., Herbert, J., Bicknell, R., Falciani, F., & Bikfalvi, A. (2010). Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model. BMC GENOMICS, 11. doi:10.1186/1471-2164-11-495

    DOI: 10.1186/1471-2164-11-495

    2008

    Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage (Journal article)

    Sameith, K., Antczak, P., Marston, E., Turan, N., Maier, D., Stankovic, T., & Falciani, F. (2008). Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. BIOINFORMATICS, 24(22), 2602-2607. doi:10.1093/bioinformatics/btn489

    DOI: 10.1093/bioinformatics/btn489