Recent Highlights


CRABP2 -- A novel biomarker for high risk endometrial cancer. Egan D et al. Gynecologic Oncology. 2022 September 24

Control of cell state transitions.
 Rukhlenko O et al. Nature. 2022 September 14

Interaction of LATS1 with SMAC links the MST2/Hippo pathway with apoptosis in an IAP-dependent manner. Garcia-Gutierrez L et al. Cell Death & Disease. 2022 August 8

A Systems Biology Approach to Investigate Kinase Signal Transduction Networks That Are Involved in Triple Negative Breast Cancer Resistance to Cisplatin. Mukherjee N et al. Journal of Personalized Medicine. 2022 August 3

Hypoxia-inducible factor (HIF) as a bridge between healthy barrier function, wound healing, and fibrosis. Steiner CA et al. AJP Cell Physiology. 2022 August 1

Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. Bokharaie H et al. Biomolecules. 2022 July 17

Prolyl Hydroxylase Inhibition Mitigates Allograft Injury During Liver Transplantation. Harnoss J et al. Transplantation. 2022 July 11

Machine learning based prediction and the influence of complement - Coagulation pathway proteins on clinical outcome: Results from the NEURAPRO trial. Susai SR et al. Brain, behavior and immunity. 2022 July 1

A comparative analysis of extracellular vesicles (EVs) from human and feline plasma. Howard J et al. Scientific Reports. 2022 June 27

The effect of HIF on metabolism and immunity. Cormac Taylor and Carsten Scholz. Nature Reviews Nephrology. 2022 June 20

Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. Nolan A et al. Genes. 2022 April 10

Emerging RAS-directed therapies for cancer. Conroy M et al. Cancer Drug Resistance. 2022 April 8

Reconstruction and analysis of a large-scale binary Ras-effector signaling network. Catozzi S et al. Cell Communication and Signaling. 2022 March 4

Investigating a clinically actionable BRAF mutation for monitoring low-grade serous ovarian cancer: A case report. Silva R et al. Case Reports in Women's Health. 2022 February 6

Suppressive effects of the obese tumor microenvironment on CD8 T cell infiltration and effector function. Dyck L er al. Journal of Experimental Medicine. 2022 February 1

Clinico-biological features of T-cell acute lymphoblastic leukemia with fusion proteins. Steimle T et al. Blood Cancer Journal. 2022 January 26

HOMELETTE: a unified interface to homology modelling software. Philipp Junk, Christina Kiel. Bioinformatics. 2021 December 25

Can Systems Biology Advance Clinical Precision Oncology? Andrea Rocca, Boris N. Kholodenko. Cancers. 2021 December 16

Effects of Curcumin Analogues DMC and EF24 in Combination with the Cytokine TRAIL against Kidney Cancer. McMorrow T et al. Molecules. 2021 October 18

Autosomal dominant Shwachman-Diamond syndrome with a novel heterozygous missense variant in the SRP54 gene causing severe phenotypic features. Smith O et al. British Journal of Haematology. 2021 September 22

Immunological assessment of SARS-CoV-2 infection in pregnancy from diagnosis to delivery: A multicentre prospective study. Brennan D et al. PLOS One. 2021 September 20

Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Ryan CJ et al. Cell Systems. 2021 September 15

Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. Nwaokorie A, Fey D. International Journal of Molecular Sciences. 2021 September 15



Interaction of LATS1 with SMAC links the MST2/Hippo pathway with apoptosis in an IAP-dependent manner. Garcia-Gutierrez L et al. Cell Death & Disease. 2022 August 8

Hypoxia-inducible factor (HIF) as a bridge between healthy barrier function, wound healing, and fibrosis. Steiner CA et al. AJP Cell Physiology. 2022 August 1

Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. Bokharaie H et al. Biomolecules. 2022 July 17

Prolyl Hydroxylase Inhibition Mitigates Allograft Injury During Liver Transplantation. Harnoss J et al. Transplantation. 2022 July 11

Machine learning based prediction and the influence of complement - Coagulation pathway proteins on clinical outcome: Results from the NEURAPRO trial. Susai SR et al. Brain, behavior and immunity. 2022 July 1

A comparative analysis of extracellular vesicles (EVs) from human and feline plasma. Howard J et al. Scientific Reports. 2022 June 27

The effect of HIF on metabolism and immunity. Cormac Taylor and Carsten Scholz. Nature Reviews Nephrology. 2022 June 20

Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. Nolan A et al. Genes. 2022 April 10

Emerging RAS-directed therapies for cancer. Conroy M et al. Cancer Drug Resistance. 2022 April 8

Reconstruction and analysis of a large-scale binary Ras-effector signaling network. Catozzi S et al. Cell Communication and Signaling. 2022 March 4

Investigating a clinically actionable BRAF mutation for monitoring low-grade serous ovarian cancer: A case report. Silva R et al. Case Reports in Women's Health. 2022 February 6

Suppressive effects of the obese tumor microenvironment on CD8 T cell infiltration and effector function. Dyck L er al. Journal of Experimental Medicine. 2022 February 1

Clinico-biological features of T-cell acute lymphoblastic leukemia with fusion proteins. Steimle T et al. Blood Cancer Journal. 2022 January 26


HOMELETTE: a unified interface to homology modelling software. Philipp Junk, Christina Kiel. Bioinformatics. 2021 December 25

Can Systems Biology Advance Clinical Precision Oncology? Andrea Rocca, Boris N. Kholodenko. Cancers. 2021 December 16

Network pharmacology: curing causal mechanisms instead of treating symptoms. Schmidt H et al. Trends in Pharmacological Sciences. 2021 December 9

Effects of Curcumin Analogues DMC and EF24 in Combination with the Cytokine TRAIL against Kidney Cancer. McMorrow T et al. Molecules. 2021 October 18

Autosomal dominant Shwachman-Diamond syndrome with a novel heterozygous missense variant in the SRP54 gene causing severe phenotypic features. Smith O et al. British Journal of Haematology. 2021 September 22

Immunological assessment of SARS-CoV-2 infection in pregnancy from diagnosis to delivery: A multicentre prospective study. Brennan D et al. PLOS One. 2021 September 20

Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Ryan CJ et al. Cell Systems. 2021 September 15

Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. Nwaokorie A, Fey D. International Journal of Molecular Sciences. 2021 September 15

Cell Adhesion Molecules in Normal Skin and Melanoma. Cian D'Arcy, Christina Kiel. Biomolecules. 2021 August 15

KBoost: a new method to infer gene regulatory networks from gene expression data. Kolch W et al. Scientific Reports. 2021 July 29

Engineering of Biological Pathways: Complex Formation and Signal Transduction. Junk P, Kiel C. Computational Design of Membrane Proteins. 2021 July 25

Modeling the Nonlinear Dynamics of Intracellular Signaling Networks. Rukhlenko OS, Kholodenko BN. Bio-Protocol. 2021 July 20

Channeling macrophage polarization by rocaglates increases macrophage resistance to Mycobacterium tuberculosis. Kramnik I et al. iScience. 2021 July 10

Reengineering protein-phosphorylation switches. Kholodenko, BN and Okada M. Science. 2021 July 02

Modeling Cervical Cancer Screening Strategies With Varying Levels of Human Papillomavirus Vaccination. Brennan D et al. JAMA Network Open. 2021 June 30

Nonvalvular atrial fibrillation patients anticoagulated with rivaroxaban compared with warfarin exhibit reduced circulating extracellular vesicles with attenuated pro-inflammatory protein signatures. Maguire P et al. Journal of Thrombosis and Haemostasis. 2021 June 23

A systematic analysis of signaling reactivation and drug resistance. Rukhlenko O et al. Cell Reports. 2021 May 25

Immature acute leukaemias: lessons from the haematopoietic roadmap. Bond J et al. The FEBS Journal. 2021 May 24

Detection and quanititation of host cell proteins in monoclonal antibody drug products using automated sample perparation and data-independent acquisition LC-MS/MS.Bones J et al. Journal of Pharmaceutical Analysis. 2021 May 20

Comparing 3D models of placenta accreta spectrum to surgical findings. Brennan D et al. International Journal of Gynaecology and Obstetrics. 2021 May 17 

Personalized Medicine for Neuroblastoma: Moving from Static Genotypes to Dynamic Simulations of Drug Response. Croucher D et al. MDPI: Journal of Personalised Medicine. 2021 May 11

A Chemo-Genomic Approach Identifies Diverse Epigenetic Therapeutic Vulnerabilities in MYCN-Amplified Neuroblastoma. Duffy D et al. Frontiers in Cell and Developmental Biology. 2021 April 21

Proteomic signatures of radioresistance: Alteration of inflammation, angiogenesis and metabolism-related factors in radioresistant oesophageal adenocarcinoma. Marcone S et al. Cancer Treatment and Research Communications. 2021 April 18

Von Willebrand Factor, Factor VIII, and other acute phase reactants as biomarkers of inflammation and endothelial dysfunction in chronic Graft-versus-Host Disease. Lelas A et al. Frontiers in Immunology. 2021 April 12

Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. Nolan A et al. Genes. 2021 April 10

Signaling pathways in intestinal homeostasis and colorectal cancer: KRAS at centre stage. Ternet C and Kiel C. Cell Communication and Signaling. 2021 March 10

Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells. Parkhitko AA et al. PLoS Genetics. 2021 Feb 17

IQGAP1 Is a Scaffold of the Core Proteins of the Hippo Pathway and Negatively Regulates the Pro-Apoptotic Signal Mediated by This Pathway. Quinn N et al. Cells. 2021 Feb 13

Predicted 'wiring landscape' of Ras-effector interactions in 29 human tissues. Catozzi S et al. NPJ Systems Biology and Applications. 2021 Feb 12

BAX and SMAC regulate bistable properties of the apoptotic caspase system. McKenna S et al. Scientific Reports. 2021 Feb 8

The Ins and Outs of RAS Effector Complexes. Kiel C et al. Biomolecules. 2021 Feb 7

Mid-luteal uterine artery Doppler indices in the prediction of pregnancy outcome in nulliparous women undergoing assisted reproduction. Crosby DA et al. Human Fertility. 2021 Jan 13



Signaling Dynamics Regulating Crosstalks between T-Cell Activation and Immune Checkpoints. Kreileder M et al. Trends in Cell Biology. 2020 Dec 30

Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs. Seidel C et al. Nanotoxicology. 2020 Dec 17

Perinatal Derivatives: Where Do We Stand? A Roadmap of the Human Placenta and Consensus for Tissue and Cell Nomenclature. Silini AR et al. Frontiers in Bioengineering and Biotechnology. 2020 Dec 17

N-Linked glycosylation profiles of therapeutic induced senescent (TIS) triple negative breast cancer cells (TNBC) and their extracellular vesicle (EV) progeny. Kavanagh EL et al. Molecular omics. 2020 Dec 16

Examination and characterisation of the effect of amitriptyline therapy for chronic neuropathic pain on neuropeptide and proteomic constituents of human cerebrospinal fluid. Royds J et al. Brain, Behavior, & Immunity - Health. 2020 Dec 7

