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Zhang, W., Chronis, C., Chen, X., Zhang, H., Spalinskas, R., Pardo, M., Chen, L., Wu, G., Zhu, Z., Yu, Y., et al. (2019). The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation. Cell stem cell, Vol.24 (1), pp. 138-152.e8.

Moens, T.G., Niccoli, T., Wilson, K.M., Atilano, M.L., Birsa, N., Gittings, L.M., Holbling, B.V., Dyson, M.C., Thoeng, A., Neeves, J., et al. (2019). C9orf72 arginine-rich dipeptide proteins interact with ribosomal proteins in vivo to induce a toxic translational arrest that is rescued by eIF1A. Acta neuropathologica, Vol.137 (3), pp. 487-500.

Roumeliotis, T.I., Weisser, H. & Choudhary, J.S. (2019). Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression. Journal of proteome research, Vol.18 (3), pp. 1433-1440.

Gentzel, M., Pardo, M., Subramaniam, S., Stewart, A.F. & Choudhary, J.S. (2019). Proteomic navigation using proximity-labeling. Methods, Vol.164-165, pp. 67-72.

Frankish, A., Diekhans, M., Ferreira, A.-., Johnson, R., Jungreis, I., Loveland, J., Mudge, J.M., Sisu, C., Wright, J., Armstrong, J., et al. (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic acids research, Vol.47 (D1), pp. D766-D773.

Hillier, C., Pardo, M., Yu, L., Bushell, E., Sanderson, T., Metcalf, T., Herd, C., Anar, B., Rayner, J.C., Billker, O., et al. (2019). Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality. Cell reports, Vol.28 (6), pp. 1635-1647.e5.

Liess, A.K., Kucerova, A., Schweimer, K., Yu, L., Roumeliotis, T.I., Diebold, M., Dybkov, O., Sotriffer, C., Urlaub, H., Choudhary, J.S., et al. (2019). Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination. Structure, Vol.27 (8), pp. 1195-1210.e7.

Bianco, J.N., Bergoglio, V., Lin, Y.-., Pillaire, M.-., Schmitz, A.-., Gilhodes, J., Lusque, A., Mazières, J., Lacroix-Triki, M., Roumeliotis, T.I., et al. (2019). Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner. Nature communications, Vol.10 (1).

Capalbo, L., Bassi, Z.I., Geymonat, M., Todesca, S., Copoiu, L., Enright, A.J., Callaini, G., Riparbelli, M.G., Yu, L., Choudhary, J.S., et al. (2019). The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. Nature communications, Vol.10 (1).

Mayer, L., Jasztal, M., Pardo, M., Aguera de Haro, S., Collins, J., Bariana, T.K., Smethurst, P.A., Grassi, L., Petersen, R., Nurden, P., et al. (2018). Nbeal2 interacts with Dock7, Sec16a, and Vac14. Blood, Vol.131 (9), pp. 1000-1011.  show abstract

Steinberg, J., Brooks, R.A., Southam, L., Bhatnagar, S., Roumeliotis, T.I., Hatzikotoulas, K., Zengini, E., Wilkinson, J.M., Choudhary, J.S., McCaskie, A.W., et al. (2018). Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis. Rheumatology, Vol.57 (8), pp. 1481-1489.

Gozdecka, M., Meduri, E., Mazan, M., Tzelepis, K., Dudek, M., Knights, A.J., Pardo, M., Yu, L., Choudhary, J.S., Metzakopian, E., et al. (2018). UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs. Nature genetics, Vol.50 (6), pp. 883-894.

Barreiro-Alonso, A., Lamas-Maceiras, M., García-Díaz, R., Rodríguez-Belmonte, E., Yu, L., Pardo, M., Choudhary, J.S. & Cerdán, M.E. (2018). Delineating the HMGB1 and HMGB2 interactome in prostate and ovary epithelial cells and its relationship with cancer. Oncotarget, Vol.9 (27).

Bakos, G., Yu, L., Gak, I.A., Roumeliotis, T.I., Liakopoulos, D., Choudhary, J.S. & Mansfeld, J. (2018). An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. Nature communications, Vol.9 (1).

Raouf, R., Lolignier, S., Sexton, J.E., Millet, Q., Santana-Varela, S., Biller, A., Fuller, A.M., Pereira, V., Choudhary, J.S., Collins, M.O., et al. (2018). Inhibition of somatosensory mechanotransduction by annexin A6. Science signaling, Vol.11 (535), pp. eaao2060-eaao2060.

Modrzynska, K., Pfander, C., Chappell, L., Yu, L., Suarez, C., Dundas, K., Gomes, A.R., Goulding, D., Rayner, J.C., Choudhary, J., et al. (2017). A Knockout Screen of ApiAP2 Genes Reveals Networks of Interacting Transcriptional Regulators Controlling the Plasmodium Life Cycle. Cell host & microbe, Vol.21 (1), pp. 11-22.

