Recent Highlights

 

VGll3 operates via Tead1, Tead3 and Tead4 to influence myogenesis in skeletal muscle. Figeac N et al. Journal of Cell Science. 2019 May 28

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation. Charitou T et al. British Journal of Cancer. 2019 May 28

Loss of RAF kinase inhibitor protein is involved in myelomonocytic differentiation and aggravates RAS-driven myeloid leukemogenesis. Caraffini V et al. Haematologica. 2019 May 16

Hypoxia-inducible factor (HIF) hydroxylase inhibition enhances the protective effects of cyclosporine in colitis. Taylor C and colleagues. American Journal of Physiology - Gastrointestinal and Liver Physiology. 2019 May 09

Protein Hydroxylation by Hypoxia-Inducible Factor (HIF) Hydroxylases: Unique or Ubiquitous? Taylor C and colleagues. Cells. 2019 April 26

Targeting promiscuous heterodimerization overcomes innate resistance to ERBB2 dimerization inhibitors in breast cancer. Kennedy S et al. Breast Cancer Research. 2019 March 21

An Integrated Global Analysis of Compartmentalized HRAS Signaling. Santra T et al. Cell Reports. 2019 March 12

Understanding the role of distance, direction and cue salience in an associative model of landmark learning. Commins S, Fey D. Scientific Reports. 2019 Feb 14

Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival. Oser MG et al. Cancer Discovery. 2019 Feb

Hydroxylase Inhibition Selectively Induces Cell Death in Monocytes. Crifo B et al. The Journal of Immunology. 2019 Jan 30

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. Erickson KE et al. PLoS Comput Biol. 2019 Jan 17

Pharmacologic inhibition of hypoxia inducible factor (HIF)-hydroxylases ameliorates allergic contact dermatitis. Manresa M et al. Allergy. 2018 Nov 5

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Thomaseth C et al. Scientific Reports. 2018 Nov 1

Structure-based assessment and network analysis of targeting 14-3-3 proteins in prostate cancer. Root A et al. Molecular Cancer. 2018 Oct 31

Synthetic Lethality and Cancer – Penetrance as the Major Barrier. Ryan C et al. Trends in Cancer 2018 October

Gut adaptation after metabolic surgery and its influences on the brain, liver and cancer. Sinclair P et al. Nature Reviews Gastroenterology & Hepatology. 2018 Sep 4

From oncogenic mutation to dynamic code. Kolch W et al. Science. 2018 Aug 1

Nanoparticles Can Wrap Epithelial Cell Membranes and Relocate Them Across the Epithelial Cell Layer. Urbancic I et al. Nano Letters. 2018 July 24

ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation. Monypenny J et al. Cell Rep. 2018 Jul 17

Dissecting RAF Inhibitor Resistance by Structure-based Modelling Reveals Ways to Overcome Oncogenic RAS Signalling. Rukhlenko OS et al. Cell Syst. 2018 Jul 11

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. Ebhardt HA et al. npj Systems Biology and Applications. 2018 Jul 2

Polycomb Repressive Complex 2 haploinsufficiency identifies a high-risk subgroup of pediatric acute myeloid leukemia. Bond J et al. Leukemia 2018 June 27

Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer. Brough R et al. Nature Oncogene 2018 June 18.

RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73. Papaspyropoulos A et al. Nature Communications 2018 Jan 30

2019

VGll3 operates via Tead1, Tead3 and Tead4 to influence myogenesis in skeletal muscle. Figeac N et al. Journal of Cell Science. 2019 May 28

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation. Charitou T et al. British Journal of Cancer. 2019 May 28

Loss of RAF kinase inhibitor protein is involved in myelomonocytic differentiation and aggravates RAS-driven myeloid leukemogenesis. Caraffini V et al. Haematologica. 2019 May 16

Hypoxia-inducible factor (HIF) hydroxylase inhibition enhances the protective effects of cyclosporine in colitis. Taylor C and colleaguesAmerican Journal of Physiology - Gastrointestinal and Liver Physiology. 2019 May 09

Protein Hydroxylation by Hypoxia-Inducible Factor (HIF) Hydroxylases: Unique or Ubiquitous? Taylor C and colleagues. Cells. 2019 April 26

Targeting promiscuous heterodimerization overcomes innate resistance to ERBB2 dimerization inhibitors in breast cancer. Kennedy S et al. Breast Cancer Research. 2019 March 21

An Integrated Global Analysis of Compartmentalized HRAS Signaling. Santra T et al. Cell Reports. 2019 March 12

Understanding the role of distance, direction and cue salience in an associative model of landmark learning. Commins S, Fey D. Scientific Reports. 2019 Feb 14

Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival. Oser MG et al. Cancer Discovery. 2019 Feb

Hydroxylase Inhibition Selectively Induces Cell Death in Monocytes. Crifo B et al. The Journal of Immunology. 2019 Jan 30

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. Erickson KE et al. PLoS Comput Biol. 2019 Jan 17

2018

VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants. Radusky L et al. Frontiers in Genetics. 2018 Dec 6

Pharmacologic inhibition of hypoxia inducible factor (HIF)-hydroxylases ameliorates allergic contact dermatitis. Manresa M et al. Allergy. 2018 Nov 5

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Thomaseth C et al. Scientific Reports. 2018 Nov 1

Association of Implementing a Multidisciplinary Team Approach in the Management of Morbidly Adherent Placenta With Maternal Morbidity and Mortality. Bartels HC et al. Obstetrics and Gynecology. 2018 Nov 1

Structure-based assessment and network analysis of targeting 14-3-3 proteins in prostate cancer. Root A et al. Molecular Cancer. 2018 Oct 31

Synthetic Lethality and Cancer – Penetrance as the Major Barrier. Ryan C et al. Trends in Cancer 2018 October

Gut adaptation after metabolic surgery and its influences on the brain, liver and cancer. Sinclair P et al. Nature Reviews Gastroenterology & Hepatology. 2018 Sep 4

Molecular basis of distinct oestrogen responses in endometrial and breast cancer. Baxter E et al. Society for Endocrinology Endocrine-Related Cancer. 2018 Aug 1

Opportunities and Challenges of Whole-Cell and -Tissue Simulations of the Outer Retina in Health and Disease. Luthert P et al. Annual Reviews 2018 July

Quantitative Biology: Theory, Computational Methods, and Models (The MIT Press). Editors: Brian Munsky, William S. Hlavacek, Lev S. Tsimring (2018).

Integration of Omics Approaches and Systems Biology for Clinical Applications A. Vlahou, H. Mischak, J. Zoidakis, & F. Magni (Eds.), Introduction into the Concept of Systems Medicine (pp. 408-433). Logotheti, & Kolch, W. (2018).

Sievers, F., Higgins, D.G. (2018) Clustal Omega for making accurate alignments of many protein sequences, Protein Science [10.1002/pro.3290]

Jauniaux, E., Chantraine, F., Silver, R.M., Langhoff-Roos, J., Duncombe, G., Klaritsch, P., Chantraine, F., Kingdom, J., Grønbeck, L., Rull, K., Nigatu, B., Tikkanen, M., Sentilhes, L., Asatiani, T., Leung, W.-C., AIhaidari, T., Brennan, D., Kondoh, E., Yang, J.-I., Seoud, M., Jegasothy, R., Espino y Sosa, S., Jacod, B., D'Antonio, F., Shah, N., Bomba-Opon, D., Ayres-de-Campos, D., Jeremic, K., Kok, T.L., Soma-Pillay, P., Tul Mandić, N., Lindqvist, P., Arnadottir, T.B., Hoesli, I., Jaisamrarn, U., Al Mulla, A., Robson, S., Cortez, R. (2018) FIGO consensus guidelines on placenta accreta spectrum disorders: Epidemiology, International Journal of Gynecology and Obstetrics [10.1002/ijgo.12407]

Jauniaux, E., Bhide, A., Kennedy, A., Woodward, P., Hubinont, C., Collins, S., Duncombe, G., Klaritsch, P., Chantraine, F., Kingdom, J., Grønbeck, L., Rull, K., Nigatu, B., Tikkanen, M., Sentilhes, L., Asatiani, T., Leung, W.-C., AIhaidari, T., Brennan, D., Kondoh, E., Yang, J.-I., Seoud, M., Jegasothy, R., Espino y Sosa, S., Jacod, B., D'Antonio, F., Shah, N., Bomba-Opon, D., Ayres-de-Campos, D., Jeremic, K., Kok, T.L., Soma-Pillay, P., Tul Mandić, N., Lindqvist, P., Arnadottir, T.B., Hoesli, I., Jaisamrarn, U., Al Mulla, A., Robson, S., Cortez, R. (2018) FIGO consensus guidelines on placenta accreta spectrum disorders: Prenatal diagnosis and screening, International Journal of Gynecology and Obstetrics [10.1002/ijgo.12408]

Sentilhes, L., Kayem, G., Chandraharan, E., Palacios-Jaraquemada, J., Jauniaux, E., Duncombe, G., Klaritsch, P., Chantraine, F., Kingdom, J., Grønbeck, L., Rull, K., Nigatu, B., Tikkanen, M., Sentilhes, L., Asatiani, T., Leung, W.-C., AIhaidari, T., Brennan, D., Kondoh, E., Yang, J.-I., Seoud, M., Jegasothy, R., Espino y Sosa, S., Jacod, B., D'Antonio, F., Shah, N., Bomba-Opon, D., Ayres-de-Campos, D., Jeremic, K., Kok, T.L., Soma-Pillay, P., Tul Mandić, N., Lindqvist, P., Arnadottir, T.B., Hoesli, I., Jaisamrarn, U., Al Mulla, A., Robson, S., Cortez, R. (2018) FIGO consensus guidelines on placenta accreta spectrum disorders: Conservative management, International Journal of Gynecology and Obstetrics [10.1002/ijgo.12410]

Nguyen, L.K., Kholodenko, B.N., von Kriegsheim, A. (2018) Rac1 and RhoA: Networks, loops and bistability, Small GTPases [10.1080/21541248.2016.1224399]

Allen, L., Jauniaux, E., Hobson, S., Papillon-Smith, J., Belfort, M.A., Duncombe, G., Klaritsch, P., Chantraine, F., Kingdom, J., Grønbeck, L., Rull, K., Nigatu, B., Tikkanen, M., Sentilhes, L., Asatiani, T., Leung, W.-C., AIhaidari, T., Brennan, D., Kondoh, E., Yang, J.-I., Seoud, M., Jegasothy, R., Espino y Sosa, S., Jacod, B., D'Antonio, F., Shah, N., Bomba-Opon, D., Ayres-de-Campos, D., Jeremic, K., Kok, T.L., Soma-Pillay, P., Tul Mandić, N., Lindqvist, P., Arnadottir, T.B., Hoesli, I., Jaisamrarn, U., Al Mulla, A., Robson, S., Cortez, R. (2018) FIGO consensus guidelines on placenta accreta spectrum disorders: Nonconservative surgical management, International Journal of Gynecology and Obstetrics [10.1002/ijgo.12409]

Kolch, W., Cleveland, J.L., Rapp, U.R. (2018) Role of oncogenes in the abrogation of growth factor requirements of hemopoietic cells, Growth Regulation and Carcinogenesis: Volume I [10.1201/9781351072328]

Kennel, K.B., Burmeister, J., Schneider, M., Taylor, C.T. (2018) The PHD1 oxygen sensor in health and disease, Journal of Physiology [10.1113/JP275327]

Roguev, A., Ryan, C.J., Xu, J., Colson, I., Hartsuiker, E., Krogan, N. (2018) Genetic interaction score (S-score) calculation, clustering, and visualization of genetic interaction profiles for yeast, Cold Spring Harbor Protocols [10.1101/pdb.prot091983]

Herrero, A., Reis-Cardoso, M., Jiménez-Gómez, I., Doherty, C., Agudo-Ibañez, L., Pinto, A., Calvo, F., Kolch, W., Crespo, P., Matallanas, D. (2018) Characterisation of HRas local signal transduction networks using engineered site-specific exchange factors, Small GTPases [10.1080/21541248.2017.1406434]

Jauniaux, E., Ayres-de-Campos, D., Duncombe, G., Klaritsch, P., Chantraine, F., Kingdom, J., Grønbeck, L., Rull, K., Nigatu, B., Tikkanen, M., Sentilhes, L., Asatiani, T., Leung, W.-C., AIhaidari, T., Brennan, D., Kondoh, E., Yang, J.-I., Seoud, M., Jegasothy, R., Espino y Sosa, S., Jacod, B., D'Antonio, F., Shah, N., Bomba-Opon, D., Ayres-de-Campos, D., Jeremic, K., Kok, T.L., Soma-Pillay, P., Tul Mandić, N., Lindqvist, P., Arnadottir, T.B., Hoesli, I., Jaisamrarn, U., Al Mulla, A., Robson, S., Cortez, R. (2018) FIGO consensus guidelines on placenta accreta spectrum disorders: Introduction, International Journal of Gynecology and Obstetrics [10.1002/ijgo.12406]

Roguev, A., Ryan, C.J., Hartsuiker, E., Krogan, N.J. (2018) High-throughput quantitative genetic interaction mapping in the fission yeast schizosaccharomyces pombe, Cold Spring Harbor Protocols [10.1101/pdb.top079905]