Accurate prediction of kinase-substrate networkds using knowledge graphs. Novacek V et al. PLoS Computational Biology. 2020 Dec 3

An Investigation into Proteomic Constituents of Cerebrospinal Fluid in Patients with Chronic Peripheral Neuropathic Pain Medicated with Opioids- a Pilot Study. Royds J et al. Journal of Neuroimmune Pharmacology. 2020 Nov 20

SnapShot: APC/T Cell Immune Checkpoints. Shrager S and Kiel C. Cell. 2020 Nov 12

Improving response to progestin treatment of low-grade endometrial cancer. Baxter E at al. International Journal of Gynecological Cancer. 2020 Nov 1

Differential responses of murine alveolar macrophages to elongate mineral particles of asbestiform and non-asbestiform varieties: Cytotoxicity, cytokine secretion and transcriptional changes. Khaliullin TO et al. Toxicology & Applied Pharmacology. 2020 Oct 24

Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing. Rukhlenko O et al. Current Opinion in Structural Biology. 2020 October 23

Prediction of chronic inflammation for inhaled particles: the impact of material cycling and quarantining in the lung epithelium. Kokot H et al. Advanced Materials. 2020 Oct 19

The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology. Wilkinson M et al. Life (Basel). 2020 Sept 10

Resolving the Interactome of the Human Immune Regulator MACIR with Enhanced Membrane Protein Preparation and Affinity Proteomics. McGauran G et al. Proteomics. 2020 Aug 31

Combining Gene-Disease Associations with Single-Cell Gene Expression Data Provides Anatomy-Specific Subnetworks in Age-Related Macular Degeneration. Luther PJ, Kiel C. Network and Systems Medicine. 2020 Aug 3 

Applications of personalised signalling network models in precision oncology. Hastings JF et al. Pharmacology & Therapeutics. 2020 Aug 1

Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. Bolado-Carrancio A et al. eLife. 2020 July 24

Examination and characterisation of burst spinal cord stimulation on cerebrospinal fluid cellular and protein constituents in patient responders with chronic neuropathic pain - A Pilot Study. Royds J et al. Journal of Neuroimmunology. 2020 July 15

A transcriptomic continuum of differentiation arrest identifies myeloid interface acute leukemias with poor prognosis. Bond J et al. Leukemia. 2020 July 13

Toxicity of TiO2 Nanoparticles: Validation of Alternative Models. Leroux MM et al. International Journal of Molecular Sciences. 2020 July 9

Fertility-sparing treatment in early endometrial cancer: current state and future strategies. Obermair A et al. Obstetrics & Gynecology Science. 2020 July 8

Characterization of the renal cortical transcriptome following Roux-en-Y gastric bypass surgery in experimental diabetic kidney disease. Nair M et al. BMJ Open Diabetes Research & Care. 2020 July 1

Increased extracellular vesicles mediate inflammatory signalling in cystic fibrosis. Useckaite Z et al. Thorax. 2020 June 1

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. Lord CJ et al. eLife. 2020 May 28

Adverse outcome pathways as a tool for the design of testing strategies to support the safety assessment of emerging advanced materials at the nanoscale. Halappanavar S et al. Particle and Fibre Toxicology. 2020 May 25

Curcumin Sensitizes Kidney Cancer Cells to TRAIL-Induced Apoptosis via ROS Mediated Activation of JNK-CHOP Pathway and Upregulation of DR4. Obaidi I et al. Biology (Basel). 2020 May 1

Demodex: A skin resident in Man and his best friend. Foley R et al. Journal of the European Academy of Dermatology and Venereology. 2020 April 15

Acute Phase Response as a Biological Mechanism‐of‐Action of (Nano)particle‐Induced Cardiovascular Disease. Hadrup N et al. Small. 2020 March 29

The Impact of Sarcopenia and Low Muscle Attenuation on Overall Survival in Epithelial Ovarian Cancer: A Systematic Review and Meta-analysis. McSharry V et al. Gynecologic Oncology. 2020 March 27

Genetic Deletion of Zebrafish Rab28 Causes Defective Outer Segment Shedding, but Not Retinal Degeneration. Carter S et al. Frontiers in Cell and Developmental Biology. 2020 March 17

Genes expression profiling of alveolar macrophages exposed to non-functionalized, anionic and cationic multi-walled carbon nanotubes shows three different mechanisms of toxicity. Nahle S et al. Journal of Nanobiotechnology. 2020 Feb 24

A Quantitative Genetic Interaction Map of HIV Infection. Krogan N et al. Molecular Cell. 2020 Feb 20

Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Kiel C et al. Small GTPases. 2020 Feb 14

Mitogen-Activated Protein Kinase (MAPK) and Obesity-Related Cancer. Donohoe F et al. International Journal of Molecular Sciences. 2020 Feb 13

Targeting MAPK Signaling in Cancer: Mechanisms of Drug Resistance and Sensitivity. Kolch W et al. International Journal of Molecular Sciences (Special Issue: Targeting MAPK in Cancer). 2020 Feb 7

Patient perceptions and understanding of obesity related endometrial cancer. Brennan DJ et al. Gynecologic Oncology Reports. 2020 May (online 31 Jan 2020)

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D. Kolch W. Nature Communications. 2020 Jan 24

RASSF1A Tumour Suppressor: Target the Network for Effective Cancer Therapy. Matallanas D et al. Cancers. 2020 January 17

CBFβ-SMMHC Affects Genome-wide Polycomb Repressive Complex 1 Activity in Acute Myeloid Leukemia. Cordonnier G et al. Cell Reports. 2020 Jan 14

Repository of proposed pathways and protein-protein interaction networks in age-related macular degeneration. Pool FM et al. NPJ Aging and Mechanisms of Disease. 2020 Jan 7



Pharmacologic inhibition of hypoxia inducible factor (HIF)-hydroxylases ameliorates allergic contact dermatitis. Manresa, M.C. et al. Allergy. 2019;74(4): 753‐766

The extracellular matrix as a key regulator of intracellular signalling networks. Hastings, J.F. et al. British journal of pharmacology. 2019; 176(1): 82-92

A feasibility study of a multimodal stimulation bioreactor for the conditioning of stem cell seeded cardiac patches via electrical impulses and pulsatile perfusion. Herrmann, F.E.M. et al. Bio-medical materials and engineering. 2019; 30(1): 37-48

Mapping connections in signaling networks with ambiguous modularity. Lill, D. et al. NPJ systems biology and applications. 2019; 5, 19

Platelet-Derived Microparticles From Obese Individuals: Characterization of Number, Size, Proteomics, and Crosstalk With Cancer and Endothelial Cells. Grande, R. et al. Frontiers in pharmacology. 2019; 10, 7

Molecular basis of distinct oestrogen responses in endometrial and breast cancer Baxter, E. et al. Endocr Relat Cancer. 2019; 26(1): 31-46

DNMT3A mutation is associated with increased age and adverse outcome in adult T-acute lymphoblastic leukemia. Bond J. et al. Haematologica. 2019; 104(8): 1617‐1625.

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor.  Erickson, K.E. et al. PLOS Comutational Biology. 2019; 17;15(1)

Hydroxylase Inhibition Selectively Induces Cell Death in Monocytes.  Crifo, B. et al. The Journal of Immunology. 2019; 204(8)

Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival. Oser, M.G. et al. Cancer discovery. 2019; 9(2)

New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling.  Erickson, K.E. et al. Seminars in Cancer biology. 2019; 54: 162-173

Understanding the role of distance, direction and cue salience in an associative model of landmark learning. Commins, S. & Fey, D. Scientific reports. 2019; 9(1), 2026

CBFβ-MYH11 interferes with megakaryocyte differentiation via modulating a gene program that includes GATA2 and KLF1. Yi, G. et al. Blood cancer journal.  2019; 9(3): 33

An Integrated Global Analysis of Compartmentalized HRAS Signaling. Santra, T. et al. Cell reports. 2019; 26(11): 3100‐3115

Targeting promiscuous heterodimerization overcomes innate resistance to ERBB2 dimerization inhibitors in breast cancer. Kennedy, S.P. et al. Breast Cancer Research. 2019; 21(1): 43

Evaluation of Demodex mite viability using motility and scattered light intensity Gatault, S. et al. Experimental and Applied Acarology. 2019; 77: 463-469

Protein Hydroxylation by Hypoxia-Inducible Factor (HIF) Hydroxylases: Unique or Ubiquitous?  Moritz, J. et al. Cells. 2019; 8(5): 384

All over the place: deciphering HRAS signaling from different subcellular compartments Kolch, K. & Matallanas, D. Molecular & Cellular Oncology. 2019; 6(5): e1605821

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation. Charitou, T. et al. British journal of cancer. 2019; 121(1): 37‐50

An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity. Zhernovkov, V. et al. Toxicological sciences : an official journal of the Society of Toxicology. 2019; Online Preprint:kfz151

VGLL3 operates via TEAD1, TEAD3 and TEAD4 to influence myogenesis in skeletal muscle. Figeac N. et al. Journal of cell science. 2019; 132(13): jcs225946

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Bouchal, P. et al. Cell reports. 2019; 28(3): 832-843

Hypoxia-inducible factor (HIF) hydroxylase inhibition enhances the protective effects of cyclosporine in colitis.  Taylor, C.T. et al. American Journal of Physiology, Gastrointestinal and Liver Physiology. 2019; 317(2): G99-G97

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines. De Kegel, B. & Ryan, C.J. PLoS genetics. 2019; 15(10): e1008466

Neutrophil gelatinase-associated lipocalin (NGAL) is localised to the primary cilium in renal tubular epithelial cells - A novel source of urinary biomarkers of renal injury. Cassidy, H. et al. Biochimica et biophysica acta. Molecular basis of disease. 2019; 1865(12): 165532

Mechanisms and consequences of oxygen-and carbon dioxide-sensing in mammals.  Cummins, E.P. et al. Physiological Reviews. 2020; 100(1): 463‐488

Loss of RAF kinase inhibitor protein is involved in myelomonocytic differentiation and aggravates RAS-driven myeloid leukemogenesis. Caraffini, V. et al. Haematologica. 2020; 105(2): 375‐386

Epigenetics of paediatric acute myeloid leukaemia. Jones, L., McCarthy, P. & Bond, J. British journal of haematology. 2020; 188(1): 63‐76

Prolyl Hydroxylase Inhibition Mitigates Pouchitis Harnoss, J.M. et al. Inflamatory Bowel Disease. 2020; 26(2): 192‐205

Protein and lipid homeostasis altered in rat macrophages after exposure to metallic oxide nanoparticles. Zahra, D. et al. Cell biology and toxicology. 2020;36(1):65‐82


Hypoxia in the Gut Taylor, C.T.. Cellular and Molecular Gastroenterology and Hepatology. 2017; 5(1): 61-62

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. Ebhardt H.A. et al. NPJ Systems Biology and Applications. 2018; 4: 26