Scanlan, E., Yu, L., Maskell, D., Choudhary, J. & Grant, A. (2017). A quantitative proteomic screen of the Campylobacter jejuni flagellar-dependent secretome. Journal of proteomics, Vol.152, pp. 181-187.

Jia, Y., Marq, J., Bisio, H., Jacot, D., Mueller, C., Yu, L., Choudhary, J., Brochet, M. & Soldati‐Favre, D. (2017). Crosstalk between PKA and PKG controls pH ‐dependent host cell egress of Toxoplasma gondii. The embo journal, Vol.36 (21), pp. 3250-3267.

Thomas, D.C., Clare, S., Sowerby, J.M., Pardo, M., Juss, J.K., Goulding, D.A., van der Weyden, L., Storisteanu, D., Prakash, A., Espéli, M., et al. (2017). Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity. The journal of experimental medicine, Vol.214 (4), pp. 1111-1128.  show abstract

Weisser, H. & Choudhary, J.S. (2017). Targeted Feature Detection for Data-Dependent Shotgun Proteomics. Journal of proteome research, Vol.16 (8), pp. 2964-2974.

Yeung, A.T., Hale, C., Lee, A.H., Gill, E.E., Bushell, W., Parry-Smith, D., Goulding, D., Pickard, D., Roumeliotis, T., Choudhary, J., et al. (2017). Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis. Nature communications, Vol.8 (1).

Bayés, À., Collins, M.O., Reig-Viader, R., Gou, G., Goulding, D., Izquierdo, A., Choudhary, J.S., Emes, R.D. & Grant, S.G. (2017). Evolution of complexity in the zebrafish synapse proteome. Nature communications, Vol.8 (1).

Roumeliotis, T.I., Williams, S.P., Gonçalves, E., Alsinet, C., Del Castillo Velasco-Herrera, M., Aben, N., Ghavidel, F.Z., Michaut, M., Schubert, M., Price, S., et al. (2017). Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. Cell reports, Vol.20 (9), pp. 2201-2214.

Schlaffner, C.N., Pirklbauer, G.J., Bender, A. & Choudhary, J.S. (2017). Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes. Cell systems, Vol.5 (2), pp. 152-156.e4.

Weisser, H. & Choudhary, J.S. (2017). Targeted Feature Detection for Data-Dependent Shotgun Proteomics. Journal of proteome research, Vol.16 (8), pp. 2964-2974.

Gialitakis, M., Tolaini, M., Li, Y., Pardo, M., Yu, L., Toribio, A., Choudhary, J.S., Niakan, K., Papayannopoulos, V. & Stockinger, B., et al. (2017). Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development. Stem cell reports, .

Fernández, E., Collins, M.O., Frank, R.A., Zhu, F., Kopanitsa, M.V., Nithianantharajah, J., Lemprière, S.A., Fricker, D., Elsegood, K.A., McLaughlin, C.L., et al. (2017). Arc Requires PSD95 for Assembly into Postsynaptic Complexes Involved with Neural Dysfunction and Intelligence. Cell reports, Vol.21 (3), pp. 679-691.

Berger, C.N., Crepin, V.F., Roumeliotis, T.I., Wright, J.C., Carson, D., Pevsner-Fischer, M., Furniss, R.C., Dougan, G., Dori-Bachash, M., Yu, L., et al. (2017). Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo. Cell metabolism, Vol.26 (5), pp. 738-752.e6.

Invergo, B.M., Brochet, M., Yu, L., Choudhary, J., Beltrao, P. & Billker, O. (2017). Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation. Cell reports, Vol.21 (7), pp. 2017-2029.

Steinberg, J., Ritchie, G.R., Roumeliotis, T.I., Jayasuriya, R.L., Clark, M.J., Brooks, R.A., Binch, A.L., Shah, K.M., Coyle, R., Pardo, M., et al. (2017). Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis. Scientific reports, Vol.7 (1).

Pardo, M., Yu, L., Shen, S., Tate, P., Bode, D., Letney, B.L., Quelle, D.E., Skarnes, W. & Choudhary, J.S. (2017). Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells. Scientific reports, Vol.7 (1).

Collins, M.O., Woodley, K.T. & Choudhary, J.S. (2017). Global, site-specific analysis of neuronal protein S-acylation. Scientific reports, Vol.7 (1).

Weisser, H., Wright, J.C., Mudge, J.M., Gutenbrunner, P. & Choudhary, J.S. (2016). Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. Journal of proteome research, Vol.15 (12), pp. 4686-4695.