Brown, E., Taylor, C.T. (2018) Hypoxia-sensitive pathways in intestinal inflammation, Journal of Physiology [10.1113/JP274350]

Hughes, G.M., Boston, E.S.M., Finarelli, J.A., Murphy, W.J., Higgins, D.G., Teeling, E.C. (2018) The birth and death of olfactory receptor gene families in Mammalian niche adaptation, Molecular Biology and Evolution [10.1093/molbev/msy028]

Smith, D., Stewart, C.J.R., Clarke, E.M., Lose, F., Davies, C., Armes, J., Obermair, A., Brennan, D., Webb, P.M., Nagle, C.M., Spurdle, A.B. (2018) ER and PR expression and survival after endometrial cancer, Gynecologic Oncology [10.1016/j.ygyno.2017.11.027]

Taylor, C.T. (2018) Hypoxia in the Gut, Cellular and Molecular Gastroenterology and Hepatology [10.1016/j.jcmgh.2017.09.005]

Verlande, A., Krafčíková, M., Potěšil, D., Trantírek, L., Zdráhal, Z., Elkalaf, M., Trnka, J., Souček, K., Rauch, N., Rauch, J., Kolch, W., Uldrijan, S. (2018) Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization, EMBO Reports [10.15252/embr.201744524]

Campbell, J., Ryan, C.J., Lord, C.J. (2018) Identifying genetic dependencies in cancer by analyzing siRNA screens in tumor cell line panels, Methods in Molecular Biology [10.1007/978-1-4939-7493-1_5]

Papaspyropoulos, A., Bradley, L., Thapa, A., Leung, C.Y., Toskas, K., Koennig, D., Pefani, D.-E., Raso, C., Grou, C., Hamilton, G., Vlahov, N., Grawenda, A., Haider, S., Chauhan, J., Buti, L., Kanapin, A., Lu, X., Buffa, F., Dianov, G., Von Kriegsheim, A., Matallanas, D., Samsonova, A., Zernicka-Goetz, M., O'Neill, E. (2018) RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73, Nature Communications [10.1038/s41467-017-02786-5]

Cavadas, M.A.S., Taylor, C.T., Cheong, A. (2018) Acquisition of temporal HIF transcriptional activity using a secreted luciferase assay, Methods in Molecular Biology [10.1007/978-1-4939-7665-2_4]

Pickel, C., Taylor, C.T., Scholz, C.C. (2018) Genetic knockdown and pharmacologic inhibition of hypoxia-inducible factor (HIF) hydroxylases, Methods in Molecular Biology [10.1007/978-1-4939-7665-2_1]

Bond, J., Touzart, A., Nadal, N., Trinquand, A., Thouvenin, S., Da Cruz, V., Bonté, P.-E., Radford-Weiss, I., Garnier, N., Stéphan, J.-L., Macintyre, E. (2018) Early thymic precursor-like lymphomatous presentation of the ETV6-NCOA2 translocation, British Journal of Haematology [10.1111/bjh.14579]

Magi, S., Iwamoto, K., Yumoto, N., Hiroshima, M., Nagashima, T., Ohki, R., Garcia-Munoz, A., Volinsky, N., Kriegsheim, A.V., Sako, Y., Takahashi, K., Kimura, S., Kholodenko, B.N., Okada-Hatakeyama, M. (2018) Transcriptionally inducible pleckstrin homology-like domain, family a, member 1, attenuates ERBB receptor activity by inhibiting receptor oligomerization, Journal of Biological Chemistry [10.1074/jbc.M117.778399]

Erickson, K.E., Rukhlenko, O.S., Posner, R.G., Hlavacek, W.S., Kholodenko, B.N. (2018) New insights into RAS biology reinvigorate interest in mathematical modelling of RAS signalling, Seminars in Cancer Biology [10.1016/j.semcancer.2018.02.008]

Donovan, P.D., Gonzalez, G., Higgins, D.G., Butler, G., Ito, K. (2018) Identification of fungi in shotgun metagenomics datasets, PLoS ONE [10.1371/journal.pone.0192898]

Shields, S., Conroy, E., O'Grady, T., McGoldrick, A., Connor, K., Ward, M.P., Useckaite, Z., Dempsey, E., Reilly, R., Fan, Y., Chubb, A., Matallanas, D.G., Kay, E.W., O'Connor, D., McCann, A., Gallagher, W.M., Coppinger, J.A. (2018) BAG3 promotes tumour cell proliferation by regulating EGFR signal transduction pathways in triple negative breast cancer, Oncotarget [10.18632/oncotarget.24590]

Bond, J., Quang, C.T., Hypolite, G., Belhocine, M., Bergon, A., Cordonnier, G., Ghysdael, J., Macintyre, E., Boissel, N., Spicuglia, S., Asnafi, V. (2018) Novel Intergenically spliced chimera, NFATC3- PLA2G15, is associated with aggressive T-ALL biology and outcome, Molecular Cancer Research [10.1158/1541-7786.MCR-17-0442]

Johnston, D., Malo Estepa, I., Ebhardt, H.A., Crowe, M.A., Diskin, M.G. (2018) Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle, Theriogenology [10.1016/j.theriogenology.2018.04.008]

Rogers, S., McCloy, R.A., Parker, B.L., Gallego-Ortega, D., Law, A.M.K., Chin, V.T., Conway, J.R.W., Fey, D., Millar, E.K.A., O'Toole, S., Deng, N., Swarbrick, A., Chastain, P.D., Cesare, A.J., Timpson, P., Caldon, C.E., Croucher, D.R., James, D.E., Watkins, D.N., Burgess, A. (2018) MASTL overexpression promotes chromosome instability and metastasis in breast cancer, Oncogene [10.1038/s41388-018-0295-z]

Santra, T., Rukhlenko, O., Zhernovkov, V., Kholodenko, B.N. (2018) Reconstructing static and dynamic models of signalling pathways using Modular Response Analysis, Current Opinion in Systems Biology [10.1016/j.coisb.2018.02.003]

Brough, R., Gulati, A., Haider, S., Kumar, R., Campbell, J., Knudsen, E., Pettitt, S.J., Ryan, C.J., Lord, C.J. (2018) Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer, Oncogene [10.1038/s41388-018-0368-z]

Bond, J., Labis, E., Marceau-Renaut, A., Duployez, N., Labopin, M., Hypolite, G., Michel, G., Ducassou, S., Boutroux, H., Nelken, B., Bertrand, Y., Baruchel, A., Petit, A., Asnafi, V., Leverger, G., Preudhomme, C., Macintyre, E., Lapillonne, H. (2018) Polycomb repressive complex 2 haploinsufficiency identifies a high-risk subgroup of pediatric acute myeloid leukemia, Leukemia [10.1038/s41375-018-0187-9]

Rukhlenko, O.S., Khorsand, F., Krstic, A., Rozanc, J., Alexopoulos, L.G., Rauch, N., Erickson, K.E., Hlavacek, W.S., Posner, R.G., Gómez-Coca, S., Rosta, E., Fitzgibbon, C., Matallanas, D., Rauch, J., Kolch, W., Kholodenko, B.N. (2018) Dissecting RAF Inhibitor Resistance by Structure-based Modelling Reveals Ways to Overcome Oncogenic RAS Signalling, Cell Systems [10.1016/j.cels.2018.06.002]

Duffy, D.J., Konietzny, A., Krstic, A., Mehta, J.P., Halasz, M., Kolch, W. (2018) Identification of a MYCN and Wnt-related VANGL2-ITLN1 fusion gene in neuroblastoma, Gene Reports [10.1016/j.genrep.2018.06.018]

Bajrami, I., Marlow, R., van De Ven, M., Brough, R., Pemberton, H.N., Frankum, J., Song, F., Rafiq, R., Konde, A., Krastev, D.B., Menon, M., Campbell, J., Gulati, A., Kumar, R., Pettitt, S.J., Gurden, M.D., Cardenosa, M.L., Chong, I., Gazinska, P., Wallberg, F., Sawyer, E.J., Martin, L.-A., Dowsett, M., Linardopoulos, S., Natrajan, R., Ryan, C.J., Derksen, P.W.B., Jonkers, J., Tutt, A.N.J., Ashworth, A., Lord, C.J. (2018) E-Cadherin/ROS1 inhibitor synthetic lethality in breast cancer, Cancer Discovery [10.1158/2159-8290.CD-17-0603]

Donovan, P.D., Holland, L.M., Lombardi, L., Coughlan, A.Y., Higgins, D.G., Wolfe, K.H., Butler, G. (2018) TPP riboswitch-dependent regulation of an ancient Thiamin transporter in Candida, PLoS Genetics [10.1371/journal.pgen.1007429]

Rodriguez, J., Herrero, A., Li, S., Rauch, N., Quintanilla, A., Wynne, K., Krstic, A., Acosta, J.C., Taylor, C., Schlisio, S., von Kriegsheim, A. (2018) PHD3 Regulates p53 Protein Stability by Hydroxylating Proline 359, Cell Reports [10.1016/j.celrep.2018.06.108]

Root, A., Ebhardt, H.A. (2018) A two-drug combination simulation study for metastatic castrate resistant prostate cancer, Prostate [10.1002/pros.23694]

Fioredda, F., Iacobelli, S., Korthof, E.T., Knol, C., van Biezen, A., Bresters, D., Veys, P., Yoshimi, A., Fagioli, F., Mats, B., Zecca, M., Faraci, M., Miano, M., Arcuri, L., Maschan, M., O'Brien, T., Diaz, M.A., Sevilla, J., Smith, O., Peffault de Latour, R., de la Fuente, J., Or, R., Van Lint, M.T., Tolar, J., Aljurf, M., Fisher, A., Skorobogatova, E.V., Diaz de Heredia, C., Risitano, A., Dalle, J.-H., Sedláček, P., Ghavamzadeh, A., Dufour, C. (2018) Outcome of haematopoietic stem cell transplantation in dyskeratosis congenita, British Journal of Haematology [10.1111/bjh.15495]

Holme, H., Gulati, A., Brough, R., Fleuren, E.D.G., Bajrami, I., Campbell, J., Chong, I.Y., Costa-Cabral, S., Elliott, R., Fenton, T., Frankum, J., Jones, S.E., Menon, M., Miller, R., Pemberton, H.N., Postel-Vinay, S., Rafiq, R., Selfe, J.L., Von Kriegsheim, A., Munoz, A.G., Rodriguez, J., Shipley, J., Van Der Graaf, W.T.A., Williamson, C.T., Ryan, C.J., Pettitt, S., Ashworth, A., Strauss, S.J., Lord, C.J. (2018) Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness, Scientific Reports [10.1038/s41598-018-29043-z]

Monypenny, J., Milewicz, H., Flores-Borja, F., Weitsman, G., Cheung, A., Chowdhury, R., Burgoyne, T., Arulappu, A., Lawler, K., Barber, P.R., Vicencio, J.M., Keppler, M., Wulaningsih, W., Davidson, S.M., Fraternali, F., Woodman, N., Turmaine, M., Gillett, C., Franz, D., Quezada, S.A., Futter, C.E., Von Kriegsheim, A., Kolch, W., Vojnovic, B., Carlton, J.G., Ng, T. (2018) ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation, Cell Reports [10.1016/j.celrep.2018.06.066]

Urbančič, I., Garvas, M., Kokot, B., Majaron, H., Umek, P., Cassidy, H., Škarabot, M., Schneider, F., Galiani, S., Arsov, Z., Koklic, T., Matallanas, D., Čeh, M., Muševič, I., Eggeling, C., Štrancar, J. (2018) Nanoparticles Can Wrap Epithelial Cell Membranes and Relocate Them Across the Epithelial Cell Layer, Nano Letters [10.1021/acs.nanolett.8b02291]

Besray Unal, E., Kiel, C., Benisty, H., Campbell, A., Pickering, K., Blüthgen, N., Sansom, O.J., Serrano, L. (2018) Systems level expression correlation of Ras GTPase regulators, Cell Communication and Signalling [10.1186/s12964-018-0256-8]

Testi, A.M., Pession, A., Diverio, D., Grimwade, D., Gibson, B., Cardoso de Azevedo, A., Moran, L., Leverger, G., Elitzur, S., Hasle, H., van der Werff ten Bosch, J., Smith, O., De Rosa, M., Piciocchi, A., Lo Coco, F., Foà, R., Locatelli, F., Kaspers, G.J.L. (2018) Risk-adapted treatment of acute promyelocytic leukemia: Results from the international consortium for childhood APL, Blood [10.1182/blood-2018-03-836528]

Holme, H., Gulati, A., Brough, R., Fleuren, E.D.G., Bajrami, I., Campbell, J., Chong, I.Y., Costa-Cabral, S., Elliott, R., Fenton, T., Frankum, J., Jones, S.E., Menon, M., Miller, R., Pemberton, H.N., Postel-Vinay, S., Rafiq, R., Selfe, J.L., von Kriegsheim, A., Munoz, A.G., Rodriguez, J., Shipley, J., van der Graaf, W.T.A., Williamson, C.T., Ryan, C.J., Pettitt, S., Ashworth, A., Strauss, S.J., Lord, C.J. (2018) Erratum to: Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness (Scientific Reports, (2018), 8, 1, (10614), 10.1038/s41598-018-29043-z), Scientific Reports [10.1038/s41598-018-30922-8]

Kolch, W., Kiel, C. (2018) From oncogenic mutation to dynamic code, Science [10.1126/science.aau8059]

Ebhardt, H.A., Root, A., Liu, Y., Gauthier, N.P., Sander, C., Aebersold, R. (2018) Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer, npj Systems Biology and Applications [10.1038/s41540-018-0064-1]

2017

Bendtsen, C., Degasperi, A., Ahlberg, E., Carlsson, L. (2017). Improving machine learning in early drug discovery. Annals of Mathematics and Artificial Intelligence.

