Publications

Selected Publications 

• Myall, Ashleight C., Simon Perkins, David Rushton, David Jonathan, Phillippa Spencer, Andrew R. Jones, and Philipp Antczak. 2020. “Identifying Robust Biomarkers of Infection through an Omics-Based Meta-Analysis.” MedRxiv 2020.07.28.20163329.
• Perkins, Edward J., Kalyan Gayen, Jason E. Shoemaker, Philipp Antczak, Lyle Burgoon, Francesco Falciani, Steve Gutsell, Geoff Hodges, Aude Kienzler, Dries Knapen, Mary McBride, Catherine Willett, Francis J. Doyle, and Natàlia Garcia-Reyero. 2019. “Chemical Hazard Prediction and Hypothesis Testing Using Quantitative Adverse Outcome Pathways.” Altex 36(1):91–102.
• Basili, Danilo, Ji Liang Zhang, John Herbert, Kevin Kroll, Nancy D. Denslow, Christopher J. Martyniuk, Francesco Falciani, and Philipp Antczak. 2018. “In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass (Micropterus Salmoides).” Environmental Science and Technology 52(13):7553–65.
• Murphy, Cheryl A., Roger M. Nisbet, Philipp Antczak, Natàlia Garcia-Reyero, Andre Gergs, Konstadia Lika, Teresa Mathews, Erik B. Muller, Diane Nacci, Angela Peace, Christopher H. Remien, Irvin R. Schultz, Louise M. Stevenson, and Karen H. Watanabe. 2018. “Incorporating Suborganismal Processes into Dynamic Energy Budget Models for Ecological Risk Assessment.” Integrated Environmental Assessment and Management 14(5):615–24.
• Antczak, Philipp, Thomas Andrew White, Anirudha Giri, Francesco Frank Michelangeli, Mark R. Viant, Mark T. D. D. Cronin, Chris Vulpe, Francesco Falciani, Francesco Frank Michelangeli, Mark R. Viant, Chris Vulpe, and Francesco Falciani. 2014. “A Systems Biology Approach Reveals a Novel Calcium-Dependent Mechanism for Basal Toxicity in Daphnia Magna.” Environmental Science & Technology 49(18):11132–40.

2020

• Mathews, Teresa, Louise Stevenson, Paul C. Pickhardt, Cheryl A. Murphy, Roger M. Nisbet, Philipp Antczak, Natàlia Garcia‐Reyero, and Andre Gergs. 2020. “The Effect of Dietary Exposure to Coal Ash Contaminants Within Food Ration on Growth and Reproduction in Daphnia Magna.” Environmental Toxicology and Chemistry etc.4819.
• Myall, Ashleight C., Simon Perkins, David Rushton, David Jonathan, Phillippa Spencer, Andrew R. Jones, and Philipp Antczak. 2020. “Identifying Robust Biomarkers of Infection through an Omics-Based Meta-Analysis.” MedRxiv 2020.07.28.20163329.
• Sleight, Victoria A., Philipp Antczak, Francesco Falciani, Melody S. Clark, and Lenore Cowen. 2020. “Computationally Predicted Gene Regulatory Networks in Molluscan Biomineralization Identify Extracellular Matrix Production and Ion Transportation Pathways” edited by L. Cowen. Bioinformatics 36(5):1326–32.

2019

• Perkins, Edward J., Kalyan Gayen, Jason E. Shoemaker, Philipp Antczak, Lyle Burgoon, Francesco Falciani, Steve Gutsell, Geoff Hodges, Aude Kienzler, Dries Knapen, Mary McBride, Catherine Willett, Francis J. Doyle, and Natàlia Garcia-Reyero. 2019. “Chemical Hazard Prediction and Hypothesis Testing Using Quantitative Adverse Outcome Pathways.” Altex 36(1):91–102.
• Salem, Shebl E., Rachael Hough, Chris Probert, Thomas W. Maddox, Philipp Antczak, Julian M. Ketley, Nicola J. Williams, Sarah J. Stoneham, and Debra C. Archer. 2019. “A Longitudinal Study of the Faecal Microbiome and Metabolome of Periparturient Mares.” PeerJ 7:e6687.
• Salem, Shebl E., Thomas W. Maddox, Philipp Antczak, Julian M. Ketley, Nicola J. Williams, and Debra C. Archer. 2019. “Acute Changes in the Colonic Microbiota Are Associated with Large Intestinal Forms of Surgical Colic.” Veterinary Research.

