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1Academic Journal
المؤلفون: Szklarczyk, D., Nastou, K., Koutrouli, M., Kirsch, R., Mehryary, F., Hachilif, R., Hu, D., Peluso, M.E., Huang, Q., Fang, T., Doncheva, N.T., Pyysalo, S., Bork, P., Jensen, L.J., von Mering, C.
وصف الملف: application/pdf
Relation: https://edoc.mdc-berlin.de/id/eprint/24917/1/24917oa.pdf; The STRING database in 2025: protein networks with directionality of regulation. Szklarczyk, D., Nastou, K., Koutrouli, M., Kirsch, R., Mehryary, F., Hachilif, R., Hu, D., Peluso, M.E., Huang, Q., Fang, T., Doncheva, N.T., Pyysalo, S., Bork, P., Jensen, L.J. and von Mering, C. Nucleic Acids Research 18 November 2024 (In Press); PMID:39558183; https://doi.org/10.1093/nar/gkae1113
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2Academic Journal
المؤلفون: Karakulak, T., Szklarczyk, D., Saylan, C.C., Moch, H., von Mering, C., Kahraman, A.
المصدر: Bioinformatics advances, vol. 3, no. 1, pp. vbad050
وصف الملف: application/pdf
Relation: info:eu-repo/semantics/altIdentifier/pmid/37123454; info:eu-repo/semantics/altIdentifier/eissn/2635-0041; info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_843529F1ADE55; https://serval.unil.ch/notice/serval:BIB_843529F1ADE5; https://serval.unil.ch/resource/serval:BIB_843529F1ADE5.P001/REF.pdf
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3Academic Journal
المؤلفون: Fullam, A., Letunic, I., Schmidt, T.S.B., Ducarmon, Q.R., Karcher, N., Khedkar, S., Kuhn, M., Larralde, M., Maistrenko, O.M., Malfertheiner, L., Milanese, A., Rodrigues, J.F.M., Sanchis-López, C., Schudoma, C., Szklarczyk, D., Sunagawa, S., Zeller, G., Huerta-Cepas, J., von Mering, C., Bork, P., Mende, D.R.
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/22848/1/22848oa.pdf; proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Fullam, A. and Letunic, I. and Schmidt, T.S.B. and Ducarmon, Q.R. and Karcher, N. and Khedkar, S. and Kuhn, M. and Larralde, M. and Maistrenko, O.M. and Malfertheiner, L. and Milanese, A. and Rodrigues, J.F.M. and Sanchis-López, C. and Schudoma, C. and Szklarczyk, D. and Sunagawa, S. and Zeller, G. and Huerta-Cepas, J. and von Mering, C. and Bork, P. and Mende, D.R. Nucleic Acids Research 51 (D1): D760-D766. 6 January 2023
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4Academic Journal
المؤلفون: Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A.L., Fang, T., Doncheva, N.T., Pyysalo, S., Bork, P., Jensen, L.J., von Mering, C.
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/22652/1/22652oa.pdf; The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Szklarczyk, D. and Kirsch, R. and Koutrouli, M. and Nastou, K. and Mehryary, F. and Hachilif, R. and Gable, A.L. and Fang, T. and Doncheva, N.T. and Pyysalo, S. and Bork, P. and Jensen, L.J. and von Mering, C. Nucleic Acids Research 51 (D1): D638-D646. 6 January 2023
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5Academic Journal
المؤلفون: Gable, A.L., Szklarczyk, D., Lyon, D., Matias Rodrigues, J.F., von Mering, C.