Ebhardt HA, Degen S, Tadini V, Schilb A, Johns N, Greig CA, Fearon KCH, Aebersold R, Jacobi C. (2017). Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study. Journal of Cachexia, Sarcopenia and Muscle.

Kelly E. Nissen, Christina M. Homer, Colm J. Ryan, Michael Shales, Nevan J. Krogan, Kristin L. Patrick, and Christine Guthrie (2017). The histone variant H2A. Z promotes splicing of weak introns. Genes & Development.

Stephen Bridgett, James Campbell, Christopher J. Lord, Colm J. Ryan (2017). CancerGD: A Resource for Identifying and Interpreting Genetic Dependencies in Cancer. Cell Systems.

Sun C, De Mello V, Mohamed A, Ortuste Quiroga HP, Garcia-Munoz A, Al Bloshi A, Tremblay AM, von Kriegsheim A, Collie-Duguid E, Vargesson N, Â Matallanas D, Wackerhage H, Zammit PS. (2017). Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function. Stem Cells.

Duffy DJ, Krstic A, Â Halasz M, Schwarzl T, Konietzny A, Iljin K, Higgins DG, Kolch W. (2017). Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance Genome Medicine.

Radic-Sarikas B, Â Halasz M, Huber KVM, Winter GE, Tsafou KP, Papamarkou T, Brunak S, Kolch W, Superti-Furga G. (2017). Lapatinib potentiates cytotoxicity of YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter. Scientific Reports.

Schaible B, Rodriguez J, Garcia A, von Kriegsheim A, McClean S, Hickey C, Keogh CE, Brown E, Schaffer K, Broquet A, Taylor CT. (2017). Hypoxia Reduces the Pathogenicity of Pseudomonas aeruginosa by Decreasing the Expression of Multiple Virulence Factors. J Infect Dis.

Le Q, Sievers F, Higgins DG. (2017). Protein multiple sequence alignment benchmarking through secondary structure prediction. Bioinformatics.

Santra T, Roche S, Conlon N, O'Donovan N, Crown J, O'Connor R, Kolch W. (2017). Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models. PLOS ONE.

Latosinska A, Mokou M, Makridakis M, Mullen W, Zoidakis J, Lygirou V, Frantzi M, Katafigiotis I, Stravodimos K, Hupe MC, Dobrzyński M, Kolch W, Merseburger AS, Mischak H, Roubelakis MG, Vlahou A. (2017). Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention. Oncotarget.

Fasterius E, Raso C, Kennedy S, Rauch N, Lundin P, Kolch W, Uhlén M, Al-Khalili Szigyarto C. (2017). A novel RNA sequencing data analysis method for cell line authentication. PLoS ONE.

Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC. (2017). Vascular Endothelial Growth Factor (VEGF) Promotes Assembly of the p130Cas Interactome to Drive Endothelial Chemotactic Signalling and Angiogenesis. Mol Cell Proteomics.

Frank, T. D. (2017). Nambu bracket formulation of nonlinear biochemical reactions beyond mass action kinetics. Journal of Nonlinear Mathematical Physics.

Santra, T, Roche, S, Donovan, N.O., Crown, J, O'Connor, R, Kolch, W. (2017). Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models. PLOS one.

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

Daly C, Shine L, Heffernan T, Deeti S, Reynolds AL, O'Connor JJ, Dillon ET, Duffy DJ, Kolch W, Cagney G, Kennedy BN. (2017). A Brain-Derived Neurotrophic Factor Mimetic Is Sufficient to Restore Cone Photoreceptor Visual Function in an Inherited Blindness Model. Scientific Reports.

Degasperi A, Fey D, Kholodenko BN. (2017). Performance of objective functions and optimisation procedures for parameter estimation in system biology models. NPJ Systems Biology and Applications.

Roguev A, Ryan CJ, Hartsuiker E, Krogan NJ. (2017). High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe. Cold Spring Harbour Protocols.

Roguev A, Ryan CJ, Xu J, Colson I, Hartsuiker E, Krogan N. (2017). Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast. Cold Spring Harbour Protocols.

Manresa MC, Taylor CT. (2017). Hypoxia Inducible Factor (HIF) Hydroxylases as Regulators of Intestinal Epithelial Barrier Function. Cell Mol GastroenterolHepato.

Fagundes RR, Taylor CT. (2017). Determinants of hypoxia inducible factor (HIF) activity in the intestinal mucosa. J Appl Physiol.

Cavadas MAS, Cheong A, Taylor CT (2017). The regulation of transcriptional repression in hypoxia. Exp Cell Res.

Rauch J, Kolch W. (2017). Spatial regulation of ARAF controls the MST2-Hippo pathway. Small GTPases.

Kolch, W, Fey, D. (2017). Personalized Computational Models as Biomarkers. Journal of Personalised Medicine.

 

2016

Scholz CC., Rodriguez J., Von Kriegsheim A., Fabrizio J., Pickel C., Cavadas MA., Crifo B., Halligan Doug N., Wenger R., Peet D., Cummins EP, Taylor CT. (2016). FIH regulates cellular metabolism through hydroxylation of the deubiquitinase OTUB1, PLOS Biology.

Bryan, K., Jarboui, M.-A., Raso, C., Bernal Llinares, M., McCann, B., Rauch, J., Boldt, K., and Lynn, D.J. (2016). HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data, Journal of proteome research.

Rauch, J., Vandamme, D., Mack, B., McCann, B., Volinsky, N., Blanco, A., Gires, O., and Kolch, W. (2016). Differential localization of A-Raf regulates MST2-mediated apoptosis during epithelial differentiation, Cell Death and Differentiation.

Baljuls, A., Dobrzyński, M., Rauch, J., Rauch, N., and Kolch, W. (2016). Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF., Cellular Signalling .

Rodriguez J, Pilkington R, Garcia Munoz A, Nguyen LK, Rauch N, Kennedy S, Monsefi N, Herrero A, Taylor CT, von Kriegsheim A. (2016). Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signalling Pathways, CELL Reports.

Zsolt Fabian, Cormac T. Taylor, Lan K. Nguyen. (2016). Understanding complexity in the HIF signalling pathway using systems biology and mathematical modelling, Journal of Molecular Medicine.

Beaton H, Andrews D, Parsons M, Murphy M, Gaffney A, Kavanagh D, McKay GJ, Maxwell AP, Taylor CT, Cummins EP, Godson C, Higgins DF, Murphy P, Crean J. (2016). Wnt6 regulates epithelial cell differentiation and is dysregulated in renal fibrosis, American Journal of Physiology.

Selfridge AC, Cavadas MA, Scholz CC, Campbell EL, Welch LC, Lecuona E, Colgan SP, Barrett KE, Sporn PH, Sznajder JI, Cummins EP, Taylor CT. (2016). Hypercapnia Suppresses the HIF-dependent Adaptive Response to Hypoxia, The Journal of Biological Chemistry.

Cummins EP, Keogh CE, Crean D, Taylor CT. (2016). The role of HIF in immunity and inflammation, Molecular Aspects of Medicine.

Crifo B, Taylor CT. (2016). Crosstalk between toll-like receptors and hypoxia-dependent pathways in health and disease, Journal of Investigative Medicine.

Campbell J, Ryan CJ, Brough R, Bajrami I, Pemberton HN, Chong IY, Costa-Cabral S, Frankum J, Gulati A, Holme H, Miller R, Postel-Vinay S, Rafiq R, Wei W, Williamson CT, Quigley DA, Tym J, Al-Lazikani B, Fenton T, Natrajan R, Strauss SJ, Ashworth A, Lord CJ. (2016). Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines, Cell Reports.

Byrne KM, Monsefi N, Dawson JC, Degasperi A, Bukowski-Wills JC, Volinsky N, Dobrzyński M, Birtwistle MR, Tsyganov MA, Kiyatkin A, Kida K, Finch AJ, Carragher NO, Kolch W, Nguyen LK, von Kriegsheim A, Kholodenko BN. (2016). Bistability in the Rac1, PAK, and RhoA Signalling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches, Cell Systems.

Samuel Rogers, Dirk Fey, Rachael A. McCloy, Benjamin L. Parker, Nicholas J. Mitchell, Richard J. Payne, Roger J. Daly, David E. James, C. Elizabeth Caldon, D. Neil Watkins, David R. Croucher, and Andrew Burgess. (2016). PP1 initiates the dephosphorylation of MASTL, triggering mitotic exit and bistability in human cells, Journal of Cell Science.

Rinaldi L, Datta D, Serrat J, Morey L, Solanas G, Avgustinova A, Blanco E, Pons JI, Matallanas D, Von Kriegsheim A, Di Croce L, Benitah SA. (2016). Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis, Cell Stem Cell.

Halasz M, Kholodenko BN, Kolch W, Santra T. (2016). Integrating network reconstruction with mechanistic modelling to predict cancer therapies, Science Signalling.

Santra, T., Delatola, E. A. (2016). Bayesian algorithm for detecting differentially expressed proteins and its application in breast cancer research, Scientific Reports.

Iglesius Martinez, LF, Kolch W., Santra, T. (2016). BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research, Scientific Reports

Ian M Evans, Susan A Kennedy, Ketevan Paliashvili, Tapesh Santra, Maiko Yamaji, Ruth C Lovering, Gary Britton, Paul Frankel, Walter Kolch and Ian C Zachary. (2016). VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis, Molecular and Cellular Proteomics.

Zhang, R., Fruhwirth, G. O., Coban, O., Barrett, J. E., Burgoyne, T., Lee, S. H., Simonson, P. D., Baday, M., Kholodenko, B. N., Futter, C. E., Ng, T., Selvin, P. R. (2016). Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy, ACS Nano.

Weitsman G, Barber PR, Nguyen LK, Lawler K, Patel G, Woodman N, Kelleher MT, Pinder SE, Rowley M, Ellis PA, Purushotham AD, Coolen AC, Kholodenko BN, Vojnovic B, Gillett C, Ng T. (2016). HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status, Oncotarget.

Nguyen LK, Kholodenko BN, von Kriegsheim A. (2016). Rac1 and RhoA: networks, loops and bistability, Small GTPases.

Frank, T. D., Kiyatkin, A., Cheong, A., Kholodenko, B. N. (2016). Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data, Mathematical Medicine and Biology.

Chris T. Williamson, Rowan Miller, Helen N. Pemberton, Samuel E. Jones, James Campbell, Asha Konde, Nicholas Badham, Rumana Rafiq, Rachel Brough, Aditi Gulati, Colm J. Ryan, Jeff Francis, Peter B. Vermulen, Andrew R. Reynolds, Philip M. Reaper, John R. Pollard, Alan Ashworth & Christopher J. Lord. (2016). ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A, Nature Communications.

Angela Baljuls, Maciej Dobrzyński, Jens Rauch, Nora Rauch, Walter Kolch. (2016). Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF, Cellular Signalling.

Stanley E, Delatola E, Nkuipou-Kenfack, Spooner W, Kolch W, Schanstra JP, Mischak H, Koeck T. (2016). Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease., BMC Bioinformatics.

Sánchez-Sanz G, Tywoniuk B, Matallanas D, Romano D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. (2016). SARAH Domain-Mediated MST2-RASSF Dimeric Interactions, PLoS Comput Biol.

Cavadas MAS, Mesnieres M, Crifo B, Manresa MC, Selfridge AC, Keogh CE, Fabian Z, Scholz CC, Nolan KA, Rocha LMA, Tambuwala MM, Brown S, Wdowicz A, Corbett D, Murphy KJ, Godson C, Cummins EP, Taylor CT* & Cheong A.*(2016). REST is a hypoxia-responsive transcriptional repressor, Scientific Reports.

Rodriguez J, Pilkington R, Garcia Munoz A, Nguyen LK, Rauch N, Kennedy S, Monsefi N, Herrero A, Taylor CT, von Kriegsheim A. (2016). Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signalling Pathways. Cell Reports

Okada H, Ebhardt HA, Vonesch S, Aebersold R, Hafen E. (2016). Proteome-wide association studies identify biochemical modules associated with a wing size phenotype in Drosophila melanogaster, Nature Communications.

Dernayka, L., Rauch, N., Jarboui, M.-A., Zebisch, A., Texier, Y., Horn, N., Romano, D., Gloeckner, C.J., Kriegsheim, A.V., Ueffing, M., Kolch, W., Boldt, K. (2016). Autophosphorylation on S614 inhibits the activity and the transforming potential of BRAF, Cellular Signalling.