2018

• Basili, Danilo, Ji Liang Zhang, John Herbert, Kevin Kroll, Nancy D. Denslow, Christopher J. Martyniuk, Francesco Falciani, and Philipp Antczak. 2018. “In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass (Micropterus Salmoides).” Environmental Science and Technology 52(13):7553–65.
• Flamini, Valentina, Rachel S. Ghadiali, Philipp Antczak, Amy Rothwell, Jeremy E. Turnbull, and Addolorata Pisconti. 2018. “The Satellite Cell Niche Regulates the Balance between Myoblast Differentiation and Self-Renewal via P53.” Stem Cell Reports 10(3):970–83.
• Murphy, Cheryl A., Roger M. Nisbet, Philipp Antczak, Natàlia Garcia-Reyero, Andre Gergs, Konstadia Lika, Teresa Mathews, Erik B. Muller, Diane Nacci, Angela Peace, Christopher H. Remien, Irvin R. Schultz, Louise M. Stevenson, and Karen H. Watanabe. 2018. “Incorporating Suborganismal Processes into Dynamic Energy Budget Models for Ecological Risk Assessment.” Integrated Environmental Assessment and Management 14(5):615–24.
• Murphy, Cheryl A., Roger M. Nisbet, Philipp Antczak, Natàlia Garcia-Reyero, Andre Gergs, Konstadia Lika, Teresa Mathews, Erik B. Muller, Diane Nacci, Angela Peace, Christopher H. Remien, Irvin R. Schultz, and Karen H. Watanabe. 2018. “Linking Adverse Outcome Pathways to Dynamic Energy Budgets: A Conceptual Model.” Pp. 281–302 in A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment. Cham: Springer International Publishing.
• Salem, Shebl E., Thomas W. Maddox, Adam Berg, Philipp Antczak, Julian M. Ketley, Nicola J. Williams, and Debra C. Archer. 2018. “Variation in Faecal Microbiota in a Group of Horses Managed at Pasture over a 12-Month Period.” Scientific Reports 8(1).

2017

• Brockmeier, Erica K., Geoff Hodges, Philipp Antczak, Thomas H. Hutchinson, Emma Butler, Markus Hecker, Knut Erik Tollefsen, Natalia Garcia-Reyero, Peter Kille, Dörthe Becker, Kevin Chipman, John Colbourne, Timothy W. Collette, Andrew Cossins, Mark Cronin, Peter Graystock, Steve Gutsell, Dries Knapen, Ioanna Katsiadaki, Anke Lange, Stuart Marshall, Stewart F. Owen, Edward J. Perkins, Stewart Plaistow, Anthony Schroeder, Daisy Taylor, Mark Viant, Gerald Ankley, and Francesco Falciani. 2017. “The Role of Omics in the Application of Adverse Outcome Pathways for Chemical Risk Assessment.” Toxicological Sciences 158(2):252–62.
• Feswick, April, Meghan Isaacs, Adam Biales, Robert W. Flick, David C. Bencic, Rong Lin Wang, Chris Vulpe, Marianna Brown-Augustine, Alex Loguinov, Francesco Falciani, Philipp Antczak, John Herbert, Lorraine Brown, Nancy D. Denslow, Kevin J. Kroll, Candice Lavelle, Viet Dang, Lynn Escalon, Natàlia Garcia-Reyero, Christopher J. Martyniuk, and Kelly R. Munkittrick. 2017. “How Consistent Are We? Interlaboratory Comparison Study in Fathead Minnows Using the Model Estrogen 17Α-Ethinylestradiol to Develop Recommendations for Environmental Transcriptomics.” Environmental Toxicology and Chemistry 36(10):2614–23.

2016

• Trevino, Victor, Alberto Cassese, Zsuzsanna Nagy, Xiaodong Zhuang, John Herbert, Philipp Antczak, Kim Clarke, Nicholas Davies, Ayesha Rahman, Moray J. Campbell, Michele Guindani, Roy Bicknell, Marina Vannucci, and Francesco Falciani. 2016. “A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells.” PLoS Computational Biology 12(4).