Maggiore, L., Yu, L., Omasits, U., Rossi, O., Dougan, G., Thomson, N.R., Saul, A., Choudhary, J.S. & Gerke, C. (2016). Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations. International journal of medical microbiology, Vol.306 (2), pp. 99-108.

Bode, D., Yu, L., Tate, P., Pardo, M. & Choudhary, J. (2016). Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells. Molecular & cellular proteomics, Vol.15 (3), pp. 878-891.

Petryszak, R., Keays, M., Tang, Y.A., Fonseca, N.A., Barrera, E., Burdett, T., Füllgrabe, A., Fuentes, A.M., Jupp, S., Koskinen, S., et al. (2016). Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants. Nucleic acids research, Vol.44 (D1), pp. D746-D752.

Wright, J.C., Mudge, J., Weisser, H., Barzine, M.P., Gonzalez, J.M., Brazma, A., Choudhary, J.S. & Harrow, J. (2016). Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. Nature communications, Vol.7 (1).

Röst, H.L., Sachsenberg, T., Aiche, S., Bielow, C., Weisser, H., Aicheler, F., Andreotti, S., Ehrlich, H.-., Gutenbrunner, P., Kenar, E., et al. (2016). OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature methods, Vol.13 (9), pp. 741-748.

Tay, C.L., Jones, M.L., Hodson, N., Theron, M., Choudhary, J.S. & Rayner, J.C. (2016). Study ofPlasmodium falciparumDHHC palmitoyl transferases identifies a role for PfDHHC9 in gametocytogenesis. Cellular microbiology, Vol.18 (11), pp. 1596-1610.

Blohmke, C.J., Darton, T.C., Jones, C., Suarez, N.M., Waddington, C.S., Angus, B., Zhou, L., Hill, J., Clare, S., Kane, L., et al. (2016). Interferon-driven alterations of the host’s amino acid metabolism in the pathogenesis of typhoid fever. The journal of experimental medicine, Vol.213 (6), pp. 1061-1077.  show abstract

Hodson, N., Invergo, B., Rayner, J.C. & Choudhary, J.S. (2015). Palmitoylation and palmitoyl-transferases in Plasmodium parasites. Biochemical society transactions, Vol.43 (2), pp. 240-245.  show abstract

Peltier, J., Shaw, H.A., Couchman, E.C., Dawson, L.F., Yu, L., Choudhary, J.S., Kaever, V., Wren, B.W. & Fairweather, N.F. (2015). Cyclic diGMP Regulates Production of Sortase Substrates ofClostridium difficileand Their Surface Exposure through ZmpI Protease-mediated Cleavage. Journal of biological chemistry, Vol.290 (40), pp. 24453-24469.

Kunowska, N., Rotival, M., Yu, L., Choudhary, J. & Dillon, N. (2015). Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis. Nucleic acids research, Vol.43 (3), pp. 1418-1432.

Mehla, K., Magotra, A., Choudhary, J., Singh, A.K., Mohanty, A.K., Upadhyay, R.C., Srinivasan, S., Gupta, P., Choudhary, N., Antony, B., et al. (2014). Genome-wide analysis of the heat stress response in Zebu (Sahiwal) cattle. Gene, Vol.533 (2), pp. 500-507.

Purcell, S.M., Moran, J.L., Fromer, M., Ruderfer, D., Solovieff, N., Roussos, P., O’Dushlaine, C., Chambert, K., Bergen, S.E., Kähler, A., et al. (2014). A polygenic burden of rare disruptive mutations in schizophrenia. Nature, Vol.506 (7487), pp. 185-190.

Wen, B., Li, G., Wright, J.C., Du, C., Feng, Q., Xu, X., Choudhary, J.S. & Wang, J. (2014). The OMSSAPercolator: An automated tool to validate OMSSA results. Proteomics, Vol.14 (9), pp. 1011-1014.

Collins, M.O., Wright, J.C., Jones, M., Rayner, J.C. & Choudhary, J.S. (2014). Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation. Journal of proteomics, Vol.103, pp. 1-14.

Bayés, À., Collins, M.O., Galtrey, C.M., Simonnet, C., Roy, M., Croning, M.D., Gou, G., van de Lagemaat, L.N., Milward, D., Whittle, I.R., et al. (2014). Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes. Molecular brain, Vol.7 (1).

Pettit, L.J., Browne, H.P., Yu, L., Smits, W., Fagan, R.P., Barquist, L., Martin, M.J., Goulding, D., Duncan, S.H., Flint, H.J., et al. (2014). Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism. Bmc genomics, Vol.15 (1), pp. 160-160.