Cahill, E.F., Sax, T., Hartmann, I., Haffner, S., Holler, E., Holler, B., Huss, R., Günther, C., Parolini, O., Kolch, W., Eissner, G. (2016). Mesenchymal Stromal Cells Protect Endothelial Cells from Cytotoxic T Lymphocyte-Induced Lysis Scandinavian Journal of Immunology

Duffy, D.J., Krstic, A., Schwarzl, T., Halasz, M., Iljin, K., Fey, D., Haley, B., Whilde, J., Haapa-Paananen, S., Fey, V., Fischer, M., Westermann, F., Henrich, K.-O., Bannert, S., Higgins, D.G., Kolch, W. (2016). Wnt signalling is a bi-directional vulnerability of cancer cells, Oncotarget.

Rauch, N., Rukhlenko, O.S., Kolch, W., Kholodenko, B.N. (2016). MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance, Current Opinion in Structural Biology.

Fey, D., Matallanas, D., Rauch, J., Rukhlenko, O.S., Kholodenko, B.N. (2016). The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells, Seminars in Cell and Developmental Biology.

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

Taylor, C.T., Doherty, G., Fallon, P.G., Cummins, E.P. (2016). Hypoxia-dependent regulation of inflammatory pathways in immune cells Journal of Clinical Investigation.

2015

Vandamme D, Herrero A; Al-Mulla F; Kolch W (2015) 'Regulation of the MAPK pathway by raf kinase inhibitory protein'. Critical reviews in oncogenesis, 19 (6):405-415.

Volinsky, N., McCarthy, C. J., Von Kriegsheim, A., Saban, N., Okada-Hatakeyama, M., Kolch, W., Kholodenko, B. N. (2015) 'Signalling mechanisms regulating phenotypic changes in breast cancer cells'. Biosci Rep, .

Milewska M, Romano D; Herrero A; Guerriero ML; Birtwistle M; Quehenberger F; Hatzl S; Kholodenko BN; Segatto O; Kolch W; Zebisch A (2015) 'Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation'. PLoS ONE, 10 (6).

Nguyen LK, Matallanas DG; Romano D; Kholodenko BN; Kolch W (2015) 'Competing to coordinate cell fate decisions: the MST2-Raf-1 signalling device'. Cell Cycle, 14 (2):189-199.

Kilinc D, Lesniak A; Rashdan SA; Gandhi D; Blasiak A; Fannin PC; von Kriegsheim A; Kolch W; Lee GU (2015) 'Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK'. Advanced healthcare materials, 4 (3):395-404.

Tortolina L, Duffy DJ; Maffei M; Castagnino N; Carmody AM; Kolch W; Kholodenko BN; De Ambrosi C; Barla A; Biganzoli EM; Nencioni A; Patrone F; Ballestrero A; Zoppoli G; Verri A; Parodi S (2015) 'Advances in dynamic modelling of colorectal cancer signalling-network regions, a path toward targeted therapies'. Oncotarget, 6 (7):5041-5058.

Kim TH, Monsefi N; Song JH; von Kriegsheim A; Vandamme D; Pertz O; Kholodenko BN; Kolch W; Cho KH (2015) 'Network-based identification of feedback modules that control RhoA activity and cell migration'. Journal of molecular cell biology, 7 (3):242-252.

Ryan CM, Brown JA; Bourke E; Prendergast; M; Kavanagh C; Liu Z; Owens P; Shaw G; Kolch W; O'Brien T ; Barry FP (2015) 'ROCK activity and the G¿¿¿¿ complex mediate chemotactic migration of mouse bone marrow-derived stromal cells'. Stem Cell Research and Therapy, 6 .

Kolch W, Halasz M; Granovskaya M; Kholodenko BN (2015) 'The dynamic control of signal transduction networks in cancer cells'. Nature Reviews Cancer, 15 (9):515-527.

Schwarzl T, Higgins DG; Kolch W; Duffy DJ (2015) 'Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification'. Molecular Biology, 427 (21):3368-3374.

Varusai TM, Kolch W; Kholodenko BN; Nguyen LK (2015) 'Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses'. Molecular BioSystems, 11 (10):2750-2762.

Lesniak A, Kilinc D; Rashdan SA; von Kriegsheim A; Ashall B; Zerulla D; Kolch W; Lee GU (2015) 'In vitro study of the interaction of heregulin-functionalized magnetic-optical nanorods with MCF7 and MDA-MB-231 cells'. Faraday Discussions, 175 :189-201.

Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, Weir TL, Ehrentraut SF, Pickel C, Kuhn KA, Lanis JM, Nguyen V, Taylor CT, Colgan SP. "Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function Cell Host Microbe" (2015)

Bastiaens P, Birtwistle MR, Bluthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV & Kholodenko BN. "Silence on the relevant literature and errors in implementation" Nature Biotechnology (2015)

Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C. "Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast." PLOS Genetics (2015)

Nguyen LK, Cavadas MA, Kholodenko BN, Frank TD, Cheong A. "Species differential regulation of COX2 can be described by an NFkB-dependent logic AND gate" Cellular and Molecular Life Sciences (2015)

Nolan KA, Brennan EP, Scholz CC, Cullen C, Ryan A, Taylor CT, Godson C. "Paricalcitol protects against TGF1-induced fibrotic responses in hypoxia and stabilises HIF in renal epithelia." Exp Cell Res (2015)

Nagashima T, Inoue N, Yumoto N, Saeki Y, Magi S, Volinsky N, Sorkin A, Kholodenko BN, Okada-Hatakeyama M. "Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity" The FEBS Journal (2015)

Schaffer K, Taylor CT. "The impact of hypoxia on bacterial infection." FEBS Journal (2015)

Nguyen LK, Cavadas MA, Scholz CC, Fitzpatrick SF, Bruning U, Cummins EP, Tambuwala MM, Manresa MC, Kholodenko BN, Taylor CT, Cheong A. (2015) 'A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network'. Journal of Cell Science.

Nguyen LK, Degasperi A, Cotter P, Kholodenko BN. (2015) 'DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks'. Scientific Reports.

Kholodenko BN (2015) 'Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects'. Cell Reports.

Nguyen LK, Kholodenko BN. (2015) 'Feedback regulation in cell signalling: Lessons for cancer therapeutics'. Seminars in Cell and Developmental Biology.

Sanchez-Sanz, G; Matallanas, D; Nguyen, LK; Kholodenko, BN; Rosta, E; Kolch, W; Buchete, NV (2015) 'MST2-RASSF protein-protein interactions through SARAH domains'. Briefings in bioinformatics.

2014

Tortolina L, Duffy DJ, Maffei M, Castagnino N, Carmody AM, Kolch W, Kholodenko BN, De Ambrosi C, Barla A, Biganzoli EM, Nencioni A, Patrone F, Ballestrero A, Zoppoli G, Verri A, Parodi S. "Advances in dynamic modelling of colorectal cancer signalling-network regions, a path toward targeted therapies." OncoTarget (2014)

Dreidax, D., Bannert, S., Henrich, K.-O., Schröder, C., Bender, S., Oakes, C. C., Lindner, S., Schulte, J., Duffy, D., Schwarzl, T. et al. "p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas." Human Molecular Genetics (2014)

Guerriero Maria Luisa, Akman Ozgur E, van Ooijen Gerben. "Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure" Frontiers in Plant Science (2014)

Kilinc D, Lesniak A, Rashdan SA, Gandhi D, Blasiak A, Fannin PC, von Kriegsheim A, Kolch W, Lee GU. "Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK." Advanced Healthcare Materials (2014)

den Breems N, Nguyen LK, Kulasiri D. "Integrated signalling pathway and gene expression regulatory model to dissect dynamics of Escherichia coli challenged mammary epithelial cells." BioSystems (2014)

Nguyen LK, Zhao Q, Varusai TM, Kholodenko BN. "Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing" IET Systems Biology (2014)

Diggle CP, Moore DJ, Mali G, Zur Lage P, Ait-Lounis A, Schmidts M, Shoemark A, Garcia Munoz A, Halachev MR, Gautier P, Yeyati PL, Bonthron DT, Carr IM, Hayward B, Markham AF, Hope JE, von Kriegsheim A, Mitchison HM, Jackson IJ, Durand B, Reith W, Sheridan E, Jarman AP, Mill P. "HEATR2 Plays a Conserved Role in Assembly of the Ciliary Motile Apparatus" PloS Genet (2014)

Maciej Dobrzyński, Lan K. Nguyen, Marc R. Birtwistle, Alexander von Kriegsheim, Alfonso Blanco-Fernandez, Alex Cheong, Walter Kolch, Boris N. Kholodenko. "Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses" J. R. Soc. Interface (2014)

Romano D, Matallanas D, Frederick DT, Flaherty KT, Kolch W. "One Hippo and many masters: differential regulation of the Hippo pathway in cancer." Biochem Soc Trans (2014)

Junil Kim, Drieke Vandamme, Jeong-Rae Kim, Amaya Garcia Munoz, Walter Kolch, Kwang-Hyun Cho. "Robustness and Evolvability of the Human Signalling Network" PLOS Computational Biology (2014)

David J. Duffy, Aleksandar Krstic, Thomas Schwarzl, Desmond G. Higgins and Walter Kolch. "GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signalling" Mol Cancer Ther (2014)

James A.L. Brown, Tapesh Santra, Sharon A. Glynn, Peter Owens, Frank P. Barry. "Primary cilium-associated genes mediate bone marrow stromal cell response to hypoxia" Stem Cell Research (2014)

D Romano, LK Nguyen, D Matallanas, M Halasz, C Doherty, BN Kholodenko and W Kolch. "Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling" Nature Cell Biology (2014)

M Jiwaji, ME Sandison, J Reboud, R Stevenson, R Daly, G Barkess, K Faulds, W Kolch, D Graham, MA Girolami, JM Cooper and AR Pitt . "Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells." PLoS ONE (2014)

GEO Borgstahl, K Brader, A Mosel, S Liu, E Kremmer, KA Goettsch, C Kolar, HP Nasheuer, GG Oakley. "Interplay of DNA damage and cell cycle signalling at the level of human replication protein A" DNA Repair (2014)

J Farrell, C Kelly, J Rauch, K Kida, A Garcia-Muñoz, N Monsefi, B Turriziani, C Doherty, JP Mehta, D Matallanas, JC Simpson, W Kolch and A von Kriegsheim. "HGF Induces Epithelial-to-Mesenchymal Transition by Modulating the Mammalian Hippo/MST2 and ISG15 Pathways" Journal of Proteome Research (2014)

G Illuzzi, E Fouquerel, JC Amé, A Noll, K Rehmet, HP Nasheuer, F Dantzer, V Schreiber. "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)

Horvath G, Reglodi D, Brubel R, Halasz M, Barakonyi A, Tamas A, Fabian E, Opper B, Toth G, Cohen M, Szereday L. "Investigation of the possible functions of PACAP in human trophoblast cells" J Mol Neurosci (2014)

Tapesh Santra. "A Bayesian framework that integrates heterogeneous data for inferring gene regulatory networks". Frontiers in Bioengineering and Biotechnology (2014)

GEO Borgstahl, K Brader, A Mosel, S Liu, E Kremmer, KA Goettsch, C Kolar, HP Nasheuer, GG Oakley. "Interplay of DNA damage and cell cycle signalling at the level of human replication protein A" DNA Repair (2014)

Taylor CT, Kent BD, Crinion SJ, McNicholas WT, Ryan S. "Human adipocytes are highly sensitive to intermittent hypoxia induced NF-kappaB activity and subsequent inflammatory gene expression." Biochemical and Biophysical Research Communications (2014)

M Milewska and W Kolch. "Mig-6 participates in the regulation of cell senescence and retinoblastoma protein phosphorylation." Cellular Signalling (2014)

B Turriziani, A Garcia-Munoz, R Pilkington, C Raso, W Kolch and A von Kriegsheim. "On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction Proteomics" Biology (2014)

Song JH, Huels DJ, Ridgway RA, Sansom OJ, Kholodenko BN, Kolch W, Cho KH. "The APC network regulates the removal of mutated cells from colonic crypts." Cell Reports (2014)

Z Fábián, S Ramadurai, G Shaw, H P Nasheuer, W Kolch, C Taylor and F Barry. "Basic fibroblast growth factor modifies the hypoxic response of human bone marrow stromal cells by ERK-mediated enhancement of HIF-1 activity" Stem Cell Research (2014)

A Shilo, V Ben Hur, P Denichenko, I Stein, E Pikarsky, J Rauch, W Kolch, L Zender and R Karni. "Splicing factor hnRNP A2 activates the Ras-MAPK-ERK pathway by controlling A-Raf splicing in hepatocellular carcinoma development" RNA (A publication of the RNA Society) (2014)

T Santra, W Kolch, BN Kholodenko. "Navigating the Multilayered Organization of Eukaryotic Signalling: A New Trend in Data Integration" PLOS Computational Biology (2014)

A Degasperi, M Birtwistle, N Volinsky, J Rauch, W Kolch and BN Kholodenko. "Evaluating Strategies to Normalise Biological Replicates of Western Blot Data" PLOS One   (2014)

LK Nguyen, M Dobrzyński, D Fey, BN Kholodenko. "Polyubiquitin chain assembly and organisation determine the dynamics of protein activation and degradation" Frontiers in Physiology (2014)

Ryan CJ, Lord CJ, Ashworth A. "DAISY: picking synthetic lethals from cancer genomes." Cancer Cell (2014)