المصدر: Briefings in bioinformatics, vol. 23, no. 5, pp. bbac355
مصطلحات موضوعية: Databases, Factual, Genetic, Genomics/methods, Humans, Software, Gene Ontology, STRING, benchmark, functional annotation, gene set enrichment, pathways
وصف الملف: application/pdf
Relation: info:eu-repo/semantics/altIdentifier/pmid/36088548; info:eu-repo/semantics/altIdentifier/eissn/1477-4054; info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_9C804159875D1; https://serval.unil.ch/notice/serval:BIB_9C804159875D; https://serval.unil.ch/resource/serval:BIB_9C804159875D.P001/REF.pdf
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6Academic Journal
المؤلفون: Orakov, A., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B., Bork, P.
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/20358/1/20358oa.pdf; http://edoc.mdc-berlin.de/20358/7/20358oa.pdf; GUNC: detection of chimerism and contamination in prokaryotic genomes. Orakov, A. and Fullam, A. and Coelho, L.P. and Khedkar, S. and Szklarczyk, D. and Mende, D.R. and Schmidt, T.S.B. and Bork, P. Genome Biology 22 (1): 178. 13 June 2021
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7Academic Journal
المؤلفون: Szklarczyk, D., Gable, A.L., Nastou, K.C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N.T., Legeay, M., Fang, T., Bork, P., Jensen, L.J., von Mering, C.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/19668/1/19668oa.pdf; The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Szklarczyk, D. and Gable, A.L. and Nastou, K.C. and Lyon, D. and Kirsch, R. and Pyysalo, S. and Doncheva, N.T. and Legeay, M. and Fang, T. and Bork, P. and Jensen, L.J. and von Mering, C. Nucleic Acids Research 49 (D): D605-D612. 8 January 2021
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8Academic Journal
المؤلفون: Altenhoff, A.M., Garrayo-Ventas, J., Cosentino, S., Emms, D., Glover, N.M., Hernández-Plaza, A., Nevers, Y., Sundesha, V., Szklarczyk, D., Fernández, J.M., Codó, L., For Orthologs Consortium, T.Q., Gelpi, J.L., Huerta-Cepas, J., Iwasaki, W., Kelly, S., Lecompte, O., Muffato, M., Martin, M.J., Capella-Gutierrez, S., Thomas, P.D., Sonnhammer, E., Dessimoz, C.
المصدر: Nucleic acids research, vol. 48, no. W1, pp. W538-W545
مصطلحات موضوعية: Animals, Benchmarking, Consensus, Genomics, Humans, Mice, Multigene Family, Phylogeny, Proteome, Rats, Software
وصف الملف: application/pdf
Relation: info:eu-repo/semantics/altIdentifier/pmid/32374845; info:eu-repo/semantics/altIdentifier/eissn/1362-4962; info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_EBF2C2C4065D8; https://serval.unil.ch/notice/serval:BIB_EBF2C2C4065D; https://serval.unil.ch/resource/serval:BIB_EBF2C2C4065D.P001/REF.pdf
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9Academic Journal
المؤلفون: Altenhoff, AM, Garrayo-Ventas, J, Cosentino, S, Emms, D, Glover, NM, Hernández-Plaza, A, Nevers, Y, Sundesha, V, Szklarczyk, D, Fernández, JM, Codó, L, Quest for Orthologs Consortium, Gelpi, JL, Huerta-Cepas, J, Iwasaki, W, Kelly, S, Lecompte, O, Muffato, M, Martin, MJ, Capella-Gutierrez, S, Thomas, PD, Sonnhammer, E, Dessimoz, C
المصدر: Nucleic Acids Research (2020) (In press).