Sea turtle fibropapilloma tumors share genomic drivers and therapeutic vulnerabilities with human cancers. Duffy D.J. et al. Communications Biology. 2018; 1: 63

Increased Virulence of Bloodstream Over Peripheral Isolates of P. aeruginosa Identified Through Post-transcriptional Regulation of Virulence Factors. Hickey, C. et al. Frontiers in Cellular and Infection Microbiology. 2018; 8: 357

Acquisition of temporal HIF transcriptional activity using a secreted luciferase assay Cavadas, M.A.S, Taylor, C.T. & Cheong, A.. Methods in Molecular Biology. 2018; 1742: 37‐44

Characterisation of HRas local signal transduction networks using engineered site-specific exchange factors Herrero, A. et al. Small GTPases. 2017; 1‐13

Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels Campbell, J., Ryan, C.J. & Lord, C.J.. Methods in Molecular Biology. 2018;1711:83‐99

Integration of Omics Approaches and Systems Biology for Clinical Applications (Chapter 13. Introduction into the Concept of Systems Medicine) Vlahou, A. et al. John Wiley & Sons, Inc. DOI:10.1002/9781119183952

RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73. Papaspyropoulos, A. et al. Nature communications. 2018; 9(424)

ER and PR expression and survival after endometrial cancer Smith, D. et al. Gynecologic Oncology. 2018;148(2):258‐266

High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe. Roguev, A. et al. Cold Spring Harbor Protocols. 2018;2018(2):10.1101

Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast Roguev, A. et al. Cold Spring Harbor Protocols. 2018;2018(2):10.1101

Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization. Verlande, A. et al. EMBO reports. 2018;19(2):320‐336

FIGO consensus guidelines on placenta accreta spectrum disorders: Introduction Jauniaux, E. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 261-264

FIGO consensus guidelines on placenta accreta spectrum disorders: Prenatal diagnosis and screening Jauniaux, E. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 274-280

FIGO consensus guidelines on placenta accreta spectrum disorders: Nonconservative management Allen, L. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 281-290

FIGO consensus guidelines on placenta accreta spectrum disorders: Conservative management Sentilhes, L. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 291-298

FIGO consensus guidelines on placenta accreta spectrum disorders: Epidemiology Jauniaux, E. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 265-273

Transcriptionally inducible Pleckstrin homology-like domain, family A, member 1, attenuates ErbB receptor activity by inhibiting receptor oligomerization Magi, S. et al. Journal of Biological Chemistry. 2018;293(6):2206‐2218

The PHD1 oxygen sensor in health and disease Kennel, K.B. et al. The Journal of Physiology. 2018;596(17):3899‐3913

Identification of fungi in shotgun metagenomics datasets Donovan, P.D. et al. PLoS ONE. 2018; 13 (2)

Novel Intergenically Spliced Chimera, NFATC3-PLA2G15, Is Associated with Aggressive T-ALL Biology and Outcome. Bond, J. et al. Molecular Cancer Research. 2018; 16(3): 470-475

New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling Erickson, K.E. et al. Seminars in Cancer Biology. 2018; 54:162-173

The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche Adaptation Hughes, G.M. et al. Mol Biol Evol. 2018; 35(6):139-1406

BAG3 promotes tumour cell proliferation by regulating EGFR signal transduction pathways in triple negative breast cancer. Shields, S. et al. Oncotarget. 2018; 9(21):15673-15690

E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer. Bajrami, I. et al. Cancer discovery. 2018; 8(4): 498-515

Enhancing Understanding of the Visual Cycle by Applying CRISPR/Cas9 Gene Editing in Zebrafish Ward, R. et al. Frontiers Media. 2018; 6(37)

Early thymic precursor-like lymphomatous presentation of the ETV6-NCOA2 translocation. Bond, J. et al. British journal of haematology. 2018; 181(3): 392-394

Risk-adapted treatment of acute promyelocytic leukemia: results from International Consortium for Childhood APL Testi, A.M. et al. Blood. 2018; 132(4)

TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida Donovan, P.D. et al. PLoS Genetics . 2018; 14(5)

Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer. Brough, R. et al. Oncogene. 2018; 37:5701-5718

Polycomb repressive complex 2 haploinsufficiency identifies a high-risk subgroup of pediatric acute myeloid leukemia. Bond, J. et al. Leukemia. 2018; 32(8): 1878-1882

Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle. Johnston, D. et al. Theriogenology. 2018; 114: 301-307

Identification of a MYCN and Wnt-related VANGL2-ITLN1 fusion gene in neuroblastoma Duffy D.J. et al. Gene Reports. 2018; 12: 187-200

Outcome of haematopoietic stem cell transplantation in dyskeratosis congenita Fioredda, F. et al. British Journal of Haematology. 2018; 183(1): 110-118

Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness Holme, H. et al. Scientific Reports. 2018; 8(1)

ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation. Monypenny, J. et al. Cell reports. 2018; 24(3): 630-641

PHD3 Regulates p53 Protein Stability by Hydroxylating Proline 359. Rodriguez, J. et al. Cell reports. 2018; 24(5): 1316-1329

Hypoxia‐sensitive pathways in intestinal inflammation Brown, E. & Taylor, C.T.. The Journal of Physiology. 2018: 596(15): 2985–2989

MASTL overexpression promotes chromosome instability and metastasis in breast cancer. Rogers, S. et al. Oncogene. 2018; 37(33): 4518-4533

Nanoparticles Can Wrap Epithelial Cell Membranes and Relocate Them Across the Epithelial Cell Layer. Urbančič, I. et al. Nano letters. 2018; 18(8): 5294-5305

Systems level expression correlation of Ras GTPase regulators. Besray Unal, E. et al. Cell Communication and Signaling. 2018; 16(1): 46

Author Correction: Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness. Holme, H. et al. Scientific Reports volume . 2018; 8(1)

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Rukhlenko, O.S. et al. Cell systems. 2018; 7(2): 161-179

From oncogenic mutation to dynamic code. Kolch, W. & Kiel, C.. Science. 2018; 361(6405): 44-845

Gut adaptation after metabolic surgery and its influences on the brain, liver and cancer Sinclair, P., Brennan, D.J. & le Roux, C.W.. Nature Reviews Gastroenterology & Hepatology. 2018; 15(10): 606–624

Synthetic Lethality and Cancer - Penetrance as the Major Barrier Ryan, C.J., Bajrami, I. & Lord, C.J.. Trends Cancer. 2018; 4(10): 671-683

Systems biology: old news or new stimulus for biochemistry. Kolch, W., Fey, D. & Ryan, C.J.. Essays in biochemistry. 2018; 62(4): 483-486

Structure-based assessment and network analysis of targeting 14-3-3 proteins in prostate cancer. Root, A., Beizaei, A. & Ebhardt, H.A.. Molecular cancer. 2018; 17: 156

A two-drug combination simulation study for metastatic castrate resistant prostate cancer. Root, A. & Ebhardt, H.A.. The Prostate. 1196-1200

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Thomaseth, C. et al. Scientific reports. 2018; 8, 16217

VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants Radusky, L. et al. Front. Genet.. 2018; 9: 620

Quantitative Biology Theory, Computational Methods, and Models Munsky, B. et al. The MIT Press. ISBN: 9780262038089

Opportunities and Challenges of Whole-Cell and -Tissue Simulations of the Outer Retina in Health and Disease Luthert, P.J., Serrano, L. & Kiel, C.. Annual Review of Biomedical Data Science. 2018; 1: 131-152131-152

Association of Implementing a Multidisciplinary Team Approach in the Management of Morbidly Adherent Placenta With Maternal Morbidity and Mortality Bartels, H. et al. Obstetrics & Gynecology. 2018; 132(5): 1167–1176

Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis Santra, T. et al. Current Opinion in Systems Biology. 2018; 9: 11-21

Clustal Omega for making accurate alignments of many protein sequences Sievers, F. & Higgins, D.G.. Protein Science. 2018; 27(1): 135–145


Improving machine learning in early drug discovery. Bendtsen, C. et al. Annals of Mathematics and Artificial Intelligence. 2017; 81,155-166.

Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study. Ebhardt, H.A. et al. Journal of Cachexia, Sarcopenia and Muscle. 2017; 8(4): 567–582.

The histone variant H2A. Z promotes splicing of weak introns. Kelly, E. et al. Genes & Development. 2017; 1;31(7): 688-701

CancerGD: A Resource for Identifying and Interpreting Genetic Dependencies in Cancer. Bridgett, S. Cell Systems. 2017; 26;5(1): 82-86.e3

Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function. Sun, C. Stem Cells. 2017; 35(8): 1958–1972.

Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance. Duffy, D.J. et al Genome Medicine. 2017; 9: 15.

Lapatinib potentiates cytotoxicity of YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter. Radic-Sarikas, B. et al Scientific Reports. 2017; 7: 3091.

Hypoxia Reduces the Pathogenicity of Pseudomonas aeruginosa by Decreasing the Expression of Multiple Virulence Factors. Schaible, B. et al J Infect Dis. 2017; 1;215(9): 1459-1467

Protein multiple sequence alignment benchmarking through secondary structure prediction. Le, Q., Sievers, F. & Higgins, D.G. Bioinformatics. 2017; 1;33(9):1331-1337

Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models. Santra, T. et al PLOS ONE. 2017; 8;12(5):e0177058

Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention. Latosinska, A. et al Oncotarget. 2017; 19; 8(41): 69435–69455

A novel RNA sequencing data analysis method for cell line authentication. Fasterius, E. et al PLoS ONE. 2017; 13;12(2): e0171435

Vascular Endothelial Growth Factor (VEGF) Promotes Assembly of the p130Cas Interactome to Drive Endothelial Chemotactic Signalling and Angiogenesis. Evans, I.M. et al Mol Cell Proteomics. 2017; 16(2): 168-180.

Nambu bracket formulation of nonlinear biochemical reactions beyond mass action kinetics. Frank, T.D. Journal of Nonlinear Mathematical Physics. 2017; 19(1): 81-97.

Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models. Santra, T. et al PLOS one. 2017; 8;12(5): e0177058

A Bayesian non-parametric method for clustering high-dimensional binary data. Santra, T. Arxiv, 2017; 1603.02494

A Brain-Derived Neurotrophic Factor Mimetic Is Sufficient to Restore Cone Photoreceptor Visual Function in an Inherited Blindness Model. Daly, C. Scientific Reports. 2017; 12;7(1):11320

Performance of objective functions and optimisation procedures for parameter estimation in system biology models. Degasperi, A., Fey, D., Kholodenko, B.N. NPJ Systems Biology and Applications. 2017; 3: 20.