Taylor CT, Scholz CC. "Editorial: A PHD in macrophage survival" J Leukoc Biol. (2014)

Vandamme D, Minke BA, Fitzmaurice W, Kholodenko BN, Kolch W. "Systems biology-embedded target validation: improving efficacy in drug discovery." Wiley Interdiscip Rev Syst Biol Med. (2014)

2013

Sullivan C, Barry F, Porter R, Ritter T, Evans C, O'Flatharta C, Shaw G, Murphy M. "Allogeneic murine mesenchymal stem cells: migration to inflamed joints in vivo and amelioration of collagen induced arthritis when transduced to express CTLA4Ig." Stem cells dev (2013)

Scholz CC, Cavadas MA, Tambuwala MM, Hams E, Rodríguez J, Kriegsheim Av, Cotter P, Bruning U, Fallon PG, Cheong A, Cummins EP, Taylor CT. "Regulation of IL-1-induced NF-B by hydroxylases links key hypoxic and inflammatory signalling pathways." Proc Natl Acad Sci U S A. (2013)

Claudia Sibilski, Thomas Mueller, Laxmikanth Kollipara, René P. Zahedi, Ulf R. Rapp, Thomas Rudel, Angela Baljuls. "Tyr728 in the Kinase Domain of the Murine Kinase Suppressor of RAS 1 regulates Binding and Activation of the Mitogen-activated Protein Kinase Kinase" J Biol Chem (2013)

Scholz CC, Cavadas MA, Tambuwala MM, Hams E, Rodríguez J, Kriegsheim Av, Cotter P, Bruning U, Fallon PG, Cheong A, Cummins EP, Taylor CT. "Regulation of IL-1-induced NF-B by hydroxylases links key hypoxic and inflammatory signalling pathways." Proc Natl Acad Sci USA (2013)

von Thun A, Preisinger C, Rath O, Schwarz JP, Ward C, Monsefi N, Rodríguez J, Garcia-Munoz A, Birtwistle M, Bienvenut W, Anderson KI, Kolch W, von Kriegsheim A. "Extracellular signal-regulated kinase regulates RhoA activation and tumor cell plasticity by inhibiting guanine exchange factor H1 activity." Mol Cell Biol (2013)

Ronan Broderick, Michael D. Rainey, Corrado Santocanale, Heinz Peter Nasheuer. "Cell cycle-dependent formation of Cdc45-Claspin complexes in human cells are compromised by UV-mediated DNA damage." FEBS Journal (2013)

Jacquemet G, Green DM, Bridgewater RE, von Kriegsheim A, Humphries MJ, Norman JC, Caswell PT. "RCP-driven α5β1 recycling suppresses Rac and promotes RhoA activity via the RacGAP1-IQGAP1 complex." J Cell Biol (2013)

Nguyen, L. K., Kolch, W., Kholodenko, B., N. "When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling." Cell communication and signalling  (2013)

Elena Nikonova, Mikhail A. Tsyganov, Walter Kolch, Dirk Fey and Boris N. Kholodenko. "Control of the G-protein Cascade Dynamics by GDP Dissociation Inhibitors." Molecular Biosystems (2013)

Veronika Reiterer, Dirk Fey, Walter Kolch, Boris N. Kholodenko and Hesso Farhan. "Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2." Proc Natl Acad Sci U S A (2013)

Zheng Y, Zhang C, Croucher DR, Soliman MA, St-Denis N, Pasculescu A, Taylor L, Tate SA, Hardy WR, Colwill K, Dai AY, Bagshaw R, Dennis JW, Gingras AC, Daly RJ, Pawson T. "Temporal regulation of EGF signalling networks by the scaffold protein Shc1." Nature (2013)

Par G, Szereday L, Berki T, Palinkas L, Halasz M, Miseta A, Hegedus G, Szekeres-Bartho J, Vincze A, Hunyady B, Par A. "Increased baseline proinflammatory cytokine production in chronic hepatitis C patients with rapid virological response to peginterferon plus ribavirin." PLOS One (2013)

Tapesh Santra, Boris N. Kholodenko, Walter Kolch. "Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology." BMC Systems Biology (2013)

Norkus, M; Kilmartin, L; Fay, D; Murphy, MJ; O'Laighin, G; Barry, F; . "The Effect of Temperature Elevation on Cryopreserved Mesenchymal Stem Cells" Cryo Letters (2013)

Halasz M, Polgar B, Berta G, Czimbalek L, Szekeres-Bartho J. "Progesterone-Induced Blocking Factor differentially regulates trophoblast and tumour invasion by altering matrix metalloproteinase activity." Cell. Mol. Life Sci. (2013)

Mairead Diviney, Dirk Fey and Sean Commins. "Hippocampal contribution to vector model hypothesis during cue-dependent navigation" Learn Mem (2013)

Coleman CM, Vaughan EE, Browe DC, Mooney E, Howard L, Barry F. "Growth differentiation factor-5 enhances in vitro mesenchymal stromal cell chondrogenesis and hypertrophy" Stem Cells Dev (2013)

MAS Cavadas, LK Nguyen, A Cheong. "Hypoxia-inducible factor (HIF) network: insights from mathematical models."  Cell Communication and signalling (2013)

A. Degasperi and M. Calder. "A Process Algebra Framework for Multi-Scale Modelling of Biological Systems" Theoretical Computer Science   (2013)

Hogan NM, Joyce MR, Murphy JM, Barry FP, O'Brien T, Kerin MJ, Dwyer RM. "Impact of Mesenchymal Stem Cell secreted PAI-1 on colon cancer cell migration and proliferation." Biochemical and Biophysical Research Communication (2013)

Curley GF, Ansari B, Hayes M, Devaney J, Masterson C, Ryan A, Barry F, O'Brien T, Toole DO, Laffey JG. "Effects of intratracheal mesenchymal stromal cell therapy during recovery and resolution after ventilator-induced lung injury" Anesthesiology (2013)

Brown KM, Day JP, Huston E, Zimmermann B, Hampel K, Christian F, Romano D, Terhzaz S, Lee LC, Willis MJ, Morton DB, Beavo JA, Shimizu-Albergine M, Davies SA, Kolch W, Houslay MD, Baillie GS. "Phosphodiesterase-8A binds to and regulates Raf-1 kinase" Proc Natl Acad Sci U S A. (2013)

Romano D, Maccario H, Doherty C, Quinn NP, Kolch W, Matallanas D. "The differential effects of wild-type and mutated K-Ras on MST2 signalling are determined by K-Ras activation kinetics." Mol Cell Biol. (2013)

Ganly S, Hynes SO, Sharif F, Aied A, Barron V, McCullagh K, McMahon J, McHugh P, Crowley J, Wang W, O'Brien T, Greiser U. "Liposomal surface coatings of metal stents for efficient non-viral gene delivery to the injured vasculature." Journal of Controlled Release (2013)

Nguyen LK, Cavadas MA, Scholz CC, Fitzpatrick SF, Bruning U, Cummins EP, Tambuwala MM, Manresa MC, Kholodenko BN, Taylor CT, Cheong A. "A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network." J Cell Sci. (2013)

David R. Croucher, Falko Hochgrafe, Luxi Zhang, Ling Liu, Ruth J. Lyons, Danny Rickwood, Carole M. Tactacan, Brigid C. Browne, Naveid Ali, Howard Chan, Robert Shearer, David Gallego-Ortega, Darren N. Saunders, Alexander Swarbrick, and Roger J. Daly. "Involvement of Lyn and the Atypical Kinase SgK269/PEAK1 in a Basal Breast Cancer Signalling Pathway." Cancer Research (2013)

Nash ME, Fan X, Carroll WM, Gorelov AV, Barry FP, Shaw G, Rochev YA. "Thermoresponsive substrates used for the expansion of human mesenchymal stem cells and the preservation of immunophenotype." Stem Cell Rev (2013)

Doyle B, Hagan S, Al-Mulla F, Scott L, Harden S, Paul J, Mulcahy H, Murray GI, Sheahan K, O'Sullivan J, Kolch W. "Raf kinase inhibitor protein expression combined with peritoneal involvement and lymphovascular invasion predicts prognosis in Dukes' B colorectal cancer patients." Histopathology (2013)

Till Frank. "A limit cycle oscillator model for cycling mood variations of bipolar disorder patients derived from cellular biochemical reaction equations." Communications in nonlinear science and numerical simulation (2013)

Kolch W., Kholodenko B. "Systems medicine: opportunities and challenges for systems biology approaches" FEBS journal (2013)

Barry, Frank; Murphy, Mary. "Mesenchymal stem cells in joint disease and repair." Nature Reviews Rheumatology (2013)

Cummins EP, Selfridge AC, Sporn PH, Sznajder JI, Taylor CT. "Carbon dioxide-sensing in organisms and its implications for human disease" Cell Mol Life Sci (2013)

Markus S Schröder, Dermot Harnett, Benedikt A Minke, Preethy Sasidharan Nair & Committee Member Consortium. "Organizing a PhD symposium: an inside view." EMBO reports (2013)

Volinsky N., Kholodenko, B.N. "Complexity of receptor tyrosine kinase signal processing." Cold Spring Harbor perspectives in biology. (2013)

Vandamme D, Fitzmaurice W, Kholodenko B, Kolch W. "Systems medicine: helping us understand the complexity of disease" QJM (2013)

Scholz CC, Taylor CT. "Targeting the HIF pathway in inflammation and immunity." Curr Opin Pharmacol (2013)

Scholz CC, Taylor CT. "Hydroxylase-dependent regulation of the NF-κB pathway." Biol Chem (2013)

Jens Rauch, Walter Kolch, Sophie Laurent, and Morteza Mahmoudi. "Big Signals from Small Particles: Regulation of Cell Signalling Pathways by Nanoparticles." Chemical Reviews (2013)

Halasz M, Szekeres-Bartho J. "The role of progesterone in implantation and trophoblast invasion." J Reprod Immunol. (2013)

Miguel Cavadas and Alex Cheong. "Monitoring of Transcriptional Dynamics of HIF and NF-κB" Bioluminescent Imaging (2013)

Rauch J. and Kolch W. "Encyclopedia of Signalling Molecules: A-Raf kinase." Encyclopedia of Signalling Molecules (2013)

2012

Mahdi Ghavami, Meisam Rezaei, Reza Ejtehadi, Mina Lotfi, Mohammad A Shokrgozar, Baharak Abd Emamy, Jens Rauch, and Morteza Mahmoudi. "Physiological Temperature Has a Crucial Role in Amyloid Beta in the Absence and Presence of Hydrophobic and Hydrophilic Nanoparticles" ACS Chem. Neurosci. (2012)

Jiwaji M1, Daly R, Gibriel A, Barkess G, McLean P, Yang J, Pansare K, Cumming S, McLauchlan A, Kamola PJ, Bhutta MS, West AG, West KL, Kolch W, Girolami MA, Pitt AR. "Unique Reporter-Based Sensor Platforms to Monitor Signalling in Cells." PLOS One (2012)

Tierney EG1, McSorley K, Hastings CL, Cryan SA, O'Brien T, Murphy MJ, Barry FP, O'Brien FJ, Duffy GP. "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." Journal of Controlled Release (2012)

R. M. Mackenzie, I. P. Salt, W. H. Miller, A. Logan, H. A. Ibrahim, A. Degasperi, J. A. Dymott, C. A. Hamilton, M. P. Murphy, C. Delles and A. F Dominiczak. "Mitochondrial reactive oxygen species enhance AMPK activation in the endothelium of patients with coronary artery disease and diabetes." Clinical Science (2012)

Jens Rauch, Walter Kolch & Morteza Mahmoudi. "Cell Type-Specific Activation of AKT and ERK Signalling Pathways by Small Negatively-Charged Magnetic Nanoparticles." Sci. Rep (2012)

Cruet-Hennequart S, Prendergast ÁM, Shaw G, Barry FP, Carty MP. "Doxorubicin induces the DNA damage response in cultured human mesenchymal stem cells." Int J Hematol. (2012)

Byrne, M., Newell, J., Coffey, N., O Hara, M. C., Cooke, D. and Dineen, S.F. "Predictors of quality of life gains among people with type 1 diabetes participating in the Dose Adjustment for Normal Eating (DAFNE) structured education programme." Diabetes Res Clin Pract. (2012)

Dirk Fey, David R Croucher, Walter Kolch, Boris N Kholodenko. "Crosstalk and signalling switches in mitogen-activated protein kinase cascades." Frontiers in Physiology (2012)

Marc R Birtwistle, Alex von Kriegsheim, Maciej DobrzyDski, Boris Kholodenko, and Walter Kolch. "Mammalian Protein Expression Noise: Scaling Principles and the Implications for Knockdown Experiments." Mol. BioSyst. (2012)

Labusca L, Zugun-Eloae F, Shaw G, Botez P, Barry F, Mashayekhi K. "Isolation and Phenotypic Characterisation of Stem Cells from late Stage Osteoarthritic Mesenchymal Tissues." Curr Stem Cell Res Ther. (2012)

Preisinger C, Schwarz JP, Bleijerveld OB, Corradini E, Müller PJ, Anderson KI, Kolch W, Scholten A, Heck AJ. "Imatinib-dependent tyrosine phosphorylation profiling of Bcr-Abl-positive chronic myeloid leukemia cells." Leukemia. (2012)

Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej DobrzyDski, Jan B Hoek, Walter Kolch, Babatunde A Ogunnaike and Boris N Kholodenko. "Emergence of bimodal cell population responses from the interplay between analog single-cell signalling and protein expression noise." BMC Syst Biol (2012)

Vaara, M., Itkonen, H., Hillukkala, T., Liu, Z., Nasheuer, H.P., Schaarschmidt, D., Pospiech, H. and Syvaoja, J.E. "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." J Biol Chem (2012)

Davina Tondeleir, Anja Lambrechts, Matthias Muller, Veronique Jonckheere, Thierry Doll, Drieke Vandamme, Karima Bakkali, Davy Waterschoot, Marianne Lemaistre, Olivier Debeir, Christine Decaestecker, Boris Hinz, An Staes, Evy Timmerman, Niklaas Colaert, Kris Gevaert, Joel Vandekerckhove, Christophe Ampe "Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity." Molecular & Cellular Proteomics (2012)

Mooney E, Mackle JN, Blond DJ, O'Cearbhaill E, Shaw G, Blau WJ, Barry FP, Barron V, Murphy JM. "The electrical stimulation of carbon nanotubes to provide a cardiomimetic cue to MSCs." Biomaterials (2012)

Steven Watterson, Maria Luisa Guerriero, Mathieu Blanc, Alexander Mazein, Laurence Loewe, Kevin A. Robertson, Holly Gibbs, Guanghou Shui, Markus R. Wenk, Jane Hillston, and Peter Ghazal. "A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction." Biochimie (2012)

Drakulic D, Krstic A, Stevanovic M. "Establishment and initial characterization of SOX2-overexpressing NT2/D1 cell clones." Genetics and Molecular Research (2012)

Moloney TC, Hoban DB, Barry FP, Howard L, Dowd E. "Kinetics of thermally induced heat shock protein 27 and 70 expression by bone marrow-derived mesenchymal stem cells" Protein Sci. (2012)

Norkus M, Fay D, Murphy MJ, Barry F, ÓLaighin G, Kilmartin L. "On the application of active learning and gaussian processes in postcryopreservation cell membrane integrity experiments." IEEE/ACM Trans Comput Biol Bioinform (2012)

Hastings CL, Kelly HM, Murphy MJ, Barry FP, O'Brien FJ, Duffy GP. "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." J Control Release (2012)

Cuturilo G, Drakulic D, Krstic A, Gradinac M, Ilisic T, Parezanovic V, Milivojevic M, Stevanovic M, Jovanovic I. "The role of modern imaging techniques in the diagnosis of malposition of the branch pulmonary arteries and possible association with microdeletion 22q11.2." Cardiology in the Young (2012)

Oliver KM, Lenihan CR, Bruning U, Cheong A, Laffey JG, McLoughlin P, Taylor CT, Cummins EP. "Hypercapnia induces cleavage and nuclear localization of Rel B giving insight into CO2 sensing and signalling." J Biol Chem. (2012)

Broderick, R., Ramadurai, S., Toth, K., Togashi, D.M., Ryder, A.G., Langowski, J. and Nasheuer, H.P. "Cell Cycle-Dependent Mobility of Cdc45 Determined in vivo by Fluorescence Correlation Spectroscopy." PLoS One (2012)

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

Frank TD, Cheong A, Okada M, Kholodenko BN. "Catching transcriptional regulation by thermostatistical modelling." Phys. Biol. (2012)

Crean D, Felice L, Taylor CT, Rabb H, Jennings P, Leonard MO. "Glucose reintroduction triggers the activation of Nrf2 during experimental ischemia reperfusion." Mol Cell Biochem. (2012)

Nguyen LK. "Regulation of oscillation dynamics in biochemical systems with dual negative feedback loops." J R Soc Interface. (2012)

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

Oliver KM, Lenihan CR, Bruning U, Cheong A, Laffey JG, McLoughlin P, Taylor CT & Cummins EP. "Hypercapnia induces cleavage and nuclear localization of RELB giving insight into CO2 sensing and signalling" J. Biol. Chem. (2012)

Zebisch A, Wölfler A, Fried I, Wolf O, Lind K, Bodner C, Haller M, Drasche A, Pirkebner D, Matallanas D, Rath O, Blyth K, Delwel R, Taskesen E, Quehenberger F, Kolch W, Troppmair J, Sill H. "Frequent loss of RAF kinase inhibitor protein expression in acute myeloid leukemia." Leukemia (2012)

Tibarewal P, Zilidis G, Spinelli L, Schurch N, Maccario H, Gray A, Perera NM, Davidson L, Barton GJ, Leslie NR. "PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity." Sci Signal. (2012)

von Thun A, Birtwistle M, Kalna G, Grindlay J, Strachan D, Kolch W, von Kriegsheim A, Norman JC. "ERK2 drives tumour cell migration in three-dimensional microenvironments by suppressing expression of Rab17 and liprin- β2." J Cell Sci. (2012)

Vaughan EE, Liew A, Mashayekhi K, Dockery P, McDermott J, Kealy B, Flynn A, Duffy A, Coleman C, O'Regan A, Barry FP, O'Brien T. "Pre-treatment of Endothelial Progenitor Cells with Osteopontin Enhances Cell Therapy for Peripheral Vascular Disease." Cell Transplant. (2012)

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

Frank, T. D., Blau, J. J. C., Turvey, M. T. "Symmetry breaking analysis of prism adaptation's latent aftereffect." Cognitive Science (2012)

Cahill E, Costello CM, Rowan SC, Harkin S, Howell K, Leonard MO, Southwood M, Cummins EP, Fitzpatrick SF, Taylor C, Morrell NW, Martin F, McLoughlin P. "Gremlin Plays a Key Role in the Pathogenesis of Pulmonary Hypertension." Circulation (2012)

Birmingham E, Niebur GL, McHugh PE, Shaw G, Barry FP, McNamara LM. "Osteogenic differentiation of mesenchymal stem cells is regulated by osteocyte and osteoblast cells in a simplified bone niche." Eur Cell Mater. (2012)

Tsyganov, M. A., Kolch, W. & Kholodenko, B. N. "The topology design principles that determine the spatiotemporal dynamics of G-protein cascades." Mol Biosyst. (2012)

Frank, Till D. "Nambu bracket formulation of nonlinear biochemical reactions beyond mass action kinetics." Journal of Nonlinear Mathematical Physics (2012)

Angela Baljuls, Boris N. Kholodenko, Walter Kolch. "It takes two to tango: signalling by dimeric Raf kinases." Molecular Biosystems. (2012)

Bulman S, Barron V, Coleman C, Barry F. "Enhancing the MSC Therapeutic Response: Cell Localization and Support for Cartilage Repair." Tissue Eng Part B Rev. (2012)

Ansboro S, Greiser U, Barry F, Murphy M. "Strategies for improved targeting of therapeutic cells: implications for tissue repair." Eur Cell Mater. (2012)

Kholodenko, B., Yaffe, M. B. & Kolch, W. "Computational approaches for analyzing information flow in biological networks." Sci. Signal. (2012)

Duffy, D. J. "Instructive reconstruction: A new role for apoptosis in pattern formation." BioEssays (2012)

Nguyen, L. K., Matallanas, D., Croucher, D. R., von Kriegsheim, A. & Kholodenko, B. N. "Signalling by protein phosphatases and drug development: a systems-centered view." FEBS J. (2012)

Maciej DobrzyDski, Dirk Fey, Lan K Nguyen, and Boris N Kholodenko. "Bimodal Protein Distributions in Heterogeneous Oscillating Systems." CMSB (2012)

Dirk Fey, David R. Croucher, Walter Kolch, Boris N. Kholodenko. "Understanding cell fate decisions by identifying crucial system dynamics." New Challenges for Cancer Systems Biomedicine SIMAI Springer Series (2012)

 

2011

Liang, B., Tikhanovich, I., Nasheuer, H.P. and Folk, W.R. "Stimulation of BKV DNA replication by NFI-family transcription factor." J Virol (2011)

Matallanas D, Romano D, Al-Mulla F, O'Neill E, Al-Ali W, Crespo P, Doyle B, Nixon C, Sansom O, Drosten M, Barbacid M, Kolch W. "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." Mol Cell. (2011)

Nguyen LK, Muñoz-García J, Maccario H, Ciechanover A, Kolch W, Kholodenko BN. "Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System." PLoS Comput Biol. (2011)

Duffy, D. J., Millane, R. C. and Frank, U. "A heat shock protein and Wnt signalling crosstalk during axial patterning and stem cell proliferation." Developmental Biology (2011)

Birtwistle MR, von Kriegsheim A, Kida K, Schwarz JP, Anderson KI, Kolch W. "Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modelling." PLoS One (2011)

Bruning U, Fitzpatrick SF, Birtwistle M, Taylor CT, Cheong A. "NF-kB and HIF display synergistic behaviour during hypoxic inflammation." Cell Mol Life Sci. (2011)

Xu TR, Lu RF, Romano D, Pitt A, Houslay MD, Milligan G, Kolch W. "Eukaryotic translation initiation factor 3, subunit a, regulates the extracellular signal-regulated kinase pathway." Mol Cell Biol. (2011)

Zhang, S., Roche, K., Nasheuer, H. P., Lowndes, N. F. "Modification of histones by the sugar {beta}-N-acetylglucosamine (GlcNAc) occurs on multiple residues, including H3 serine 10, and is cell cycle regulated." J Biol Chem (2011)

Duffy MM, Pindjakova J, Hanley SA. McCarthy C, Weidhofer GA, Sweeney EM, English K, Shaw G, Murphy JM, Barry FP, Mahon BP, Beltob O, Ceredig R, Griffin MD. "Mesenchymal stem cell inhibition of T-helper 17 differentiation is triggered by cell-cell contact and mediated by prostaglandin E2 via the EP4 receptor." Eur J Immunology (2011)

Pakay JL, Diesch J, Gilan O, Yip YY, Sayan E, Kolch W, Mariadason JM, Hannan RD, Tulchinsky E, Dhillon AS. "A 19S proteasomal subunit cooperates with an ERK MAPK-regulated degron to regulate accumulation of Fra-1 in tumour cells." Oncogene (2011)

Bruning U, Cerone L, Neufeld Z, Fitzpatrick SF, Cheong A, Scholz CC, Simpson DA, Leonard MO, Tambuwala MM, Cummins EP, Taylor CT. "MicroRNA-155 Promotes Resolution of Hypoxia-Inducible Factor 1{alpha} Activity during Prolonged Hypoxia." Mol Cell Biol. (2011)

Hassett P, Curley GF, Contreras M, Masterson C, Higgins BD, O'Brien T, Devaney J, O'Toole D, Laffey JG. "Overexpression of pulmonary extracellular superoxide dismutase attenuates endotoxin-induced acute lung injury." Intensive Care Med. (2011)

Mackle JN, Blond DJ, Mooney E, McDonnell C, Blau WJ, Shaw G, Barry FP, Murphy JM, Barron V. "In vitro Characterization of an Electroactive Carbon-Nanotube-Based Nanofiber Scaffold for Tissue Engineering." Macromol Biosc. (2011)

Birtwistle MR, Kolch W. "Biology using engineering tools: The negative feedback amplifier." Cell Cycle. (2011)

Sharif F, Hynes SO, McCullagh KJ, Ganley S, Greiser U, McHugh P, Crowley J, Barry F, O'Brien T. "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." Gene Ther. (2011)

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

Dwyer RM, Ryan J, Havelin RJ, Morris JC, Miller BW, Liu Z, Foley MJ, Barrett HH, Murphy M, Barry FP, O Brien T and Kerin MJ. "Mesenchymal Stem Cell (MSC) mediated delivery of the Sodium Iodide Symporter (NIS) supports radionuclide imaging and treatment of breast cancer." Stem Cells (2011)

Aksamitiene E, Achanta S, Kolch W, Kholodenko BN, Hoek JB, Kiyatkin A. "Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signalling pathway in breast cancer cells." Cell Signal (2011)

Lopresti-Goodman, S. M., Turvey, M. T., Frank, T. D. "Behavioral dynamics of the affordance "graspable"." Attention, Perception, and Psychophysics (2011)

Frank T D. "Unifying mass-action kinetics and Newtonian mechanics by means of Nambu brackets." Journal of Biological Physics (2011)

Frank, T.D. "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." European Journal of Scientific Research (2011)

Bowes T, Finlay W, Eglon M, Liew A, O'Kennedy R, Barry FP, Taylor W, O'Brien T, Greiser U. "Developing cell-specific antibodies to endothelial progenitor cells using avian immune phage display technology." Journal of biomolecular screening (2011)

Locke P, O Brien T, Tuan RS. "Stem Cell Research & Therapy marks its first anniversary." Editorial Stem Cell Research & Therapy (2011)

Tikhanovich, I., B. Liang, C. Seoighe, W. R. Folk, and H. P. Nasheuer. "Inhibition of human BK polyomavirus replication by small non-coding RNAs." J Virol (2011)

Rauch, J., Moran-Jones, K., Albrecht, V., Schwarzl, T., Hunter, K., Gires, O., and Kolch, W. "c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathway." Cancer Research (2011)