وصف الملف: text
Relation: https://discovery.ucl.ac.uk/id/eprint/10097391/1/gkaa308.pdf; https://discovery.ucl.ac.uk/id/eprint/10097391/
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10Academic Journal
المؤلفون: Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin JY, Hescott B, Hu XZ, Mercer J, Natoli T, Narayan R, Aicheler F, Amoroso N, Arenas A, Azhagesan K, Baker A, Banf M, Batzoglou S, Baudot A, Bellotti R, Bergmann S, Boroevich KA, Brun C, Cai S, Caldera M, Calderone A, Cesareni G, Chen WQ, Chichester C, Cowen L, Cui HZ, Dao P, De Domenico M, Dhroso A, Didier G, Divine M, del Sol A, Feng XY, Flores-Canales JC, Fortunato S, Gitter A, Gorska A, Guan YF, Guenoche A, Gomez S, Hamza H, Hartmann A, He S, Heijs A, Heinrich J, Hu Y, Huang XQ, Hughitt VK, Jeon M, Jeub L, Johnson NT, Joo K, Joung I, Jung S, Kalko SG, Kamola PJ, Kang J, Kaveelerdpotjana B, Kim M, Kim YA, Kohlbacher O, Korkin D, Krzysztof K, Kunji K, Kutalik Z, Lage K, Lang-Brown S, Le TD, Lee J, Lee S, Li D, Li JY, Liu L, Loizou A, Luo ZH, Lysenko A, Ma TL, Mall R, Marbach D, Mattia T, Medvedovic M, Menche J, Micarelli E, Monaco A, Mueller F, Narykov O, Norman T, Park S, Perfetto L, Perrin D, Pirro S, Przytycka TM, Qian XN, Raman K, Ramazzotti D, Ramsahai E, Ravindran B, Rennert P, Saez-Rodriguez J, Scharfe C, Sharan R, Shi N, Shin W, Shu H, Sinha H, Slonim DK, Spinelli L, Srinivasan S, Subramanian A, Suver C, Szklarczyk D, Tangaro S, Thiagarajan S, Tichit L, Tiede T, Tripathi B, Tsherniak A, Tsunoda T, Turei D, Ullah E, Vahedi G, Valdeolivas A, Vivek J, von Mering C, Waagmeester A, Wang B, Wang YJ, Weir BA, White S, Winkler S, Xu K, Xu TS, Yan CH, Yang LQ, Yu KX, Yu XT, Zaffaroni G, Zaslavskiy M, Zeng T, Zhang JTD, Zhang L, Zhang WJ, Zhang XY, Zhang JP, Zhou X, Zhou JR, Zhu HT, Zhu JJ, Zuccon G, Stolovitzky G, Cowen LJ
المساهمون: Choobdar, S, Ahsen, Me, Crawford, J, Tomasoni, M, Fang, T, Lamparter, D, Lin, Jy, Hescott, B, Hu, Xz, Mercer, J, Natoli, T, Narayan, R, Aicheler, F, Amoroso, N, Arenas, A, Azhagesan, K, Baker, A, Banf, M, Batzoglou, S, Baudot, A, Bellotti, R, Bergmann, S, Boroevich, Ka, Brun, C, Cai, S, Caldera, M, Calderone, A, Cesareni, G, Chen, Wq, Chichester, C, Cowen, L, Cui, Hz, Dao, P, De Domenico, M, Dhroso, A, Didier, G, Divine, M, del Sol, A, Feng, Xy, Flores-Canales, Jc, Fortunato, S, Gitter, A, Gorska, A, Guan, Yf, Guenoche, A, Gomez, S, Hamza, H, Hartmann, A, He, S, Heijs, A, Heinrich, J, Hu, Y, Huang, Xq, Hughitt, Vk, Jeon, M, Jeub, L, Johnson, Nt, Joo, K, Joung, I, Jung, S, Kalko, Sg, Kamola, Pj, Kang, J, Kaveelerdpotjana, B, Kim, M, Kim, Ya, Kohlbacher, O, Korkin, D, Krzysztof, K, Kunji, K, Kutalik, Z, Lage, K, Lang-Brown, S, Le, Td, Lee, J, Lee, S, Li, D, Li, Jy, Liu, L, Loizou, A, Luo, Zh, Lysenko, A, Ma, Tl, Mall, R, Marbach, D, Mattia, T, Medvedovic, M, Menche, J, Micarelli, E, Monaco, A, Mueller, F, Narykov, O, Norman, T, Park, S, Perfetto, L, Perrin, D, Pirro, S, Przytycka, Tm, Qian, Xn
مصطلحات موضوعية: DREAM challenge, network, module, predictions
Relation: info:eu-repo/semantics/altIdentifier/wos/WOS:000484044700022; volume:16; issue:9; firstpage:843; lastpage:852; numberofpages:10; journal:NATURE METHODS; https://hdl.handle.net/11573/1660164; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85071733655
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11Academic Journal