High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe. Roguev, A. et al Cold Spring Harbour Protocols. 2018:2018(2): 10

Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast. Roguev, A. et al Cold Spring Harbour Protocols. 2018; 2018(2):10

Hypoxia Inducible Factor (HIF) Hydroxylases as Regulators of Intestinal Epithelial Barrier Function. Manresa, M.C. & Taylor, C.T. Cell Mol GastroenterolHepato. 2017; 20;3(3):303-315

Determinants of hypoxia inducible factor (HIF) activity in the intestinal mucosa. Fagundes, R.R. & Taylor, C.T. J Appl Physiol. 2017; 1;123(5):1328-1334

The regulation of transcriptional repression in hypoxia. Cavadas, M.A.S., Cheong, A. & Taylor, C.T. Exp Cell Res. 2017; 15;356(2):173-181

Spatial regulation of ARAF controls the MST2-Hippo pathway. Rauch, J. & Kolch, W. Small GTPases. 2019; 10(4):243-248.

Personalized Computational Models as Biomarkers. Kolch, W. & Fey, D. Journal of Personalised Medicine. 2017; 7(3), 9.


FIH regulates cellular metabolism through hydroxylation of the deubiquitinase OTUB1. Scholz, C.C. et al. PLOS Biology. 2016 Jan 11;14(1):e1002347

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data. Bryan, K. et al. Journal of proteome research. 2016 Jun 3;15(6):2072-9.

Differential localization of A-Raf regulates MST2-mediated apoptosis during epithelial differentiation. Cell Death and Differentiation. Rauch, J. et al. 2016 Aug;23(8):1283-95.

Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF. Baljuls, A. et al. Cellular Signalling. 2016 Oct;28(10):1451-62

Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signalling Pathways. Rodriguez, J. et al. CELL Reports. 2016 Mar 22;14(11):2745-60.

Understanding complexity in the HIF signalling pathway using systems biology and mathematical modelling. Zsolt, F., Taylor, C.T. & Nguyen, L.K. Journal of Molecular Medicine. 2016 Apr;94(4):377-90

Wnt6 regulates epithelial cell differentiation and is dysregulated in renal fibrosis. Beaton, H., et al. American Journal of Physiology. 2016 Jul 1;311(1):F35-45

Hypercapnia Suppresses the HIF-dependent Adaptive Response to Hypoxia. Selfridge, A.C. et al. The Journal of Biological Chemistry. 2016 May 27;291(22):11800-8.

The role of HIF in immunity and inflammation. Cummins, E.P. et al. Molecular Aspects of Medicine. Feb-Mar 2016;47-48:24-34.

Crosstalk between toll-like receptors and hypoxia-dependent pathways in health and disease. Crifo, B. & Taylor, C.T. Journal of Investigative Medicine. 2016 Feb;64(2):369-75.

Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines. Campbell, J. et al. Cell Reports. 2016 Mar 15;14(10):2490-501.

Bistability in the Rac1, PAK, and RhoA Signalling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches. Byrne, K.M. et al. Cell Systems. 2016 Jan 27;2(1):38-48.

PP1 initiates the dephosphorylation of MASTL, triggering mitotic exit and bistability in human cells. Rogers, S. et al. Journal of Cell Science. 2016 Apr 1;129(7):1340-54.

Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis. Rinaldi, L. et al. Cell Stem Cell. 2016 Oct 6;19(4):491-501.

Integrating network reconstruction with mechanistic modelling to predict cancer therapies. Halasz, M. et al. Science Signalling. 2016 Nov 22;9(455):ra114.

Bayesian algorithm for detecting differentially expressed proteins and its application in breast cancer research. Santra, T., Delatola, E.A. Scientific Reports. 2016 Jul 22;6:30159.

BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research. Iglesius Martinez, L.F., Kolch W., Santra, T. Scientific Reports. 2016 Nov 23;6:37140.

Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy. Zhang, R. et al. ACS Nano. 2017 Jan 24;11(1):249-257.

HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status. Weitsman, G. et al. Oncotarget. 2016 Aug 9;7(32):51012-51026.

Rac1 and RhoA: networks, loops and bistability. Nguyen, L.K., Kholodenko, B.N. & von Kriegsheim, A. Small GTPases. 2018 Jul 4;9(4):316-321.

Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data. Frank, T.D. et al. Mathematical Medicine and Biology. 2017 Jun 1;34(2):177-191

ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A. Williamson, C.T. et al. Nature Communications. 2016 Dec 13;7:13837.

Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF. Baljuls, A. et al. Cellular Signalling. 2016 Oct;28(10):1451-62.

Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease. Stanley, E. et al. BMC Bioinformatics. 2016 Dec 6;17(1):496.

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. Sánchez-Sanz, G. et al. PLoS Comput Biol. 2016 Oct 7;12(10):e1005051.

REST is a hypoxia-responsive transcriptional repressor. Cavadas, M.A.S. et al. Scientific Reports. 2016 Aug 17;6:31355.

Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signalling Pathways. Rodriguez, J. et al. Cell Reports. 2016 Mar 22;14(11):2745-60.

Proteome-wide association studies identify biochemical modules associated with a wing size phenotype in Drosophila melanogaster. Okada H. et al. Nature Communications. 2016 Sep 1;7:12649.

Autophosphorylation on S614 inhibits the activity and the transforming potential of BRAF. Dernayka, L. et al. Cellular Signalling. 2016 Sep;28(9):1432-9.

Mesenchymal Stromal Cells Protect Endothelial Cells from Cytotoxic T Lymphocyte-Induced Lysis. Cahill, E.F. et al. Scandinavian Journal of Immunology. 2016 Sep;84(3):158-64.

Wnt signalling is a bi-directional vulnerability of cancer cells. Duffy, D.J. et al. Oncotarget. 2016 Sep 13;7(37):60310-60331.

MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance. Rauch, N. et al. Current Opinion in Structural Biology. 2016 Dec;41:151-158.

The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells. Fey, D. et al. Seminars in Cell and Developmental Biology. 2016 Oct;58:96-107.

The MST/Hippo pathway and cell death: A non-canonical affair. Fallahi, E., O'Driscoll, N.A. & Matallanas, D. Genes. 2016 Jun 17;7(6):28.

Hypoxia-dependent regulation of inflammatory pathways in immune cells. Taylor, C.T. et al. Journal of Clinical Investigation. 2016 Oct 3;126(10):3716-3724

VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis. Evans, I.M. et al, Molecular and Cellular Proteomics. 2017 Feb;16(2):168-180.


Regulation of the MAPK pathway by raf kinase inhibitory protein. Vandamme, D. et al. Critical Reviews in Oncogenesis, 2014;19(6):405-15.

Signalling mechanisms regulating phenotypic changes in breast cancer cells. Volinsky, N. et al. Biosci Rep,. 2015 Mar 18;35(2):e00178.

Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation. Milewska, M. et al. PLoS ONE, 2015 Jun 12;10(6):e0129859.

Competing to coordinate cell fate decisions: the MST2-Raf-1 signalling device. Nguyen, L.K. et al. Cell Cycle. 2015;14(2):189-99.

Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK. Kilinc, D. et al. Advanced healthcare materials. 2015 Feb 18;4(3):395-404.

Advances in dynamic modelling of colorectal cancer signalling-network regions, a path toward targeted therapies. Tortolina, L. et al. Oncotarget. 2015 Mar 10;6(7):5041-58.

Network-based identification of feedback modules that control RhoA activity and cell migration. Kim, T.H. et al. Journal of Molecular Cell Biology. 2015 Jun;7(3):242-52.

ROCK activity and the Gβγ complex mediate chemotactic migration of mouse bone marrow-derived stromal cells. Ryan, C.M. et al. Stem Cell Research and Therapy. 2015 Jul 24;6:136.

The dynamic control of signal transduction networks in cancer cells. Kolch, W. et al. Nature Reviews Cancer. 2015 Sep;15(9):515-27.

Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification. Schwarzl, T. et al. Molecular Biology. 2015 Oct 23;427(21):3368-74.

Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses. Varusai, T.M. et al. Molecular BioSystems. 2015 Oct;11(10):2750-62.

In vitro study of the interaction of heregulin-functionalized magnetic-optical nanorods with MCF7 and MDA-MB-231 cells. Lesniak, A. ety al. Faraday Discussions. 2014;175:189-201.

CrosstaL.K. between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function Cell Host Microbe. Kelly, C.J. et al. Cell Host Microbe, 2015 May 13;17(5):662-71.

Silence on the relevant literature and errors in implementation. Bastiaens, P. et al. Nature Biotechnology. 2015 Apr;33(4):336-9.

Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast. Patrick, K.L. et al. PLOS Genetics. 2015 Mar 31;11(3):e1005074.

Species differential regulation of COX2 can be described by an NFkB-dependent logic AND gate Cellular and Molecular Life Sciences. Nguyen, L.K. et al. 2015 Jun;72(12):2431-43.

Paricalcitol protects against TGF1-induced fibrotic responses in hypoxia and stabilises HIF in renal epithelia. Nolan, K.A. et al. Exp Cell Res. 2015 Jan 15;330(2):371-81

Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity. Nagashima, T. et al. The FEBS Journal. 2015 Feb;282(4):613-29.

The impact of hypoxia on bacterial infection. Schaffer, K. & Taylor, C.T. FEBS Journal. 2015 Jun;282(12):2260-6.

A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network. Nguyen, L.K. et al. Journal of Cell Science. 2015 Jan 15;128(2):422.

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks. Nguyen, L.K. et al. Scientific Reports. 2015 Jul 29;5:12569.

Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects. Kholodenko, B.N. Cell Reports. 2015 Sep 22;12(11):1939-49.

Feedback regulation in cell signalling: Lessons for cancer therapeutics. Nguyen, L.K. & Kholodenko. B.N. Seminars in Cell and Developmental Biology. 2016 Feb;50:85-94.

MST2-RASSF protein-protein interactions through SARAH domains. Sanchez-Sanz, G. et al. Briefings in bioinformatics. 2016 Jul;17(4):593-602


Advances in dynamic modelling of colorectal cancer signalling-network regions, a path toward targeted therapies. Tortolina, L. et al. OncoTarget. 2015 Mar 10;6(7):5041-58.

p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas. Dreidax, D. et al. Human Molecular Genetics. 2014 Dec 20;23(25):6826-37.

Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure. Guerriero, M.L., Ozgur, A.E. & van Ooijen, G. Frontiers in Plant Science. 2014 Oct 21;5:564.

Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK. Kilinc, D. et al. Advanced Healthcare Materials. 2015 Feb 18;4(3):395-404.

Integrated signalling pathway and gene expression regulatory model to dissect dynamics of Escherichia coli challenged mammary epithelial cells. den Breems, N., Nguyen, L.K. & Kulasiri D. BioSystems. 2014 Dec;126:27-40.

Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing. Nguyen, L.K. et al. IET Systems Biology. 2014 Dec;8(6):282-92.

HEATR2 Plays a Conserved Role in Assembly of the Ciliary Motile Apparatus. Diggle, C.P. et al. PloS Genet. 2014 Sep 18;10(9):e1004577.

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses. Dobrzyński, M. et al. J. R. Soc. Interface. 2014 Sep 6;11(98):20140383.

One Hippo and many masters: differential regulation of the Hippo pathway in cancer. Romano, D. et al. Biochem Soc Trans. 2014 Aug;42(4):816-21.

Robustness and Evolvability of the Human Signalling Network. Junil, K., et al. PLOS Computational Biology. 2014 Jul 31;10(7):e1003763.

GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signalling. Duffy, D.J. et al. Mol Cancer Ther. 2014 Feb;13(2):454-67.

Primary cilium-associated genes mediate bone marrow stromal cell response to hypoxia. Brown, J.A.L. et al. Stem Cell Research. 2014 Sep;13(2):284-99.

Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling. Romano, D. et al. Nature Cell Biology. 2014 Jul;16(7):673-84.

Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells. Jiwaji, M. et al. PLoS ONE. 2014 Jun 13;9(6):e99458.

Interplay of DNA damage and cell cycle signalling at the level of human replication protein A DNA Repair. Borgstahl, G.E.O. et al. 2014 Sep;21:12-23.

HGF Induces Epithelial-to-Mesenchymal Transition by Modulating the Mammalian Hippo/MST2 and ISG15 Pathways. Farrell, J. et al. Journal of Proteome Research. 2014 Jun 6;13(6):2874-86.

Illuzzi, G. et al. PARG is dispensable for recovery from transient replicative stress but required to prevent detrimental accumulation of poly (ADP-ribose) upon prolonged replicative stress Nucleic Acids Research. 2014 Jul; 42(12):7776-92.

Investigation of the possible functions of PACAP in human trophoblast cells. Horvath, G. et al. J Mol Neurosci. 2014 Nov;54(3):320-30.

A Bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. Santra, T. Frontiers in Bioengineering and Biotechnology. 2014 May 20;2:13

Interplay of DNA damage and cell cycle signalling at the level of human replication protein A DNA Repair. Borgstahl, G.E.O. et al. 2014 Sep;21:12-23.

Human adipocytes are highly sensitive to intermittent hypoxia induced NF-kappaB activity and subsequent inflammatory gene expression. Taylor, C.T. et al. Biochemical and Biophysical Research Communications. 2014 May 16;447(4):660-5.

Mig-6 participates in the regulation of cell senescence and retinoblastoma protein phosphorylation. Milewska, M. & Kolch, W. Cellular Signalling. 2014 Sep;26(9):1870-7.

On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction. Turriziani, B. et al. Proteomics Biology. 2014 Apr 16;3(2):320-32.

The APC network regulates the removal of mutated cells from colonic crypts. Song, J.H. et al. Cell Reports. 2014 Apr 10;7(1):94-103.

Basic fibroblast growth factor modifies the hypoxic response of human bone marrow stromal cells by ERK-mediated enhancement of HIF-1 activity. Fábián, Z. et al. Stem Cell Research.

Splicing factor hnRNP A2 activates the Ras-MAPK-ERK pathway by controlling A-Raf splicing in hepatocellular carcinoma development RNA. Shilo, S. et al. 2014 Apr; 20(4): 505–515.

Navigating the Multilayered Organization of Eukaryotic Signalling: A New Trend in Data Integration. Santra, T., Kolch, W. & Kholodenko, B.N. PLOS Computational Biology. 2014 Feb 13;10(2):e1003385.

Evaluating Strategies to Normalise Biological Replicates of Western Blot Data. Degasperi, A. et al. PLOS One. 2014 Jan 27;9(1):e87293.

Polyubiquitin chain assembly and organisation determine the dynamics of protein activation and degradation. Nguyen, L.N. et al. Frontiers in Physiology. 2014 Jan 24;5:4.

DAISY: picking synthetic lethals from cancer genomes. Ryan, C.J., Lord, C.J. & Ashworth A. Cancer Cell. 2014 Sep 8;26(3):306-308

Editorial: A PHD in macrophage survival J Leukoc Biol. Taylor, C.T. & Scholz, C.C. 2014 Sep;96(3):359-61.

Systems biology-embedded target validation: improving efficacy in drug discovery. Vandamme, D. et al. Wiley Interdiscip Rev Syst Biol Med. Jan-Feb 2014;6(1):1-11.


Allogeneic murine mesenchymal stem cells: migration to inflamed joints in vivo and amelioration of collagen induced arthritis when transduced to express CTLA4Ig. Sullivan, C. et al. Stem cells dev. 2013 Dec 15;22(24):3203-13.

Regulation of IL-1-induced NF-B by hydroxylases links key hypoxic and inflammatory signalling pathways. Scholz, C.C. et al. Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18490-5.

Tyr728 in the Kinase Domain of the Murine Kinase Suppressor of RAS 1 regulates Binding and Activation of the Mitogen-activated Protein Kinase Kinase. Sibilski, C. et al. J Biol Chem. 2013 Dec 6;288(49):35237-52.

Extracellular signal-regulated kinase regulates RhoA activation and tumor cell plasticity by inhibiting guanine exchange factor H1 activity. von Thun, A. et al. Mol Cell Biol. 2013 Nov;33(22):4526-37.

Cell cycle-dependent formation of Cdc45-Claspin complexes in human cells are compromised by UV-mediated DNA damage. Broderick, R. et al. FEBS Journal. 2013 Oct;280(19):4888-902.

RCP-driven α5β1 recycling suppresses Rac and promotes RhoA activity via the RacGAP1-IQGAP1 complex. Jacquemet, G. et al. J Cell Biol. 2013 Sep 16;202(6):917-35.

When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Nguyen, L.K., Kolch, W. & Kholodenko, B.N. Cell Communication and Signalling. 2013 Jul 31;11:52.

Control of the G-protein Cascade Dynamics by GDP Dissociation Inhibitors. Nikonova, E. et al. Molecular Biosystems. 2013 Oct;9(10):2454-62.

Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2. Reiterer, V. et al. Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):E2934-43.

Temporal regulation of EGF signalling networks by the scaffold protein Shc1. Zheng, Y. et al. Nature. 2013 Jul 11;499(7457):166-71.

Increased baseline proinflammatory cytokine production in chronic hepatitis C patients with rapid virological response to peginterferon plus ribavirin. Par, al. PLOS One. 2013 Jul 9;8(7):e67770.

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology. Santra, T. et al. BMC Systems Biology. 2013 Jul 6;7:57.

The Effect of Temperature Elevation on Cryopreserved Mesenchymal. Norkus, M. et al. Stem Cells Cryo Letters. Jul-Aug 2013;34(4):349-59.

Progesterone-Induced Blocking Factor differentially regulates trophoblast and tumour invasion by altering matrix metalloproteinase activity. Halasz, M. et al. Cell. Mol. Life Sci. 2013 Dec;70(23):4617-30.

Hippocampal contribution to vector model hypothesis during cue-dependent navigation. Diviney, M., Fey, D. & Commins, S. Learn Mem. 2013 Jun 17;20(7):367-78.

Growth differentiation factor-5 enhances in vitro mesenchymal stromal cell chondrogenesis and hypertrophy. Coleman, C.M. et al. Stem Cells Dev. 2013 Jul 1;22(13):1968-76.

Hypoxia-inducible factor (HIF) network: insights from mathematical models. Cavadas, M.A.S., Nguyen, L.N., & Cheong, A. Cell Communication and signalling. 2013 Jun 10;11(1):42. #

A Process Algebra Framework for Multi-Scale Modelling of Biological Systems. Degasperi, A. & Calder, M. Theoretical Computer Science. 2013 June;488(3):15-45.

Impact of Mesenchymal Stem Cell secreted PAI-1 on colon cancer cell migration and proliferation. Hogan, N.M. et al. Biochemical and Biophysical Research Communication. 2013 Jun 14;435(4):574-9.

Effects of intratracheal mesenchymal stromal cell therapy during recovery and resolution after ventilator-induced lung injury. Curley, G.F. et al. Anesthesiology. 2013 Apr;118(4):924-32.

Phosphodiesterase-8A binds to and regulates Raf-1 kinase. Brown, K.M. et al Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):E1533-42.

The differential effects of wild-type and mutated K-Ras on MST2 signalling are determined by K-Ras activation kinetics. Romano, D. et al. Mol Cell Biol. 2013 May;33(9):1859-68.

Liposomal surface coatings of metal stents for efficient non-viral gene delivery to the injured vasculature. Ganly, S. et al. Journal of Controlled Release. 2013 Apr 28;167(2):109-19.

A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network. Nguyen, L.K. et al. J Cell Sci. 2013 Mar 15;126(Pt 6):1454-63.

Involvement of Lyn and the Atypical Kinase SgK269/PEAK1 in a Basal Breast Cancer Signalling Pathway. David, R. et al. Cancer Research. 2013 Mar 15;73(6):1969-80.

Thermoresponsive substrates used for the expansion of human mesenchymal stem cells and the preservation of immunophenotype. Nash, M.E. et al. Stem Cell Rev. 2013 Apr;9(2):148-57.

Raf kinase inhibitor protein expression combined with peritoneal involvement and lymphovascular invasion predicts prognosis in Dukes' B colorectal cancer patients. Doyle, B. et al. Histopathology. 2013 Feb;62(3):505-10.

A limit cycle oscillator model for cycling mood variations of bipolar disorder patients derived from cellular biochemical reaction equations. Frank, T.D. Communications in Nonlinear Science and Numerical Simulation. 2013 Aug;18(8):2107-2119

Systems medicine: opportunities and challenges for systems biology approaches. Kolch, W. & Kholodenko, B.N. FEBS journal. 2013 Dec;280(23):5937.

Mesenchymal stem cells in joint disease and repair. Barry, F. & Murphy, M. Nature Reviews Rheumatology. 2013 Oct;9(10):584-94.

Carbon dioxide-sensing in organisms and its implications for human disease. Cummins, E.P. et al. Cell Mol Life Sci. 2014 Mar;71(5):831-45.

Organizing a PhD symposium: an inside view. Schröder, M.S. et al. EMBO reports. 2013 Oct;14(10):856-60.

Complexity of receptor tyrosine kinase signal processing. Volinsky, N., Kholodenko, B.N. Cold Spring Harbor Perspectives in Biology. 2013 Aug 1;5(8):a009043.

Systems medicine: helping us understand the complexity of disease. Vandamme, D. et al. QJM. 2013 Oct;106(10):891-5.

Targeting the HIF pathway in inflammation and immunity. Scholz, C.C. & Taylor, C.T. Curr Opin Pharmacol. 2013 Aug;13(4):646-53.

Hydroxylase-dependent regulation of the NF-κB pathway. Scholz, C.C. & Taylor, C.T. Biol Chem. 2013 Apr;394(4):479-93.

Big Signals from Small Particles: Regulation of Cell Signalling Pathways by Nanoparticles. Rauch, J. et al. Chemical Reviews. 2013 May 8;113(5):3391-406

The role of progesterone in implantation and trophoblast invasion. Halasz, M. & Szekeres-Bartho, J. J Reprod Immunol. 2013 Mar;97(1):43-50.

Monitoring of Transcriptional Dynamics of HIF and NF-κB. Cavadas, M. & Cheong, A. Methods Mol. Biol. 2014;1098:97-105.