I. Morecroft , B. Doyle, M. Nilsen, W. Kolch, K. Mair and M. R. MacLean. "Mice lacking the Raf-1 kinase inhibitor protein exhibit exaggerated hypoxia-induced pulmonary hypertension." Br J Pharmacol. (2011)

McGinley L, McMahon J, Strappe P, Barry F, Murphy M, O'Toole D, O'Brien T. "Lentiviral Vector Mediated modification of Mesenchymal Stem Cells & enhanced survival in an in vitro mode of Ischaemia." Stem Cell Research & Therapy (2011)

Heneghan HM, Miller M, McAnena OJ, O'Brien T, Kerin MJ. "Differential miRNA expression in omental adipose tissue and in the circulation of obese patients identifies novel metabolic biomarkers." J Clin Endocrinol Metab. (2011)

Lan K. Nguyen and Don Kulasiri. "Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system." IET Syst Biol. (2011)

J. O Sullivan, S. D Arcy, F. P. Barry, J.M. Murphy, C.M. Coleman. "Mesenchymal Chondroprogenitor Cell Origin, Isolation and Therapeutic Potential." Stem Cell Research & Therapy (2011)

Fahd Al-Mulla, Milad S. Bitar, May Al-Maghrebi, Abdulla I. Behbehani, Waleed Al-Ali, Oliver Rath, Brendan Doyle, Kit Yee Tab, Andrew Pitt and Walter Kolch. "Raf Kinase Inhibitor Protein RKIP enhances signalling by Glycogen Synthase Kinase-3 b." Cancer Res (2011)

Agbor TA, Cheong A, Comerford KM, Scholz CC, Bruning U, Clarke A, Cummins EP, Cagney G, Taylor CT. "Small ubiquitin-related modifier (SUMO)-1 promotes glycolysis in hypoxia." Biol Chem. (2011)

Timpson P, McGhee EJ, Morton JP, von Kriegsheim A, Schwarz JP, Karim SA, Doyle B, Quinn JA, Carragher NO, Edward M, Olson MF, Frame MC, Brunton VG, Sansom OJ, Anderson KI. "Spatial regulation of RhoA activity during pancreatic cancer cell invasion driven by mutant p53." Cancer Research (2011)

Holladay C, Power K, Sefton M, O Brien T, Gallagher W. "Functionalized scaffold mediated interleukin-10 gene delivery significantly improves survival rates of stem cells in vivo." Mol Ther. (2011)

Frank, T.D. "Virial theorem and non-equilibrium canonical-dissipative distributions characterizing Parkinson tremor." International Journal of Modern Physics (2011)

Kulkarni MM, Greiser U, O'Brien T, Pandit A. "A Temporal Gene Delivery System based on Fibrin Microshpheres." Mol Pharm. (2011)

Jens Rauch, Natalia Volinsky, David Romano and Walter Kolch. "The secret life of kinases: functions beyond catalysis." Cell Commun Signal. (2011)

Matallanas D, Birtwistle M, Romano D, Zebisch A, Rauch J, von Kriegsheim A, Kolch W. "Raf family kinases: old dogs have learned new tricks." Genes & Cancer. (2011)

Flynn A, O'Brien T. "Stem Cell Therapy for Cardiac Disease." Expert Opinion on Biological Therapy. (2011)

Taylor CT, Cummins EP. "Regulation of gene expression by carbon dioxide." J Physiol. (2011)

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

Santra T, Kholodenko B, Kolch W. "An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells." Advances in Systems Biology, Advances in Experimental Medicine and Biology (2011)

Maciej DobrzyDski, Piotr Bernatowicz, Malgorzata Kloc, Jacek Z. Kubiak. "Evolution of Bet-Hedging Mechanisms in Cell Cycle and Embryo Development Stimulated by Weak Linkage of Stochastic Processes." Cell Cycle in Development (2011)

2010

Meesbah Jiwaji, Rónán Daly, Kshama Pansare, Pauline McLean, Jingli Yang, Walter Kolch, Andrew R Pitt. "The Renilla luciferase gene as a reference gene for normalization of gene expression intransiently transfected cells." BMC Molecular Biology (2010)

Oliver E. Sturm, Richard Orton, Joan Grindlay, Marc Birtwistle, Vladislav Vyshemirsky, David Gilbert, Muffy Calder, Andrew Pitt, Boris Kholodenko, Walter Kolch. "The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier." Science Signalling (2010)

Mohammed Dakna, Keith Harris, Alexandros Kalousis, Sebastien Carpentier, Walter Kolch, Joost PSchanstra, Marion Haubitz, Antonia Vlahou, Harald Mischak, Mark Girolami. "Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers." BMC Bioinformatics (2010)

J. Muñoz-García, Z. Neufeld, and C. Torney. "Nutrient exposure of chemotactic organisms in small scale turbulent flows." New Journal of Physics (2010)

Donnelly EM, Strappe PM, McGinley LM, Madigan NN, Geurts E, Rooney GE, Windebank AJ, Fraher J, Dockery P, O'Brien T, McMahon SS. "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." Journal of Gene Medicine (2010)

Duffy GP, D'Arcy S, Ahsan T, Nerem RM, O'Brien T, Barry F. Tissue Eng Part A. "Mesenchymal Stem Cells Overexpressing Ephrin-B2 Rapidly Adopt an Early Endothelial Phenotype with Simultaneous Reduction of Osteogenic Potential." Tissue Engineering Part A (2010)

Ward JB, Lawler K, Amu S, Taylor CT, Fallon PG, Keely SJ. "Hydroxylase inhibition attenuates colonic epithelial secretory function and ameliorates experimental diarrhea." FASEB Journal (2010)

Cummins EP, Oliver KM, Lenihan CR, Fitzpatrick SF, Bruning U, Scholz CC, Slattery C, Leonard MO, McLoughlin P, Taylor CT. "NF-κB links CO2 sensing to innate immunity and inflammation in mammalian cells." J Immunol. (2010)

Taylor CT, McElwain JC. "Ancient atmospheres and the evolution of oxygen sensing via the hypoxia inducible factor in metazoans." Physiology (2010)

Little CB, Smith MM, Cake MA, Read RA, Murphy MJ, Barry FP. "The OARSI histopathology initiative: recommendations for histological assessments of osteoarthritis in sheep and goats." Osteoarthritis and Cartilage (2010)

Shin, S. Y., Rath, O., Zebisch, A., Choo, S. M., Kolch, W., Cho, K. H. "Functional roles of multiple feedback loops in extracellular signal-regulated kinase and Wnt signalling pathways that regulate epithelial-mesenchymal transition." Cancer Res (2010)

O'Brien T, Barry F. "Introduction to Series on Mesenchymal Stromal (Stem) Cells-MSCs." Human Gene Therapy (2010)

Mischak, H., Allmaier, G., Apweiler, R., Attwood, T., Baumann, M., Benigni, A., Bennett, S. E., Bischoff, R., Bongcam-Rudloff, E., Capasso, G., Coon, J. J., D'Haese, P., Dominiczak, A. F., Dakna, M., Dihazi, H., Ehrich, J. H., Fernandez-Llama, P., Fliser, D., Frokiaer, J., Garin, J., Girolami, M., Hancock, W. S., Haubitz, M., Hochstrasser, D., Holman, R. R., Ioannidis, J. P., Jankowski, J., Julian, B. A., Klein, J. B., Kolch, W., Luider, T., Massy, Z., Mattes, W. B., Molina, F., Monsarrat, B., Novak, J., Peter, K., Rossing, P., Sanchez-Carbayo, M., Schanstra, J. P., Semmes, O. J., Spasovski, G., , Theodorescu, D. , Thongboonkerd, V, Vanholder, R., Veenstra, T. D., Weissinger, E., Yamamoto, T., Vlahou, A. "Recommendations for biomarker identification and qualification in clinical proteomics." Sci Transl Med (2010)

Moloney TC, Rooney GE, Barry FP, Howard L, Dowd E. "Potential of rat bone marrow-derived mesenchymal stem cells as vehicles for delivery of neurotrophins to the Parkinsonian rat brain." Journal of Brain Research (2010)

Vera, J., Rath, O., Balsa-Canto, E., , Banga, J. R., Kolch, W., Wolkenhauer, O. "Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models." Mol Biosyst. (2010)

Sandison, M. E., Cumming, S. A., Kolch, W., Pitt, A. R. "On-chip immunoprecipitation for protein purification." Lab Chip. (2010)

Schaible B, Schaffer KE, Taylor CT. "Hypoxia, innate immunity and infection in the lung." Respiratory Physiology and Neurobiology (2010)

Chua YL, Dufour E, Dassa EP, Rustin P, Jacobs HT, Taylor CT, Hagen T. "Stabilization of hypoxia inducible factor-1alpha protein in hypoxia occurs independently of mitochondrial reactive species production oxygen." J Biol Chem (2010)

Zhdanov AV, Ogurtsov VI, Taylor CT, Papkovsky DB. "Monitoring of cell oxygenation and responses to metabolic stimulation by intracellular oxygen sensing technique." Integrative Biology (2010)

Good DM, Zürbig P, Argilés A, Bauer HW, Behrens G, Coon JJ, Dakna M, Decramer S, Delles C, Dominiczak AF, Ehrich JH, Eitner F, Fliser D, Frommberger M, Ganser A, Girolami MA, Golovko I, Gwinner W, Haubitz M, Herget-Rosenthal S, Jankowski J, Jahn H, Jerums G, Julian BA, Kellmann M, Kliem V, Kolch W, Krolewski AS, Luppi M, Massy Z, Melter M, Neusüss C, Novak J, Peter K, Rossing K, Rupprecht H, Schanstra JP, Schiffer E, Stolzenburg JU, Tarnow L, Theodorescu D, Thongboonkerd V, Vanholder R, Weissinger EM, Mischak H, Schmitt-Kopplin P. "Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease." Mol Cell Proteomics. (2010)

Javier Munoz-Garc, Boris N. Kholodenko and Zoltan Neufeld. "Formation of Intracellular Concentration Landscapes by Multisite Protein Modification." Biophys J. (2010)

Tambuwala MM, Cummins EP, Lenihan CR, Kiss J, Stauch M, Scholz CC, Fraisl P, Lasitschka F, Mollenhauer M, Saunders SP, Maxwell PH, Carmeliet P, Fallon PG, Schneider M, Taylor CT. "Loss of Prolyl Hydroxylase-1 Protects Against Colitis Through Reduced Epithelial Cell Apoptosis and Increased Barrier Function." Gastroenterology (2010)

Zhdanov AV, Ward MW, Taylor CT, Souslova EA, Chudakov DM, Prehn JH, Papkovsky DB. "Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na(+)/Ca(2+) exchange." Biochimica et biophysica Acta (2010)

Lock FE, Underhill-Day N, Dunwell T, Matallanas D, Cooper W, Hesson L, Recino A, Ward A, Pavlova T, Zabarovsky E, Grant MM, Maher ER, Chalmers AD, Kolch W, Latif F. "The RASSF8 candidate tumor suppressor inhibits cell growth and regulates the Wnt and NF-κB signalling pathways." Oncogene (2010)

Takashi Nakakuki, Marc R. Birtwistle, Yuko Saeki, Noriko Yumoto, Kaori Ide, Takeshi Nagashima, Lutz Brusch, Babatunde A. Ogunnaike, Mariko Okada-Hatakeyama and Boris N. Kholodenko. "Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics." Cell (2010)

Edita Aksamitiene, Boris N. Kholodenko, Walter Kolch, Jan B. Hoek, Anatoly Kiyatkin. "PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells." Cell Signal. (2010)

McMahon SS, Albermann S, Rooney GE, Shaw G, Garcia Y, Sweeney E, Hynes J, Dockery P, O'Brien T, Windebank AJ, Allsopp TE, Barry FP. "Engraftment, migration and differentiation of neural stem cells in the rat spinal cord following contusion injury." Cryotherapy (2010)

Rooney GE, Nistor GI, Barry FB, Keirstead HS. "In vitro differentiation potential of human embryonic versus adult stem cells." Regenerative Medicine (2010)

O'Shea CA, Hynes SO, Shaw G, Coen BA, Hynes AC, McMahon J, Murphy M, Barry F, O'Brien T ."Bolus Delivery of Mesenchymal Stem Cells to Injured Vasculature in the Rabbit Carotid Artery Produces a Dysfunctional Endothelium." Tissue Eng Part A (2010)

Tikhanovich I, Nasheuer HP. "Host-specific replication of BK virus DNA in mouse cell extracts is independently controlled by DNA polymerase alpha-primase and inhibitory activities." Journal of Virology (2010)

Moloney TC, Dockery P, Windebank AJ, Barry FP, Howard L, Dowd E. "Survival and Immunogenicity of Mesenchymal Stem Cells from the Green Fluorescent Protein Transgenic Rat in the Adult Rat Brain." Neurorehabilitation and Neural repair (2010)

Stocki, P. Morris, N. J. Preisinger, C. Wang, X. N. Kolch, W. Multhoff, G. Dickinson, A. M. "Identification of potential HLA class I and class II epitope precursors associated with heat shock protein 70 (HSPA)." Cell Stress Chaperones (2010)