McMahon, A.C., Barnett, M.W., O'Leary, T.S., Stoney, P.N., Collins, M.O., Papadia, S., Choudhary, J.S., Komiyama, N.H., Grant, S.G., Hardingham, G.E., et al. (2012). SynGAP isoforms exert opposing effects on synaptic strength. Nature communications, Vol.3 (1).

Pardo, M. & Choudhary, J.S. (2012). Assignment of Protein Interactions from Affinity Purification/Mass Spectrometry Data. Journal of proteome research, Vol.11 (3), pp. 1462-1474.

Kirov, G., Pocklington, A.J., Holmans, P., Ivanov, D., Ikeda, M., Ruderfer, D., Moran, J., Chambert, K., Toncheva, D., Georgieva, L., et al. (2012). De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia. Molecular psychiatry, Vol.17 (2), pp. 142-153.

Sebastian, S., Brochet, M., Collins, M.O., Schwach, F., Jones, M.L., Goulding, D., Rayner, J.C., Choudhary, J.S. & Billker, O. (2012). A Plasmodium Calcium-Dependent Protein Kinase Controls Zygote Development and Transmission by Translationally Activating Repressed mRNAs. Cell host & microbe, Vol.12 (1), pp. 9-19.

Wright, J.C., Collins, M.O., Yu, L., Käll, L., Brosch, M. & Choudhary, J.S. (2012). Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator. Molecular & cellular proteomics, Vol.11 (8), pp. 478-491.

Jones, M.L., Collins, M.O., Goulding, D., Choudhary, J.S. & Rayner, J.C. (2012). Analysis of Protein Palmitoylation Reveals a Pervasive Role in Plasmodium Development and Pathogenesis. Cell host & microbe, Vol.12 (2), pp. 246-258.

Wilson, C.H., Crombie, C., van der Weyden, L., Poulogiannis, G., Rust, A.G., Pardo, M., Gracia, T., Yu, L., Choudhary, J., Poulin, G.B., et al. (2012). Nuclear receptor binding protein 1 regulates intestinal progenitor cell homeostasis and tumour formation. The embo journal, Vol.31 (11), pp. 2486-2497.

Brosch, M., Saunders, G.I., Frankish, A., Collins, M.O., Yu, L., Wright, J., Verstraten, R., Adams, D.J., Harrow, J., Choudhary, J.S., et al. (2011). Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome research, Vol.21 (5), pp. 756-767.

Chaudhuri, R.R., Yu, L., Kanji, A., Perkins, T.T., Gardner, P.P., Choudhary, J., Maskell, D.J. & Grant, A.J. (2011). Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome. Microbiology, Vol.157 (10), pp. 2922-2932.

Bayés, À., van de Lagemaat, L.N., Collins, M.O., Croning, M.D., Whittle, I.R., Choudhary, J.S. & Grant, S.G. (2011). Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nature neuroscience, Vol.14 (1), pp. 19-21.

Pagliuca, F.W., Collins, M.O., Lichawska, A., Zegerman, P., Choudhary, J.S. & Pines, J. (2011). Quantitative Proteomics Reveals the Basis for the Biochemical Specificity of the Cell-Cycle Machinery. Molecular cell, Vol.43 (3), pp. 406-417.

Mansfeld, J., Collin, P., Collins, M.O., Choudhary, J.S. & Pines, J. (2011). APC15 drives the turnover of MCC-CDC20 to make the spindle assembly checkpoint responsive to kinetochore attachment. Nature cell biology, Vol.13 (10), pp. 1234-1243.

Pagliuca, F.W., Collins, M.O. & Choudhary, J.S. (2011). Coordinating cell cycle progression via cyclin specificity. Cell cycle, Vol.10 (24), pp. 4195-4196.

Pickard, D., Toribio, A.L., Petty, N.K., van Tonder, A., Yu, L., Goulding, D., Barrell, B., Rance, R., Harris, D., Wetter, M., et al. (2010). A Conserved Acetyl Esterase Domain Targets Diverse Bacteriophages to the Vi Capsular Receptor of Salmonella enterica Serovar Typhi. Journal of bacteriology, Vol.192 (21), pp. 5746-5754.

Pardo, M., Lang, B., Yu, L., Prosser, H., Bradley, A., Babu, M.M. & Choudhary, J. (2010). An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease. Cell stem cell, Vol.6 (4), pp. 382-395.

Jones, M.L., Collins, M.O., Choudhary, J.S. & Rayner, J.C. (2010). A comprehensive survey of protein palmitoylation in late blood-stage Plasmodium falciparum. Malaria journal, Vol.9 (S2).

Jones, M.L., Collins, M.O., Choudhary, J. & Rayner, J.C. (2010). A comprehensive survey of protein palmitoylation in late blood-stage Plasmodium falciparum. Malaria journal, Vol.9 (S2).