Encyclopedia of Signalling Molecules: A-Raf kinase. Rauch, J. & Kolch, W. Encyclopedia of Signalling Molecules. ISBN:978-1-4614-6438-9


Physiological Temperature Has a Crucial Role in Amyloid Beta in the Absence and Presence of Hydrophobic and Hydrophilic Nanoparticles. Ghavami, M. et al. ACS Chem. Neurosci. 2013 Mar 20;4(3):375-8.

Unique Reporter-Based Sensor Platforms to Monitor Signalling in Cells. Jiwaji, M. et al. PLOS One. 2012;7(11):e50521.

High levels of ephrinB2 over-expression increases the osteogenic differentiation of human mesenchymal stem cells and promotes enhanced cell mediated mineralisation in a polyethyleneimine-ephrinB2 gene-activated matrix. Tierney, E.G. et al. Journal of Controlled Release. 2013 Feb 10;165(3):173-82.

Mitochondrial reactive oxygen species enhance AMPK activation in the endothelium of patients with coronary artery disease and diabetes. Mackenzie, R.M. et al. Clinical Science. 2013 Mar;124(6):403-11.

Cell Type-Specific Activation of AKT and ERK Signalling Pathways by Small Negatively-Charged Magnetic Nanoparticles. Rauch, J., Kolch, W. & Mahmoudi, M. Sci. Rep. 2012;2:868.

Doxorubicin induces the DNA damage response in cultured human mesenchymal stem cells. Cruet-Hennequart, S. et al. Int J Hematol. 2012 Nov;96(5):649-56.

Predictors of quality of life gains among people with type 1 diabetes participating in the Dose Adjustment for Normal Eating (DAFNE) structured education programme. Byrne, M. et al. Diabetes Res Clin Pract. 2012 Nov;98(2):243-8.

Crosstalk and signalling switches in mitogen-activated protein kinase cascades. Fey, D. et al. Frontiers in Physiology. 2012 Sep 18;3:355.

Mammalian Protein Expression Noise: Scaling Principles and the Implications for Knockdown Experiments. Birtwistle, M.R. et al. Mol. BioSyst. 2012 Nov;8(11):3068-76.

Isolation and Phenotypic Characterisation of Stem Cells from late Stage Osteoarthritic Mesenchymal Tissues. Labusca, L. et al. Curr Stem Cell Res Ther. 2012 Sep;7(5):319-28.

Imatinib-dependent tyrosine phosphorylation profiling of Bcr-Abl-positive chronic myeloid leukemia cells. Preisinger, C. et al. Leukemia. 2013 Mar;27(3):743-6.

Emergence of bimodal cell population responses from the interplay between analog single-cell signalling and protein expression noise. Birtwistle, M.R. et al. BMC Syst Biol. 2012 Aug 24;6:109.

Segregation of Replicative DNA Polymerases during S Phase: DNA Polymerase epsilon but not DNA Polymerases alpha/delta, are associated with lamins throughout the S phase in human cells. Vaara, M. et al. J Biol Chem. 2012 Sep 28;287(40):33327-38.

Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity. Tondeleir, D. et al. Molecular & Cellular Proteomics. 2012 Aug;11(8):255-71.

The electrical stimulation of carbon nanotubes to provide a cardiomimetic cue to MSCs. Mooney, E. et al. Biomaterials. 2012 Sep;33(26):6132-9.

A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction. Watterson, S. et al. Biochimie. 2013 Mar;95(3):613-21.

Establishment and initial characterization of SOX2-overexpressing NT2/D1 cell clones. Drakulic, D., Krstic, A. & Stevanovic, M. Genetics and Molecular Research. 2012 May 15;11(2):1385-400.

Kinetics of thermally induced heat shock protein 27 and 70 expression by bone marrow-derived mesenchymal stem cells. Moloney, T.C. et al. Protein Sci. 2012 Jun;21(6):904-9.

On the application of active learning and gaussian processes in postcryopreservation cell membrane integrity experiments. Norkus, M. et al. IEEE/ACM Trans Comput Biol Bioinform. May-Jun 2012;9(3):846-56.

Development of a thermoresponsive chitosan gel combined with human mesenchymal stem cells and desferrioxamine as a multimodal pro-angiogenic therapeutic for the treatment of critical limb ischaemia. Hastings, C.L. et al. J Control Release. 2012 Jul 10;161(1):73-80.

The role of modern imaging techniques in the diagnosis of malposition of the branch pulmonary arteries and possible association with microdeletion 22q11.2. Cuturilo, G. et al. Cardiology in the Young. 2013 Apr;23(2):181-8.

Hypercapnia induces cleavage and nuclear localization of Rel B giving insight into CO2 sensing and signalling. Oliver, K.M. et al. J Biol Chem. 2012 Apr 20;287(17):14004-11.

Cell Cycle-Dependent Mobility of Cdc45 Determined in vivo by Fluorescence Correlation Spectroscopy. Broderick, R. et al. PLoS One. 2012 April; 7(4): e35537.

Versatility of cooperative transcriptional activation: a thermodynamical modelling analysis for greater-than-additive and less-than-additive effect. Frank, T.D., Carmody, A.M. & Kholodenko, B.N. PLoS One. 2012;7(4):e34439.

Catching transcriptional regulation by thermostatistical modelling. Frank, T.D. et al. Phys. Biol. 2012 Aug;9(4):045007.

Glucose reintroduction triggers the activation of Nrf2 during experimental ischemia reperfusion. Crean, D. et al. Mol Cell Biochem. 2012 Jul;366(1-2):231-8.

Regulation of oscillation dynamics in biochemical systems with dual negative feedback loops. Nguyen, L.K. J R Soc Interface. 2012 Aug 7;9(73):1998-2010.

Oscillatory nonequilibrium Nambu systems: the canonical-dissipative Yamaleev oscillator. Mongkolsakulvong, S., Chaikan, P. & Frank, T.D. European Physical Journal B. 2012 March; 85(90)

Hypercapnia induces cleavage and nuclear localization of RELB giving insight into CO2 sensing and signalling. Oliver, K.M. et al. J. Biol. Chem. 2012 Apr 20;287(17):14004-11.

Frequent loss of RAF kinase inhibitor protein expression in acute myeloid leukemia. Zebisch, A. et al. Leukemia. 2012 Aug;26(8):1842-9.

PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity. Tibarewal P. et al. Sci Signal. 2012 Feb 28;5(213):ra18.

ERK2 drives tumour cell migration in three-dimensional microenvironments by suppressing expression of Rab17 and liprin-β2. von Thun, A. et al. J Cell Sci. 2012 Mar 15;125(Pt 6):1465-77.

Pre-treatment of Endothelial Progenitor Cells with Osteopontin Enhances Cell Therapy for Peripheral Vascular Disease. Vaughan, E.E. et al. Cell Transplant. 2012;21(6):1095-107.

Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance. Aksamitiene, E., Kiyatkin, A. & Kholodenko, B.N. Biochemical Society Transactions. 2012 Feb;40(1):139-46.

Symmetry breaking analysis of prism adaptation's latent aftereffect. Frank, T.D., Blau, J.J.C. & Turvey, M.T. Cognitive Science. May-Jun 2012;36(4):674-97.

Gremlin Plays a Key Role in the Pathogenesis of Pulmonary Hypertension. Cahill, E. et al. Circulation. 2012 Feb 21;125(7):920-30.

Osteogenic differentiation of mesenchymal stem cells is regulated by osteocyte and osteoblast cells in a simplified bone niche. Birmingham, E. et al. Eur Cell Mater. 2012 Jan 12;23:13-27.

The topology design principles that determine the spatiotemporal dynamics of G-protein cascades. Tsyganov, M.A., Kolch, W. & Kholodenko, B.N. Mol Biosyst. 2012 Mar;8(3):730-43.

Nambu bracket formulation of nonlinear biochemical reactions beyond mass action kinetics. Frank, T.D. Journal of Nonlinear Mathematical Physics. 2012 Jan; 19(1):81-97.

It takes two to tango: signalling by dimeric Raf kinases. Baljuls, A., Kholodenko, B.N. & Kolch, W. Molecular Biosystems. 2013 Apr 5;9(4):551-8.

Enhancing the MSC Therapeutic Response: Cell Localization and Support for Cartilage Repair. Bulman, S. et al. Tissue Eng Part B Rev. 2013 Feb;19(1):58-68.

Strategies for improved targeting of therapeutic cells: implications for tissue repair. Ansboro S. et al. Eur Cell Mater. 2012 Apr 21;23:310-8; discussion 318-9.

Computational approaches for analyzing information flow in biological networks. Kholodenko, B.N., Yaffe, M.B. & Kolch, W. Sci. Signal. 2012 Apr 17;5(220):re1.

Instructive reconstruction: A new role for apoptosis in pattern formation. Duffy, D.J. BioEssays. 2012 Jul;34(7):561-4.

Signalling by protein phosphatases and drug development: a systems-centered view. Nguyen, L.K. et al. FEBS J. 2013 Jan;280(2):751-65.

Bimodal Protein Distributions in Heterogeneous Oscillating Systems. DobrzyDski, M. et al. Computational Methods in Systems Biology 2012; 17-28.

Understanding cell fate decisions by identifying crucial system dynamics. Fey, D. et al. New Challenges for Cancer Systems Biomedicine. SIMAI Springer Series. 2012; 83-104


Stimulation of BKV DNA replication by NFI-family transcription factor Liang, B. et al. J Virol. 2012 Mar;86(6):3264-75.

Mutant K-Ras Activation of the Proapoptotic MST2 Pathway Is Mutant K-Ras Activation of the Proapoptotic MST2 Pathway Is Antagonized by Wild-Type K-Ras Matallanas, D. et al. Mol Cell. 2011 Dec 23;44(6):893-906.

Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System. Nguyen, L.K. et al. PLoS Comput Biol. 2011 Dec;7(12):e1002317.

A heat shock protein and Wnt signalling crosstalk during axial patterning and stem cell proliferation. Duffy, D.J. et al. Developmental Biology. 2012 Feb 15;362(2):271-81.

Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modelling. Birtwistle, M.R. et al. PLoS One. 2011;6(11):e27823.

NFκB and HIF display synergistic behaviour during hypoxic inflammation. Bruning, U. et al. Cell Mol Life Sci. 2012 Apr;69(8):1319-29.

Eukaryotic translation initiation factor 3, subunit a, regulates the extracellular signal-regulated kinase pathway. Xu, T.R. et al. Mol Cell Biol. 2012 Jan;32(1):88-95.

Modification of Histones by Sugar β-N-Acetylglucosamine (GlcNAc) Occurs on Multiple Residues, Including Histone H3 Serine 10, and Is Cell Cycle-regulated. Zhang, S. et al. J Biol Chem. 2011 Oct 28; 286(43): 37483–37495.

Mesenchymal stem cell inhibition of T-helper 17 differentiation is triggered by cell-cell contact and mediated by prostaglandin E2 via the EP4 receptor. Duffy, M.M. et al. Eur J Immunology. 2011 Oct;41(10):2840-51.