2015

• Altenburger, Rolf, Selim Ait-Aissa, Philipp Antczak, Thomas Backhaus, Damià Barceló, Thomas Benjamin Seiler, Francois Brion, Wibke Busch, Kevin Chipman, Miren López de Alda, Gisela de Aragão Umbuzeiro, Beate I. Escher, Francesco Falciani, Michael Faust, Andreas Focks, Klara Hilscherova, Juliane Hollender, Henner Hollert, Felix Jäger, Annika Jahnke, Andreas Kortenkamp, Martin Krauss, Gregory F. Lemkine, John Munthe, Steffen Neumann, Emma L. Schymanski, Mark Scrimshaw, Helmut Segner, Jaroslav Slobodnik, Foppe Smedes, Subramaniam Kughathas, Ivana Teodorovic, Andrew J. Tindall, Knut Erik Tollefsen, Karl Heinz Walz, Tim D. Williams, Paul J. Van den Brink, Jos van Gils, Branislav Vrana, Xiaowei Zhang, and Werner Brack. 2015. “Future Water Quality Monitoring - Adapting Tools to Deal with Mixtures of Pollutants in Water Resource Management.” Science of the Total Environment 512–513:540–51.
• Antczak, Philipp, Andrew Filer, Greg N. Parsonage, Holly M. Legault, Margot O’Toole, Mark J. Pearson, Andrew M. Thomas, Dagmar Scheel-Toellner, Karim Raza, Christopher D. Buckley, and Francesco Falciani. 2015. “Stromal Transcriptional Profiles Reveal Hierarchies of Anatomical Site, Serum Response and Disease and Identify Disease Specific Pathways.” Plos One 10(3):e0120917.
• Cassese, Alberto, Michele Guindani, Philipp Antczak, Francesco Falciani, and Marina Vannucci. 2015. “A Bayesian Model for the Identification of Differentially Expressed Genes in Daphnia Magna Exposed to Munition Pollutants.” Biometrics 71(3):803–11.
• Perkins, Edward J., Philipp Antczak, Lyle Burgoon, Francesco Falciani, Natàlia Garcia-Reyero, Steve Gutsell, Geoff Hodges, Aude Kienzler, Dries Knapen, Mary McBride, and Catherine Willett. 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.
• Scanlan, Leona D., Alexandre V. Loguinov, Quincy Teng, Philipp Antczak, Kathleen P. Dailey, Daniel T. Nowinski, Jonah Kornbluh, Xin Xin Lin, Erica Lachenauer, Audrey Arai, Nora K. Douglas, Francesco Falciani, Heather M. Stapleton, and Chris D. Vulpe. 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 and Technology 49(12):7400–7410.

2014

• Antczak, Philipp, Thomas Andrew White, Anirudha Giri, Francesco Frank Michelangeli, Mark R. Viant, Mark T. D. D. Cronin, Chris Vulpe, Francesco Falciani, Francesco Frank Michelangeli, Mark R. Viant, Chris Vulpe, and Francesco Falciani. 2014. “A Systems Biology Approach Reveals a Novel Calcium-Dependent Mechanism for Basal Toxicity in Daphnia Magna.” Environmental Science & Technology 49(18):11132–40.
• Cano, Isaac, Ákos Tényi, Christine Schueller, Martin Wolff, M. Mercedes Huertas Migueláñez, David Gomez-Cabrero, Philipp Antczak, Josep Roca, Marta Cascante, Francesco Falciani, and Dieter Maier. 2014. “The COPD Knowledge Base: Enabling Data Analysis and Computational Simulation in Translational COPD Research.” Journal of Translational Medicine 12(Suppl 2):S6.
• Davidsen, Peter K., John M. Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Victor I. Peinado, Constancio Gonzalez, Josep Roca, Stuart Egginton, Joan A. Barberá, and Francesco Falciani. 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(8):59.

2013

• Antczak, Philipp, HJ Hun Je HJ Jo, Seonock Woo, Leona Scanlan, Helen Poynton, Alex Loguinov, Sarah Chan, Francesco Falciani, and Chris Vulpe. 2013. “The Molecular Toxicity Identification Evaluation (MTIE) Approach Predicts Chemical Exposure in Daphnia Magna.” Environmental Science & Technology 1–20.
• Fergelot, Patricia, Jean Christophe Bernhard, Fabienne Soulet, Witold W. Kilarski, Céline Léon, Nathalie Courtois, Colette Deminière, John M. J. Herbert, Philipp Antczak, Francesco Falciani, Nathalie Rioux-Leclercq, Jean Jacques Patard, Jean Marie Ferrière, Alain Ravaud, Martin Hagedorn, and Andreas Bikfalvi. 2013. “The Experimental Renal Cell Carcinoma Model in the Chick Embryo.” Angiogenesis 16(1):181–94.
• Martyniuk, Christopher J., Melinda S. Prucha, Nicholas J. Doperalski, Philipp Antczak, Kevin J. Kroll, Francesco Falciani, David S. Barber, and Nancy D. Denslow. 2013. “Gene Expression Networks Underlying Ovarian Development in Wild Largemouth Bass (Micropterus Salmoides).” PloS One 8(3):e59093.
• Scanlan, Leona D., Robert B. Reed, Alexandre V. Loguinov, Philipp Antczak, Abderrahmane Tagmount, Shaul Aloni, Daniel Thomas Nowinski, Pauline Luong, Christine Tran, Nadeeka Karunaratne, Don Pham, Xin Xin Lin, Francesco Falciani, Christopher P. Higgins, James F. Ranville, Chris D. Vulpe, and Benjamin Gilbert. 2013. “Silver Nanowire Exposure Results in Internalization and Toxicity to Daphnia Magna.” ACS Nano 7(12):10681–94.