Tee, W.-., Pardo, M., Theunissen, T.W., Yu, L., Choudhary, J.S., Hajkova, P. & Surani, M.A. (2010). Prmt5 is essential for early mouse development and acts in the cytoplasm to maintain ES cell pluripotency. Genes & development, Vol.24 (24), pp. 2772-2777.

Brosch, M. & Choudhary, J. (2010). Scoring and Validation of Tandem MS Peptide Identification Methods. , , pp. 43-53.

Lawley, T.D., Croucher, N.J., Yu, L., Clare, S., Sebaihia, M., Goulding, D., Pickard, D.J., Parkhill, J., Choudhary, J. & Dougan, G., et al. (2009). Proteomic and Genomic Characterization of Highly Infectious Clostridium difficile 630 Spores. Journal of bacteriology, Vol.191 (17), pp. 5377-5386.

Fernández, E., Collins, M.O., Uren, R.T., Kopanitsa, M.V., Komiyama, N.H., Croning, M.D., Zografos, L., Armstrong, J.D., Choudhary, J.S. & Grant, S.G., et al. (2009). Targeted tandem affinity purification of PSD‐95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins. Molecular systems biology, Vol.5 (1), pp. 269-269.

Brosch, M., Yu, L., Hubbard, T. & Choudhary, J. (2009). Accurate and Sensitive Peptide Identification with Mascot Percolator. Journal of proteome research, Vol.8 (6), pp. 3176-3181.

Coba, M.P., Pocklington, A.J., Collins, M.O., Kopanitsa, M.V., Uren, R.T., Swamy, S., Croning, M.D., Choudhary, J.S. & Grant, S.G. (2009). Neurotransmitters Drive Combinatorial Multistate Postsynaptic Density Networks. Science signaling, Vol.2 (68), pp. ra19-ra19.

Pickard, D., Thomson, N.R., Baker, S., Wain, J., Pardo, M., Goulding, D., Hamlin, N., Choudhary, J., Threfall, J. & Dougan, G., et al. (2008). Molecular Characterization of the Salmonella enterica Serovar Typhi Vi-Typing Bacteriophage E1. Journal of bacteriology, Vol.190 (7), pp. 2580-2587.

Brosch, M., Swamy, S., Hubbard, T. & Choudhary, J. (2008). Comparison of Mascot and X!Tandem Performance for Low and High Accuracy Mass Spectrometry and the Development of an Adjusted Mascot Threshold. Molecular & cellular proteomics, Vol.7 (5), pp. 962-970.

Collins, M.O., Yu, L., Campuzano, I., Grant, S.G. & Choudhary, J.S. (2008). Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic Sequence Disorder. Molecular & cellular proteomics, Vol.7 (7), pp. 1331-1348.

Emes, R.D., Pocklington, A.J., Anderson, C.N., Bayes, A., Collins, M.O., Vickers, C.A., Croning, M.D., Malik, B.R., Choudhary, J.S., Armstrong, J.D., et al. (2008). Evolutionary expansion and anatomical specialization of synapse proteome complexity. Nature neuroscience, Vol.11 (7), pp. 799-806.

Collins, M.O. & Choudhary, J.S. (2008). Mapping multiprotein complexes by affinity purification and mass spectrometry. Current opinion in biotechnology, Vol.19 (4), pp. 324-330.

Collins, M.O., Yu, L. & Choudhary, J.S. (2007). Analysis of protein phosphorylation on a proteome-scale. Proteomics, Vol.7 (16), pp. 2751-2768.

Collins, M.O., Husi, H., Yu, L., Brandon, J.M., Anderson, C.N., Blackstock, W.P., Choudhary, J.S. & Grant, S.G. (2006). Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome. Journal of neurochemistry, Vol.97, pp. 16-23.

Collins, M.O., Yu, L., Coba, M.P., Husi, H., Campuzano, I., Blackstock, W.P., Choudhary, J.S. & Grant, S.G. (2005). Proteomic Analysis ofin VivoPhosphorylated Synaptic Proteins. Journal of biological chemistry, Vol.280 (7), pp. 5972-5982.

Collins, M.O., Yu, L., Husi, H., Blackstock, W.P., Choudhary, J.S. & Grant, S.G. (2005). Robust Enrichment of Phosphorylated Species in Complex Mixtures by Sequential Protein and Peptide Metal-Affinity Chromatography and Analysis by Tandem Mass Spectrometry. Science signaling, Vol.2005 (298), pp. pl6-pl6.

Choudhary, J. & Grant, S.G. (2004). Proteomics in postgenomic neuroscience: the end of the beginning. Nature neuroscience, Vol.7 (5), pp. 440-445.