A 19S proteasomal subunit cooperates with an ERK MAPK-regulated degron to regulate accumulation of Fra-1 in tumour cells. Pakay, J.L. et al. Oncogene. 2012 Apr 5;31(14):1817-24.

MicroRNA-155 Promotes Resolution of Hypoxia-Inducible Factor 1α Activity during Prolonged Hypoxia. Bruning, U. et al. Mol Cell Biol. 2011 Oct;31(19):4087-96.

Overexpression of pulmonary extracellular superoxide dismutase attenuates endotoxin-induced acute lung injury. Hassett, P. et al. Intensive Care Med. 2011 Oct;37(10):1680-7.

In vitro Characterization of an Electroactive Carbon-Nanotube-Based Nanofiber Scaffold for Tissue Engineering. Mackle, J.N. et al. Macromol Biosc. 2011 Sep 9;11(9):1272-82.

Biology using engineering tools: The negative feedback amplifier. Birtwistle, M.R. et al. Cell Cycle. 2011 Jul 1;10(13):2069-76.

Gene-eluting stents: non-viral, liposome-based gene delivery of eNOS to the blood vessel wall in vivo results in enhanced endothelialization but does not reduce restenosis in a hypercholesterolemic model. Sharif, F, et al. Gene Ther. 2012 Mar;19(3):321-8.

Stochastic processes and mean field systems defined by nonlinear Markov chains: an illustration for a model of evolutionary population dynamics. Frank, T D. Brazilian Journal of Physics. 2011; 41;129.

Mesenchymal Stem Cell (MSC) mediated delivery of the Sodium Iodide Symporter (NIS) supports radionuclide imaging and treatment of breast cancer. Dwyer, R.M. et al. Stem Cells. 2011 Jul;29(7):1149-57.

Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signalling pathway in breast cancer cells. Aksamitiene, E. et al. Cell Signal. 2011 Nov;23(11):1794-805.

Behavioral dynamics of the affordance "graspable". Lopresti-Goodman, S.M., Turvey, M.T. & Frank, T.D. Attention, Perception, and Psychophysics. 2011 Aug;73(6):1948-65.

Unifying mass-action kinetics and Newtonian mechanics by means of Nambu brackets. Frank, T.D. Journal of Biological Physics. 2011 Sep;37(4):375-85.

Rate of entropy production as a physical selection principle for mode-mode transitions in non-equilibrium systems: with an application to a non-algorithmic dynamic message buffer. Frank, T.D. European Journal of Scientific Research. 2011

Developing cell-specific antibodies to endothelial progenitor cells using avian immune phage display technology. Bowes, T. et al. Journal of biomolecular screening. 2011 Aug;16(7):744-54.

Stem Cell Research & Therapy marks its first anniversary. Locke, P., O'Brien, T. & Tuan, R.S. Editorial Stem Cell Research & Therapy. 2011; 2(3): 22.

Inhibition of human BK polyomavirus replication by small non-coding RNAs. Tikhanovich, I. et al. J Virol. 2011 June; 85(14):6930-6940.

c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathway. Rauch, J. et al. Cancer Research. 2011 Jul 1;71(13):4664-74.

Lentiviral Vector Mediated modification of Mesenchymal Stem Cells & enhanced survival in an in vitro mode of Ischaemia. McGinley, L. et al. Stem Cell Research & Therapy. 2011 Mar 7;2(2):12.

Differential miRNA expression in omental adipose tissue and in the circulation of obese patients identifies novel metabolic biomarkers. Heneghan, H.M. et al. J Clin Endocrinol Metab. 2011 May;96(5):E846-50.

Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system. Nguyen, L.N. & Kulasiri, D. IET Syst Biol. 2011 Mar;5(2):145-56.

Mesenchymal Chondroprogenitor Cell Origin, Isolation and Therapeutic Potential. O'Sullivan, J. et al. Stem Cell Research & Therapy. 2011 Feb 18;2(1):8.

Raf Kinase Inhibitor Protein RKIP enhances signalling by Glycogen Synthase Kinase-3 b. Al-Mulla, F. et al. Cancer Res. 2011 Feb 15;71(4):1334-43.

Small ubiquitin-related modifier (SUMO)-1 promotes glycolysis in hypoxia. Agbor, T.A. et al. Biol Chem. 2011 Feb 11;286(6):4718-26.

Spatial regulation of RhoA activity during pancreatic cancer cell invasion driven by mutant p53. Timpson, P. et al. Cancer Research. 2011 Feb 1;71(3):747-57.

Functionalized scaffold mediated interleukin-10 gene delivery significantly improves survival rates of stem cells in vivo. Holladay, C. et al. Mol Ther. 2011 May;19(5):969-78.

Virial theorem and non-equilibrium canonical-dissipative distributions characterizing Parkinson tremor. Frank, T.D. International Journal of Modern Physics. 2011; 25(2): 243-253

A Temporal Gene Delivery System based on Fibrin Microshpheres. Kulkarni, M.M. et al. Mol Pharm. 2011 Apr 4;8(2):439-46.

The secret life of kinases: functions beyond catalysis. Rauch, J. et al. Cell Commun Signal. 2011 Oct 28;9(1):23.

Raf family kinases: old dogs have learned new tricks. Matallanas, D. et al. Genes & Cancer. 2011 Mar;2(3):232-60.

Stem Cell Therapy for Cardiac Disease. Flynn, A. & O'Brien, T. Expert Opinion on Biological Therapy. 2011 Feb;11(2):177-87.

Regulation of gene expression by carbon dioxide. Taylor, C.T., & Cummins, E.P. J Physiol. 2011 Feb 15;589(Pt 4):797-803.

Understanding movement during performance: a recurrence quantization approach. Demos, A.P., Frank, T.D. & Chaffin, R. International Symposium on Performance Science. 2011 Jan;

An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells. Santra, T, Kholodenko B.N. & Kolch, W. Advances in Systems Biology, Advances in Experimental Medicine and Biology. 2012;736:59-80.

Evolution of Bet-Hedging Mechanisms in Cell Cycle and Embryo Development Stimulated by Weak Linkage of Stochastic Processes. Dobrzyński, M. et al. Cell Cycle in Development. 2011;53:11-30.


The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells.. Meesbah, J. et al. BMC Molecular Biology. 2010 Dec 31;11:103.

The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier.. Oliver, E. et al. Science Signalling. 2010 Dec 21;3(153):ra90.

Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers.. Dakna, M. et al. BMC Bioinformatics. 2010 Dec 10;11:594.

Nutrient exposure of chemotactic organisms in small scale turbulent flows.. Muñoz-García, J., Neufeld, Z. & Torney, C. New Journal of Physics. 2010 October; 12

Lentiviral vector-mediated knockdown of the neuroglycan 2proteoglycan or expression of neurotrophin-3 promotes neurite outgrowth in a cell culture model of the glial scar.. Donnelly, E.M. et al. Journal of Gene Medicine. 2010 Nov;12(11):863-72.

Mesenchymal Stem Cells Overexpressing Ephrin-B2 Rapidly Adopt an Early Endothelial Phenotype with Simultaneous Reduction of Osteogenic Potential.. Duffy, G.P. et al. Tissue Engineering Part A. 2010 Sep;16(9):2755-68.

Hydroxylase inhibition attenuates colonic epithelial secretory function and ameliorates experimental diarrhea.. Ward, J.B. ety al. FASEB Journal. 2011 Feb;25(2):535-43.

NF-κB links CO2 sensing to innate immunity and inflammation in mammalian cells.. Cummins, E.P. et al. J Immunol. 2010 Oct 1;185(7):4439-45.

Ancient atmospheres and the evolution of oxygen sensing via the hypoxia inducible factor in metazoans.. Taylor, C.T. & McElwain, J.C. Physiology. 2010 Oct;25(5):272-9.

The OARSI histopathology initiative: recommendations for histological assessments of osteoarthritis in sheep and goats.. Little, C.B., et al. Osteoarthritis and Cartilage. 2010 Oct;18 Suppl 3:S80-92.

Functional roles of multiple feedback loops in extracellular signal-regulated kinase and Wnt signalling pathways that regulate epithelial-mesenchymal transition.. Shin, S.Y. et al. Cancer Res. 2010 Sep 1;70(17):6715-24.

Introduction to Series on Mesenchymal Stromal (Stem) Cells-MSCs.. O'Brien, T. & Barry, F. Human Gene Therapy. 2010 Sep;21(9):1037-8.

Recommendations for biomarker identification and qualification in clinical proteomics.. Mischak, H. et al. Sci Transl Med. 2010 Aug 25;2(46):46ps42.

Potential of rat bone marrow-derived mesenchymal stem cells as vehicles for delivery of neurotrophins to the Parkinsonian rat brain.. Moloney, T.C. et al. Journal of Brain Research. 2010 Nov 4;1359:33-43.

Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models.. Vera, J. et al. Mol Biosyst. 2010 Nov;6(11):2174-91.

On-chip immunoprecipitation for protein purification.. Sandison, M.E. et al. Lab Chip. 2010 Oct 21;10(20):2805-13.

Hypoxia, innate immunity and infection in the lung.. Schaible, B., Schaffer, K.E. & Taylor, C.T. Respiratory Physiology and Neurobiology. 2010 Dec 31;174(3):235-43.

Stabilization of hypoxia inducible factor-1alpha protein in hypoxia occurs independently of mitochondrial reactive species production oxygen.. Chua, Y.L. et al. J Biol Chem. 2010 Oct 8;285(41):31277-84.

Monitoring of cell oxygenation and responses to metabolic stimulation by intracellular oxygen sensing technique.. Zhdanov, A.V. et al. Integrative Biology. 2010 Sep;2(9):443-51.

Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease.. Good, D.M. et al. Mol Cell Proteomics. 2010 Nov;9(11):2424-37.

Formation of Intracellular Concentration Landscapes by Multisite Protein Modification.. Munoz-Garc, J., Kholodenko, B.N. & Neufeld, Z. Biophys J. 2010 Jul 7;99(1):59-66.

Loss of Prolyl Hydroxylase-1 Protects Against Colitis Through Reduced Epithelial Cell Apoptosis and Increased Barrier Function.. Tambuwala, M.M. et al. Gastroenterology. 2010 Dec;139(6):2093-101.

Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na(+)/Ca(2+) exchange.. Zhdanov, A.V. et al. Biochimica et biophysica Acta. 2010 Sep;1797(9):1627-1637.

The RASSF8 candidate tumor suppressor inhibits cell growth and regulates the Wnt and NF-κB signalling pathways.. Lock, F.E. et al. Oncogene. 2010 Jul 29;29(30):4307-4316.

Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics.. Nakakuki, T. et al. Cell. 2010 May 28;141(5):884-96.

PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells.. Aksamitiene, E. et al. Cell Signal. 2010 Sep;22(9):1369-78.

Engraftment, migration and differentiation of neural stem cells in the rat spinal cord following contusion injury.. McMahon, S.S. et al. Cryotherapy. 2010 May;12(3):313-25.