2012

• Moro, Sabrina, J. Kevin Chipman, Philipp Antczak, Nil Turan, Wolfgang Dekant, Francesco Falciani, and Angela Mally. 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):336–52.
• Mura, M., R. K. Swain, X. Zhuang, H. Vorschmitt, G. Reynolds, S. Durant, J. F. J. J. Beesley, J. M. J. J. Herbert, H. Sheldon, M. Andre, S. Sanderson, K. Glen, N. T. T. Luu, H. M. McGettrick, P. Antczak, F. Falciani, G. B. Nash, Z. S. Nagy, and R. Bicknell. 2012. “Identification and Angiogenic Role of the Novel Tumor Endothelial Marker CLEC14A.” Oncogene 31(3):293–305.

2011

• Antczak, Philipp. 2011. “Moving Towards Predictive Toxicology - A Systems Biology Approach.” University of Birmingham.
• Gupta, Rita, Anna Stincone, Philipp Antczak, Sarah Durant, Roy Bicknell, Andreas Bikfalvi, and Francesco Falciani. 2011. “A Computational Framework for Gene Regulatory Network Inference That Combines Multiple Methods and Datasets.” BMC Systems Biology 5(1):52.
• Lin, Hong, John A. Halsall, Philipp Antczak, Laura P. O’Neill, Francesco Falciani, and Bryan M. Turner. 2011. “Relative Overexpression of X-Linked Genes in Mouse Embryonic Stem Cells Is Consistent with Ohno’s Hypothesis.” Nature Genetics 43(12):1169–70.
• Perkins, Edward J., J. Kevin Chipman, Stephen Edwards, Tanwir Habib, Francesco Falciani, Ronald Taylor, Graham Van Aggelen, Chris Vulpe, Philipp Antczak, and Alexandre Loguinov. 2011. “Reverse Engineering Adverse Outcome Pathways.” Environmental Toxicology and Chemistry 30(1):22–38.
• Stincone, Anna, Nazish Daudi, Ayesha S. Rahman, Philipp Antczak, Ian Henderson, Jeffrey Cole, Matthew D. Johnson, Peter Lund, and Francesco Falciani. 2011. “A Systems Biology Approach Sheds New Light on Escherichia Coli Acid Resistance.” Nucleic Acids Research 39(17):1–17.
• Trevino, Victor, Mahlet G. Tadesse, Marina Vannucci, Fatima Al-Shahrour, Philipp Antczak, Sarah Durant, Andreas Bikfalvi, Joaquin Dopazo, Moray J. Campbell, and Francesco Falciani. 2011. “Analysis of Normal-Tumour Tissue Interaction in Tumours: Prediction of Prostate Cancer Features from the Molecular Profile of Adjacent Normal Cells” edited by D. Di Bernardo. PLoS ONE 6(3):13.

2010

• Antczak, Philipp, Fernando Ortega, J. Kevin Chipman, and Francesco Falciani. 2010. “Mapping Drug Physico-Chemical Features to Pathway Activity Reveals Molecular Networks Linked to Toxicity Outcome” edited by R. Khanin. PLoS ONE 5(8):e12385.
• Antczak, Philipp, Fabienne Soulet, Witold W. Kilarski, John Herbert, Roy Bicknell, Francesco Falciani, Andreas Bikfalvi, Fabienne Soulet, Witold W. Kilarski, John Herbert, Roy Bicknell, Francesco Falciani, and Andreas Bikfalvi. 2010. “Gene Signatures in Wound Tissue as Evidenced by Molecular Profiling in the Chick Embryo Model.” BMC Genomics 11(1):495.
• Burton, Neil A., Matthew D. Johnson, Philipp Antczak, Ashley Robinson, and Peter A. Lund. 2010. “Novel Aspects of the Acid Response Network of E. Coli K-12 Are Revealed by a Study of Transcriptional Dynamics.” Journal of Molecular Biology 401(5):726–42.

2008

• Sameith, Katrin, Philipp Antczak, Elliot Marston, Nil Turan, Dieter Maier, Tanja Stankovic, and Francesco Falciani. 2008. “Functional Modules Integrating Essential Cellular Functions Are Predictive of the Response of Leukaemia Cells to DNA Damage.” Bioinformatics 24(22):2602–7.