Gan, J.-., Yu, L., Wu, J., Xu, H., Choudhary, J.S., Blackstock, W.P., Liu, W.-. & Xia, Z.-. (2004). The Three-Dimensional Structure and X-Ray Sequence Reveal that Trichomaglin Is a Novel S-like Ribonuclease. Structure, Vol.12 (6), pp. 1015-1025.

Woods, A.J., Roberts, M.S., Choudhary, J., Barry, S.T., Mazaki, Y., Sabe, H., Morley, S.J., Critchley, D.R. & Norman, J.C. (2002). Paxillin Associates with Poly(A)-binding Protein 1 at the Dense Endoplasmic Reticulum and the Leading Edge of Migrating Cells. Journal of biological chemistry, Vol.277 (8), pp. 6428-6437.

Choudhary, J.S., Blackstock, W.P., Creasy, D.M. & Cottrell, J.S. (2001). Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics, Vol.1 (5), pp. 651-667.

Choudhary, J.S., Blackstock, W.P., Creasy, D.M. & Cottrell, J.S. (2001). Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics, Vol.1 (5), pp. 651-667.

Choudhary, J.S., Blackstock, W.P., Creasy, D.M. & Cottrell, J.S. (2001). Matching peptide mass spectra to EST and genomic DNA databases. Trends in biotechnology, Vol.19 (10), pp. S17-S22.

Bell, A.W., Ward, M.A., Blackstock, W.P., Freeman, H.N., Choudhary, J.S., Lewis, A.P., Chotai, D., Fazel, A., Gushue, J.N., Paiement, J., et al. (2001). Proteomics Characterization of Abundant Golgi Membrane Proteins. Journal of biological chemistry, Vol.276 (7), pp. 5152-5165.

Rowley, A., Choudhary, J.S., Marzioch, M., Ward, M.A., Weir, M., Solari, R.C. & Blackstock, W.P. (2000). Applications of Protein Mass Spectrometry in Cell Biology. Methods, Vol.20 (4), pp. 383-397.

Husi, H., Ward, M.A., Choudhary, J.S., Blackstock, W.P. & Grant, S.G. (2000). Proteomic analysis of NMDA receptor–adhesion protein signaling complexes. Nature neuroscience, Vol.3 (7), pp. 661-669.

Zheleva, D., Sharma, J., Panico, M., Morris, H.R. & Barber, J. (1998). Isolation and Characterization of Monomeric and Dimeric CP47-Reaction Center Photosystem II Complexes. Journal of biological chemistry, Vol.273 (26), pp. 16122-16127.

Sharma, J., Panico, M., Barber, J. & Morris, H.R. (1997). Characterization of the Low Molecular Weight Photosystem II Reaction Center Subunits and Their Light-induced Modifications by Mass Spectrometry. Journal of biological chemistry, Vol.272 (7), pp. 3935-3943.

Sharma, J., Panico, M., Shipton, C.A., Nilsson, F., Morris, H.R. & Barber, J. (1997). Primary Structure Characterization of the Photosystem II D1 and D2 Subunits. Journal of biological chemistry, Vol.272 (52), pp. 33158-33166.

Sharma, J., Panico, M., Barber, J. & Morris, H.R. (1997). Purification and Determination of Intact Molecular Mass by Electrospray Ionization Mass Spectrometry of the Photosystem II Reaction Center Subunits. Journal of biological chemistry, Vol.272 (52), pp. 33153-33157.

Fang, H., Klages, N., Baechler, B., Hillner, E., Yu, L., Pardo, M., Choudhary, J. & Brochet, M. Multiple short windows of calcium-dependent protein kinase 4 activity coordinate distinct cell cycle events during Plasmodium gametogenesis. Elife, Vol.6.  show abstract

Pardo, M., Bode, D., Yu, L. & Choudhary, J.S. Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling. Journal of visualized experiments, (122).

Wright, J.C. & Choudhary, J.S. DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics. Journal of proteomics & bioinformatics, Vol.09 (06).

Abdi, A., Yu, L., Goulding, D., Rono, M.K., Bejon, P., Choudhary, J. & Rayner, J. Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome. Wellcome open research, Vol.2, pp. 50-50.  show abstract

Oshota, O., Conway, M., Fookes, M., Schreiber, F., Chaudhuri, R.R., Yu, L., Morgan, F.J., Clare, S., Choudhary, J., Thomson, N.R., et al. Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice. Plos one, Vol.12 (8), pp. e0181365-e0181365.