In vitro differentiation potential of human embryonic versus adult stem cells.. Rooney, G.E. et al. Regenerative Medicine. 2010 MAy; 5(3)

Bolus Delivery of Mesenchymal Stem Cells to Injured Vasculature in the Rabbit Carotid Artery Produces a Dysfunctional Endothelium.. O'Shea, C.A. et al. Tissue Eng Part A. 2010 May;16(5):1657-65.

Host-specific replication of BK virus DNA in mouse cell extracts is independently controlled by DNA polymerase alpha-primase and inhibitory activities.. Tikhanovich, I. & Nasheuer, H.P. Journal of Virology. 2010 Jul;84(13):6636-44.

Survival and Immunogenicity of Mesenchymal Stem Cells from the Green Fluorescent Protein Transgenic Rat in the Adult Rat Brain.. Moloney, T.C. et al. Neurorehabilitation and Neural repair. 2010 Sep;24(7):645-56.

Identification of potential HLA class I and class II epitope precursors associated with heat shock protein 70 (HSPA).. Stocki, P. et al. Cell Stress Chaperones. 2010 Sep;15(5):729-41.

Inferring Signalling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species.. Tian-Rui, X.U. et al. Sci. Signal. 2010 Mar 16;3(113):ra20

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.. Fleming, R.M. et al. Journal of Theoretical Biology. un 7;264(3):683-92.

Genetically Modified Mesenchymal Stem Cells and Their Clinical Potential in Acute Cardiovascular Disease.. Griffin, M, et al. Discovery Medicine. 2010 Mar;9(46):219-23.

Angiogenesis and blood vessel stability in inflammatory arthritis.. Kennedy, A. et al. Arthritis & Rheumatism. 2010 Mar;62(3):711-21.

Heterogeneous nuclear ribonucleoprotein H blocks MST2-mediated apoptosis in cancer cells by regulating A-Raf transcription.. Rauch, J. et al. Cancer Res. 2010 Feb 15;70(4):1679-88.

Co-operation between Raf-1 and Akt pathways for the inhibition of RASSF1A-MST2-triggered apoptosis.. Romano, D. et al. Cancer Res. 2010 Feb; 1,70(3): 1195-1203

Proapoptotic Kinase MST2 Coordinates Signalling Crosstalk between RASSF1A, Raf-1, and Akt.. Romano, D. et al. Cancer Res. 2010 Feb 1;70(3):1195-203.

Potential Role of Mesenchymal Stem Cells (MSCs) in the Breast Tumor Microenvironment: Stimulation of Epithelial to Mesenchymal Transition (EMT).. Martin, F.T. et al. Breast Cancer Research and Treatment. 2010 Nov;124(2):317-26.

Enhanced lipoplex-mediated gene expression in mesenchymal stem cells using reiterated nuclear localization sequence peptides.. Hoare, M. et al. Journal of Gene Medicine. 2010 Feb;12(2):207-18.

The Bcr-Abl kinase regulates the actin cytoskeleton via a GADS/Slp-76/Nck1 adaptor protein pathway.. Preisinger, C. & Kolch, W. Cell Signal. 2010 May;22(5):848-56.

Behavior of Human Mesenchymal Stem Cells in Fibrin-Based Vascular Tissue Engineering Constructs.. O'Cearbhaill, E.D. et al. Annals of Biomedical Engineering. 2010 Mar;38(3):649-57.

General Practioners' Attitudes and Preparedness toward Clinical Decision Support in e-Prescribing (CDS-dP) Adoption in the West of Ireland: a cross sectional study.. Peng Hor, C. et al. BMC Med Inform Decis Mak. 2010 Jan 12;10:2.

Alterations in oxidative gene expression in equine skeletal muscle following exercise and training.. Eivers, S.S. et al. Physiological Genomics. 2010 Jan 8;40(2):83-93.

New druggable targets in the Ras pathway.. Matallanas, D.& Crespo, P. Current Opinion in Molecular Therapeutics. 2010 Dec;12(6):674-83.

Compassionate use of interventions: results of a European Clinical Research Infrastructures Network (ECRIN) survey of ten European countries.. Whitfiel, K. et al. Cohen-Haguenauer, O. et al. Trials. 2010 Nov 12;11:104.

Relevance of an Academic GMP Pan-European Vector Infra-structure (PEVI).. Curr Gene Ther. 2010 Dec;10(6):414-22.

Signalling over a distance: gradient patterns and phosphorylation waves within single cells.. Muñoz-García, J. & Kholodenko, B.N. Biochem Soc Trans. 2010 Oct;38(5):1235-41.

Translation of science to surgery: linking emerging concepts in biological cartilage repair to surgical intervention.. Moran, C.J. et al. J Bone Joint Surg Br. 2010 Sep;92(9):1195-202.

Mesenchymal Stem Cells and Osteoarthritis: Remedy or Accomplice?. Coleman, C.M. et al. Hum Gene Ther. 2010 Oct;21(10):1239-50.

Functional proteomics to dissect tyrosine kinase signalling pathways in cancer.. Kolch, W. & Pitt A. Nature Reviews Cancer. 2010 Sep;10(9):618-29.

Advances in mesenchymal stem cell-mediated gene therapy for cancer.. Dwyer, R.M. et al. Stem Cell Res Ther. 2010 Aug 9;1(3):25.

Signalling Ballet in Space and Time.. Kholodenko, B.N., Hancock, J.F. & Kolch, W. Nature Reviews Molecular Cell Biology 11. 2010 Jun;11(6):414-26.

Non-viral gene therapy for myocardial engineering.. Holladay, C., O'Brien, T. & Pandit, A. Wiley Interdiscip Rev Nanomed Nanobiotechnol. May-Jun 2010;2(3):232-48.

Hypoxia: an alarm signal during intestinal inflammation.. Colgan, S.P. & Taylor, C.T. Nat Rev Gastroenterol Hepatol. 2010 May;7(5):281-7.

A-Raf.. Rauch J, Kolch W. AfCS-Nature Molecule Pages. 2010 April;

Welcome to Stem Cell Research & Therapy.. Donnelly, A. et al. Stem Cell Research & Therapy. 2010 March; 1,1

α Cell Protection by Inhibition of iNOS through Lentiviral Vector-Based Strategies.. Hynes, S.O., McCabe, C. & O'Brien, T. Methods Mol Biol. 2007 Sep;37(1):38-47.


Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions. Schilling, M. et al. Mol Syst Biol. 2009;5:334.

Gram stain/aolc screening for detection of catheter related bloodstream infection. Zach, J. et al. Journal of Infection. 2010 Mar;60(3):254-5.

Aggregation of chemotactic organisms in a differential flow. Muñoz-García, J. & Neufeld, Z. Physical Review. 2009 Dec;80(6 Pt 1):061902.

Cell fate decisions are specified by the dynamic ERK interactome. von Kriegsheim, A. et al. Nature Cell Biology. 2009 Dec;11(12):1458-64.

MST kinases monitor actin cytoskeletal integrity and signal via c-Jun N-terminal kinase stress-activated kinase to regulate p21Waf1/Cip1 stability. Densham, R.M. et al. Mol Cell Biol. 2009 Dec;29(24):6380-90.

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. Orton, R.J. et al. BMC Syst Biol. 2009 Oct 5;3:100.

Generation of antioxidant adenovirus gene transfer vectors encoding CuZnSOD, MnSOD, and catalase. Duffy, A.M., O'Brien, T. & McMahon, J.M. Methods in Molecular Biology. 2010;594:381-93.

HPLC purification of adenoviral vectors. Eglon, M., McGrath, B. & O'Brien, T. Methods in Molecular Biology. 2010;594:395-408.

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Fleming, R.M., Thiele, I. & Nasheuer, H.P. Biophysical Chemistry. 2009 Dec;145(2-3):47-56.

RASSF2 associates with and stabilizes the proapoptotic kinase MST2. Cooper, W.N. et al.Oncogene. 2009 Aug 20;28(33):2988-98.

Ionizing radiation-dependent and independent phosphorylation of the 32-kDa subunit of replication protein A during mitosis. Holger, S. et al. Nucleic Acids Research. 2009 Oct;37(18):6028-41.

Exploration of homodimer receptor: homodimer protein interactions. Vera, J. et al. Int J Bioinform Res Appl. 2009;5(4):447-57.

RAN GTPase is a RASSF1A effector involved in controlling microtubule organization. Dallol, A. et al. Cell Cycle. 2009 Jul 28;19(14):1227-32.

Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle. Kaimachnikov, N.P. & Kholodenko, B.N. FEBS Journal. 2009 Aug;276(15):4102-18.

The C-terminus of Raf-1 acts as a 14-3-3-dependent activation switch. Dhillon, A.S. et al. Cell Signal. 2009 Nov;21(11):1645-51.

Microfluidic single cell arrays to interrogate signalling dynamics of individual, patient-derived hematopoietic stem cells. Faley, S.L. et al. Lab Chip. 2009 Sep 21;9(18):2659-64.

Angiogenin protects motoneurons against hypoxic Injury. Sebastia, J. et al. Cell Death and Differentiation. 2009 May; 16:1238-1247

Multiple roles of the NF-kappaB signalling pathway regulated by coupled negative feedback circuits. Kim, D., Kolch, W. & Cho, K.H. FASEB J

Systems-level interactions between insulin-EGF networks amplify mitogenic signalling. Borisov, N. et al. Molecular Systems Biology, 2009; 5: 256.

XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase. Lévy, N. et al. Nucleic Acids Research. 2009 Jun;37(10):3177-88.

Positional information generated by spatially distributed signalling cascades. Munoz-Ga 2009 Sep;23(9):2796-802.rcia, J., Neufeld, Z. & Kholodenko, B.N. PLoS Computational Biology. 2009 Mar;5(3):e1000330.

Restriction of human polyomavirus BK virus DNA replication in murine cells and extracts. Mahon, C. et al. J Virol. 2009 Jun;83(11):5708-17.

Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor. Suenaga, A. et al. Biophysical Journal. 2009 Mar 18;96(6):2278-88.

Spatially distributed cell signalling. Kholodenko, B.N. FEBS Letters. 2009 Dec 17;583(24):4006-12.

Journeys to high altitude-risks and recommendations for travellers with preexisting medical conditions. Mieske, K., Flaherty, G. & O'Brien, T. Journal of Travel Medicine. Jan-Feb 2010;17(1):48-62.

Liposomal Gene Delivery Mediated by Tissue-Engineered Scaffolds: Trends Biotechnology. Kulkarni M. et al. Trends in Biotechnology. 2010 Jan;28(1):28-36.

Endocytosis and signalling: a meeting with mathematics. Birtwistle MR, Kholodenko BN. Mol Oncol. 2009 Aug;3(4):308-20.

Genome Stability and Human Diseases. Nasheuer, H.P. Subcell Biochem. 2010.

The use of transgenic mice in cancer and genome stability research. Conmy, S. & Nasheuer, H.P. Subcell Biochem. 2010;50:325-36.

Eukaryotic single-stranded DNA binding proteins: central factors in genome stability. Broderick, S. et al. Subcell Biochem. 2010;50:143-63.