Tian-Rui Xu, Vladislav Vyshemirsky, Amélie Gormand, Alex von Kriegsheim, Mark Girolami, George S. Baillie, Dominic Ketley, Allan J. Dunlop, Graeme Milligan, Miles D. Houslay, and Walter Kolch. "Inferring Signalling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species." Sci. Signal. (2010)

Fleming, R. M., I. Thiele, G. Provan and H. P. Nasheuer (2010). "Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism." Journal of Theoretical Biology (2010)

Griffin M, Greiser U, Barry F, O Brien T, Ritter T. "Genetically Modified Mesenchymal Stem Cells and Their Clinical Potential in Acute Cardiovascular Disease." Discovery Medicine (2010)

Kennedy A, Ng CT, Biniecka M, Saber T, Taylor C, O'Sullivan J, Veale DJ, Fearon U. "Angiogenesis and blood vessel stability in inflammatory arthritis." Arthritis & Rheumatism (2010)

Jens Rauch, Eric O´Neill, Brigitte Mack, Christoph Matthias, Markus Munz, Walter Kolch & Olivier Gires. "Heterogeneous nuclear ribonucleoprotein H blocks MST2-mediated apoptosis in cancer cells by regulating A-Raf transcription." Cancer Res (2010)

David Romano, David Matallanas, Gregory Weitsman, Christian Preisinger, TonyNg and Walter Kolch. "Co-operation between Raf-1 and Akt pathways for the inhibition of RASSF1A-MST2-triggered apoptosis." Cancer Res. (2010)

David Romano, David Matallanas, Gregory Weitsman, Christian Preisinger, Tony Ng and Walter Kolch. "Proapoptotic Kinase MST2 Coordinates Signalling Crosstalk between RASSF1A, Raf-1, and Akt." Cancer Res (2010)

Martin FT, Dwyer RM, Kelly J, Murphy JM, Curran C, Miller N, Hennessy E, Dockery P, Barry FP, O'Brien T, Kerin MJ. "Potential Role of Mesenchymal Stem Cells (MSCs) in the Breast Tumor Microenvironment: Stimulation of Epithelial to Mesenchymal Transition (EMT)." Breast Cancer Research and Treatment (2010)

Hoare M, Greiser U, Schu S, Mashayekhi K, Aydogan E, Murphy M, Barry F, Ritter T, O'Brien T. "Enhanced lipoplex-mediated gene expression in mesenchymal stem cells using reiterated nuclear localization sequence peptides." Journal of Gene Medicine (2010)

Preisinger, C. Kolch, W. "The Bcr-Abl kinase regulates the actin cytoskeleton via a GADS/Slp-76/Nck1 adaptor protein pathway." Cell Signal. (2010)

O'Cearbhaill ED, Murphy M, Barry F, McHugh PE, Barron V. "Behavior of Human Mesenchymal Stem Cells in Fibrin-Based Vascular Tissue Engineering Constructs." Annals of Biomedical Engineering (2010)

Peng Hor C, O Donnell JM, Murphy AW, O'Brien T, Krompans TJB. "General Practioners' Attitudes and Preparedness toward Clinical Decision Support in e-Prescribing (CDS-dP) Adoption in the West of Ireland: a cross sectional study." BMC Med Inform Decis Mak. (2010)

Eivers SS, McGivney BA, Fonseca RG, MacHugh DE, Menson K, Park SD, Rivero JL, Taylor CT, Katz LM, Hill EW. "Alterations in oxidative gene expression in equine skeletal muscle following exercise and training." Physiological Genomics (2010)

David Matallanas & Piero Crespo. "New druggable targets in the Ras pathway." Current Opinion in Molecular Therapeutics (2010)

Kate Whitfiel, Karl-Heinz Huemer, Diana Winter, Steffen Thirstrup, Christian Libersa, Beatrice Barraud, Christine Kubiak, Lea Stankovski, Xina Grahlert, Gabriele Dreier, Sebastian Geismann, Wolfgang Kuchinke, Anke Strenge-Hesse, Zsuza Temesvari, Gyorgy Blasko, Gabriella Kardos, Timothy O'Brien, Margaret Cooney, Siobhan Gaynor, Arrigo Schieppati, Mariantonia Serrano, Fernando de Andres, Nuria Sanz, Raquel Hernandez, German Kreis, Charlotte Asker-Hagelberg, Hanna Johansson, Adeeba Asghar, Jean-Marc Husson, Jacques Demotes and Christian Gluud. "Compassionate use of interventions: results of a European Clinical Research Infrastructures Network (ECRIN) survey of ten European countries." Trials (2010)

Odile Cohen-Haguenauer, Nicolas Creff, Pedro Cruz, Celia Tunc, Alessandro Aïuti, Christopher Baum, Fatima Bosch, Pontus Blomberg, Klaus Cichutek, Mary Collins, Olivier Danos, Frédéric Dehaut, Marc Federspiel, Eithan Galun, Henk Garritsen, Hansjörg Hauser, Martin Hildebrandt David Klatzmann, Otto Merten, Eugenio Montini, Tim O'Brien, Amos Panet, Linda Rasooly, Daniel Scherman, Manfred Schmidt, Matthias Schweitzer, Pierre Tiberghien, Thierry Vandendriessche, Holger Ziehr, Seppo Ylä- Herttuala, Christof von Kalle, Gösta Gahrton and Manuel Carrondo. "Relevance of an Academic GMP Pan-European Vector Infra-structure (PEVI)." Curr Gene Ther. (2010)

Muñoz-García J, Kholodenko BN. "Signalling over a distance: gradient patterns and phosphorylation waves within single cells." Biochem Soc Trans (2010)

Moran CJ, Shannon FJ, Barry FP, O'Byrne JM, O'Brien T, Curtin W. "Translation of science to surgery: linking emerging concepts in biological cartilage repair to surgical intervention." J Bone Joint Surg Br. (2010)

Coleman CM, Curtin C, Barry FP, O'Flatharta C, Murphy JM. "Mesenchymal Stem Cells and Osteoarthritis: Remedy or Accomplice?" Hum Gene Ther. (2010)

Kolch W, Pitt A. "Functional proteomics to dissect tyrosine kinase signalling pathways in cancer." Nature Reviews Cancer (2010)

Dwyer RM, Khan S, Barry FP, O'Brien T, Kerin MJ. "Advances in mesenchymal stem cell-mediated gene therapy for cancer." Stem Cell Res Ther. (2010)

Kholodenko BN1, Hancock JF, Kolch W. "Signalling Ballet in Space and Time." Nature Reviews Molecular Cell Biology 11 (2010)

Holladay C, O'Brien T, Pandit A. "Non-viral gene therapy for myocardial engineering." Wiley Interdiscip Rev Nanomed Nanobiotechnol. (2010)

Colgan SP, Taylor CT. "Hypoxia: an alarm signal during intestinal inflammation." Nat Rev Gastroenterol Hepatol (2010)

Rauch J, Kolch W. "A-Raf." AfCS-Nature Molecule Pages (2010)

Donnelly A, Johar S, O'Brien T, Tuan RS. "Welcome to Stem Cell Research & Therapy." Stem Cell Research&Therapy (2010)

Hynes SO, McCabe C, O'Brien T. "α Cell Protection by Inhibition of iNOS through Lentiviral Vector-Based Strategies." Methods Mol Biol. (2010)

2009

Schilling, M., Maiwald, T., Hengl, S., Winter, D., Kreutz, C., Kolch, W., Lehmann, W. D., Timmer, J. & Klingmuller, U. "Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions." Mol Syst Biol (2009)

Zach J, Zollner-Schwetz I, Krause R, Zebisch A, Rohn A, Sill H. "Gram stain/aolc screening for detection of catheter related bloodstream infection." Journal of Infection (2009)

Muñoz-García, Javier; Neufeld, Zoltán. "Aggregation of chemotactic organisms in a differential flow." Physical Review (2009)

Alex von Kriegsheim, Daniela Baiocchi, Marc Birtwistle, David Sumpton, Willy Bienvenut, Nicholas Morrice, Kayo Yamada, Angus Lamond, Gabriella Kalna, Richard Orton, David Gilbert and Walter Kolch. "Cell fate decisions are specified by the dynamic ERK interactome." Nature Cell Biology (2009)

Densham, R. M., O'Neill, E., Munro, J., Konig, I., Anderson, K., Kolch, W. & Olson, M. F. "MST kinases monitor actin cytoskeletal integrity and signal via c-Jun N-terminal kinase stress-activated kinase to regulate p21Waf1/Cip1 stability." Mol Cell Biol (2009)

Orton, R. J., Adriaens, M. E., Gormand, A., Sturm, O. E., Kolch, W. & Gilbert, D. R. "Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway." BMC Syst Biol (2009)

Duffy AM, O'Brien T, McMahon JM. "Generation of antioxidant adenovirus gene transfer vectors encoding CuZnSOD, MnSOD, and catalase." Methods in Molecular Biology (2009)

Eglon M, McGrath B, O'Brien T. "HPLC purification of adenoviral vectors." Methods in Molecular Biology (2009)

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

Cooper, W. N., Hesson, L. B., Matallanas, D., Dallol, A., von Kriegsheim, A., Ward, R., Kolch, W. & Latif, F. "RASSF2 associates with and stabilizes the proapoptotic kinase MST2." Oncogene (2009)

Stephan H1, Concannon C, Kremmer E, Carty MP, Nasheuer HP. "Ionizing radiation-dependent and independent phosphorylation of the 32-kDa subunit of replication protein A during mitosis." Nucleic Acids Research (2009)

Julio Vera, Taesoo Kwon, Ulf Schmitz, Walter Kolch, Olaf Wolkenhauer. "Exploration of homodimer receptor: homodimer protein interactions." Int J Bioinform Res Appl (2009)

Dallol A, Hesson LB, Matallanas D, Cooper WN, O'Neill E, Maher ER, Kolch W, Latif F. "RAN GTPase is a RASSF1A effector involved in controlling microtubule organization." Cell Cycle (2009)

Kaimachnikov, N. P. & Kholodenko, B. N. "Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle." FEBS Journal (2009)

Dhillon, A. S., Yip, Y. Y., Grindlay, G. J., Pakay, J. L., Dangers, M., Hillmann, M., Clark, W., Pitt, A., Mischak, H. & Kolch, W. "The C-terminus of Raf-1 acts as a 14-3-3-dependent activation switch." Cell Signal (2009)

Faley, S. L., Copland, M., Wlodkowic, D., Kolch, W., Seale, K. T., Wikswo, J. P. & Cooper, J. M.. "Microfluidic single cell arrays to interrogate signalling dynamics of individual, patient-derived hematopoietic stem cells." Lab Chip (2009)

J Sebastia, D Kieran, B Breen, MA King, DF Netteland, D Joyce, SF Fitzpatrick, CT Taylor and JHM Prehn. "Angiogenin protects motoneurons against hypoxic Injury." Cell Death and Differentiation (2009)

Kim, D., Kolch, W. & Cho, K. H. "Multiple roles of the NF-kappaB signalling pathway regulated by coupled negative feedback circuits." FASEB J (2009)

Borisov, N., Aksamitiene, E., Kiyatkin, A., Legewie, S., Berkhout, J., Maiwald, T., Kaimachnikov, N. P., Timmer, J., Hoek, J. B. & Kholodenko, B. N. "Systems-level interactions between insulin-EGF networks amplify mitogenic signalling" Molecular Systems Biology (2009)

Lévy N, Oehlmann M, Delalande F, Nasheuer HP, Van Dorsselaer A, Schreiber V, de Murcia G, Ménissier-de Murcia J, Maiorano D, Bresson A. "XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase" Nucleic Acids Research (2009)

Munoz-Garcia, J., Neufeld, Z. & Kholodenko, B. N. "Positional information generated by spatially distributed signalling cascades." PLoS Computational Biology (2009)

Mahon C, Liang B, Tikhanovich I, Abend JR, Imperiale MJ, Nasheuer HP, Folk WR. "Restriction of human polyomavirus BK virus DNA replication in murine cells and extracts" J Virol. (2009)

Suenaga, A., Hatakeyama, M., Kiyatkin, A. B., Radhakrishnan, R., Taiji, M. & Kholodenko, B. N. "Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor." Biophysical Journal (2009)

Kholodenko, Boris N. "Spatially distributed cell signalling." FEBS Letters (2009)

Mieske K, Flaherty G, O'Brien T. "Journeys to high altitude-risks and recommendations for travellers with preexisting medical conditions." Journal of Travel Medicine (2009)

Kulkarni M, Greiser U, O'Brien T, Pandit A. "Liposomal Gene Delivery Mediated by Tissue-Engineered Scaffolds: Trends Biotechnology." Trends in Biotechnology (2009)

Birtwistle MR, Kholodenko BN. "Endocytosis and signalling: a meeting with mathematics." Mol Oncol. (2009)

H. P. Nasheuer. "Genome Stability and Human Diseases." Subcell Biochem (2009)

Conmy, S. & H. P. Nasheuer. "The use of transgenic mice in cancer and genome stability research." Subcell Biochem (2009)

Broderick, S., K. Rehmet, C. Concannon & H. P. Nasheuer. "Eukaryotic single-stranded DNA binding proteins: central factors in genome stability." Subcell Biochem (2009)

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