Mousnier, A., Schroeder, G.N., Stoneham, C.A., So, E.C., Garnett, J.A., Yu, L., Matthews, S.J., Choudhary, J.S., Hartland, E.L. & Frankel, G., et al. A New Method To Determine In Vivo Interactomes Reveals Binding of the Legionella pneumophila Effector PieE to Multiple Rab GTPases. Mbio, Vol.5 (4).  show abstract

Brochet, M., Collins, M.O., Smith, T.K., Thompson, E., Sebastian, S., Volkmann, K., Schwach, F., Chappell, L., Gomes, A.R., Berriman, M., et al. Phosphoinositide Metabolism Links cGMP-Dependent Protein Kinase G to Essential Ca2+ Signals at Key Decision Points in the Life Cycle of Malaria Parasites. Plos biology, Vol.12 (3), pp. e1001806-e1001806.

Bayés, À., Collins, M.O., Croning, M.D., van de Lagemaat, L.N., Choudhary, J.S. & Grant, S.G. Comparative Study of Human and Mouse Postsynaptic Proteomes Finds High Compositional Conservation and Abundance Differences for Key Synaptic Proteins. Plos one, Vol.7 (10), pp. e46683-e46683.

Petty, N.K., Feltwell, T., Pickard, D., Clare, S., Toribio, A.L., Fookes, M., Roberts, K., Monson, R., Nair, S., Kingsley, R.A., et al. Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux. Plos pathogens, Vol.7 (4), pp. e1002018-e1002018.

Perkins, T.T., Kingsley, R.A., Fookes, M.C., Gardner, P.P., James, K.D., Yu, L., Assefa, S.A., He, M., Croucher, N.J., Pickard, D.J., et al. A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. Plos genetics, Vol.5 (7), pp. e1000569-e1000569.

Shariff, M., Choudhary, J., Zahoor, S. & Deb, M. Characterization of Streptococcus pneumoniae isolates from India with special reference to their sequence types. The journal of infection in developing countries, Vol.7 (02), pp. 101-109.  show abstract

Berger, C.N., Crepin, V.F., Roumeliotis, T.I., Wright, J.C., Serafini, N., Pevsner-Fischer, M., Yu, L., Elinav, E., Di Santo, J.P., Choudhary, J.S., et al. The Citrobacter rodentium type III secretion system effector EspO affects mucosal damage repair and antimicrobial responses. Plos pathogens, Vol.14 (10), pp. e1007406-e1007406.

Schlaffner, C.N., Pirklbauer, G.J., Bender, A., Steen, J.A. & Choudhary, J.S. A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes. Journal of visualized experiments, (135).

Pollard, D.J., Berger, C.N., So, E.C., Yu, L., Hadavizadeh, K., Jennings, P., Tate, E.W., Choudhary, J.S. & Frankel, G. Broad-Spectrum Regulation of Nonreceptor Tyrosine Kinases by the Bacterial ADP-Ribosyltransferase EspJ. Mbio, Vol.9 (2).  show abstract

Ranzani, M., Kemper, K., Michaut, M., Krijgsman, O., Aben, N., Iyer, V., Wong, K., Roumeliotis, T.I., Velasco-Herrera, M.D., Nsengimana, J., et al. A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination. , .  show abstract

Abdi, A., Yu, L., Goulding, D., Rono, M.K., Bejon, P., Choudhary, J. & Rayner, J. Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome. Wellcome open research, Vol.2, pp. 50-50.  show abstract

Bakos, G., Yu, L., Gak, I.A., Roumeliotis, T.I., Liakopoulos, D., Choudhary, J.S. & Mansfeld, J. An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. , .  show abstract

Roumeliotis, T.I., Weisser, H. & Choudhary, J.S. Evaluation of a Dual Isolation Width Acquisition (DIWA) method for isobaric labelling ratio decompression. , .  show abstract

Invergo, B.M., Brochet, M., Yu, L., Choudhary, J., Beltrao, P. & Billker, O. Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation. , .  show abstract

Zhu, F., Collins, M.O., Harmse, J., Choudhary, J.S., Grant, S.G. & Komiyama, N.H. Cell-type specific visualization and biochemical isolation of endogenous synaptic proteins in mice. , .  show abstract

Hopkins, E.G., Roumeliotis, T.I., Mullineaux-Sanders, C., Choudhary, J.S. & Frankel, G. Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection. Mbio, Vol.10 (2).  show abstract

Jackman, M., Marcozzi, C., Pardo, M., Yu, L., Tyson, A.L., Choudhary, J.S. & Pines, J. Cyclin B1-Cdk1 binding to MAD1 links nuclear pore disassembly to chromosomal stability. , .  show abstract

Roumeliotis, T.I., Williams, S.P., Gonçalves, E., Zamanzad Ghavidel, F., Aben, N., Michaut, M., Schubert, M., Wright, J.C., Yang, M., Alsinet, C., et al. Genomic determinants of protein abundance variation in colorectal cancer cells. , .  show abstract

Capalbo, L., Bassi, Z.I., Geymonat, M., Todesca, S., Copoiu, L., Enright, A., Callaini, G., Riparbelli, M.G., Yu, L., Choudhary, J., et al. The midbody interactome reveals new unexpected roles for PP1 phosphatases in cytokinesis. , .  show abstract

Steward, C.A., Roovers, J., Suner, M.-., Gonzalez, J.M., Uszczynska-Ratajczak, B., Pervouchine, D., Fitzgerald, S., Viola, M., Stamberger, H., Hamdan, F.F., et al. Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons. , .  show abstract

Schlaffner, C.N., Pirklbauer, G., Bender, A. & Choudhary, J.S. PoGo: Jumping from Peptides to Genomic Loci. , .  show abstract

Raouf, R., Lolignier, S., Sexton, J.E., Millet, Q., Santana-Varela, S., Biller, A., Fuller, A.M., Pereira, V., Choudhary, J., Collins, M., et al. Regulation of somatosensory mechanotransduction by Annexin A6. , .  show abstract

Dunstan, R.A., Pickard, D., Dougan, S., Goulding, D., Cormie, C., Hardy, J., Li, F., Grinter, R., Harcourt, K., Yu, L., et al. The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre. Molecular microbiology, .

Cano-Gamez, E., Soskic, B., Roumeliotis, T.I., So, E., Smyth, D.J., Baldrighi, M., Willé, D., Nakic, N., Esparza-Gordillo, J., Larminie, C.G., et al. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines. , .  show abstract

Mudge, J.M., Jungreis, I., Hunt, T., Gonzalez, J.M., Wright, J.C., Kay, M., Davidson, C., Fitzgerald, S., Seal, R., Tweedie, S., et al. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome research, , pp. gr.246462.118-gr.246462.118.

Carson, D., Barry, R., Hopkins, E.G., Roumeliotis, T.I., García‐Weber, D., Mullineaux‐Sanders, C., Elinav, E., Arrieumerlou, C., Choudhary, J.S. & Frankel, G., et al. Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease. Cellular microbiology, .

Zhu, F., Collins, M.O., Harmse, J., Choudhary, J.S., Grant, S.G. & Komiyama, N.H. Cell‐type‐specific visualisation and biochemical isolation of endogenous synaptic proteins in mice. European journal of neuroscience, .


Book Chapters

Wright, J.C. & Choudhary, J.S. Chapter 4 PSM Scoring and Validation. Proteome Informatics. (pp. 69-92). Royal Society of Chemistry, ISBN: 9781782624288.


Conferences

Steinberg, J., Ritchie, G., Roumeliotis, T., Jayasuriya, R., Brooks, R., Binch, A., Shah, K., Coyle, R., Pardo, M., Le Maitre, C., et al. (2017). Molecular phenotyping of patient chondrocytes reveals genes and pathways involved in osteoarthritis, Osteoarthritis and Cartilage, Vol.25, pp.S209-S210.

Thomas, D.C., Clare, S., Sowerby, J.M., Pardo, M., Juss, J.K., Goulding, D.A., Van der Weyden, L., Storisteanu, D.M., Prakash, A., Espeli, M., et al. (2016). Role of Eros, a novel transmembrane protein, in regulation of host defence, LANCET, Vol.387, p.12.

Collins, M. & Choudhary, J. (2014). Resolving Sites of Protein Palmitoylation Using Quantitative Proteomics, MOLECULAR & CELLULAR PROTEOMICS, Vol.13 (8), p.S41.

Mansfeld, J., Collin, P., Collins, M.O., Choudhary, J.S. & Pines, J. (2012). APC15 drives the turnover of MCC-Cdc20 to make the spindle assembly checkpoint responsive to kinetochore attachment, FEBS JOURNAL, Vol.279, p.556.

Hopf, C., Angrand, P.-., Gagneur, J., Heffernan, B., Mangano, R., Pickard, L., Ruffner, H., O'Sullivan, E., Stein, M., Thomas, S., et al. (2004). O2-03-05 Proteomic analysis of amyloid precursor protein processing complexes in human neuroblastoma cells by tandem affinity purification, Neurobiology of Aging, Vol.25, p.S37.

Choudhary, J.S., Husi, H., Rowley, A., Yu, L., Ma, A. & Grant, S.G. (2002). A functional proteomics analysis of the NMDA receptor., FASEB JOURNAL, Vol.16 (4), p.A522.

Rowley, A., Ward, M.A., Choudhary, J.J., Bell, A., Bergeron, J.J. & Blackstock, W.P. (2000). Identification of Golgi membrane proteins by proteomics, MOLECULAR BIOLOGY OF THE CELL, Vol.11, pp.134A-135A.