المؤلفون: Szklarczyk, D., Gable, A.L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N.T., Morris, J.H., Bork, P., Jensen, L.J., von Mering, C.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/17897/1/17897oa.pdf; STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Szklarczyk, D. and Gable, A.L. and Lyon, D. and Junge, A. and Wyder, S. and Huerta-Cepas, J. and Simonovic, M. and Doncheva, N.T. and Morris, J.H. and Bork, P. and Jensen, L.J. and von Mering, C. Nucleic Acids Research 47 (D1): D607-D613. 8 January 2019
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12Academic Journal
المؤلفون: Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S.K., Cook, H., Mende, D.R., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C., Bork, P.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/17872/1/17872oa.pdf; eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Huerta-Cepas, J. and Szklarczyk, D. and Heller, D. and Hernández-Plaza, A. and Forslund, S.K. and Cook, H. and Mende, D.R. and Letunic, I. and Rattei, T. and Jensen, L.J. and von Mering, C. and Bork, P. Nucleic Acids Research 47 (D1): D309-D314. 8 January 2019
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13Academic Journal
المؤلفون: Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., Jensen, L.J., Martin, M.J., Muffato, M., Gabaldón, T., Lewis, S.E., Thomas, P.D., Sonnhammer, E., Dessimoz, C.
المساهمون: Quest for Orthologs consortium, Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Lecompte, O., Xenarios, I., Sjölander, K., Martin, M.J., Muffato, M., Gabaldón, T., Lewis, S.E., Thomas, P.D., Sonnhammer, E., Dessimoz, C.
المصدر: Nature methods, vol. 13, no. 5, pp. 425-430
مصطلحات موضوعية: Archaea/classification, Archaea/genetics, Bacteria/classification, Bacteria/genetics, Computational Biology/methods, Computational Biology/standards, Databases, Genetic, Eukaryota/classification, Eukaryota/genetics, Gene Ontology, Genomics/methods, Genomics/standards, Models, Phylogeny, Proteomics/methods, Proteomics/standards, Sequence Analysis, Protein, Sequence Homology, Species Specificity
وصف الملف: application/pdf
Relation: info:eu-repo/semantics/altIdentifier/pmid/27043882; info:eu-repo/semantics/altIdentifier/pissn/1548-7105; info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_E8F5620D5F4F4; https://serval.unil.ch/notice/serval:BIB_E8F5620D5F4F; https://serval.unil.ch/resource/serval:BIB_E8F5620D5F4F.P001/REF.pdf
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14Academic Journal
المؤلفون: Huerta-Cepas, J., Forslund, K., Coelho, L.P., Szklarczyk, D., Jensen, L.J., von Mering, C., Bork, P.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/16431/1/16431oa.pdf; Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Huerta-Cepas, J. and Forslund, K. and Coelho, L.P. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P. Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017
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15Academic Journal
المؤلفون: Szklarczyk, D., Morris, J.H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N.T., Roth, A., Bork, P., Jensen, L.J., von Mering, C.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/16193/1/16193oa.pdf; The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Szklarczyk, D. and Morris, J.H. and Cook, H. and Kuhn, M. and Wyder, S. and Simonovic, M. and Santos, A. and Doncheva, N.T. and Roth, A. and Bork, P. and Jensen, L.J. and von Mering, C. Nucleic Acids Research 45 (D1): D362-D368. 4 January 2017
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16Academic Journal
المؤلفون: Altenhoff, AM, Boeckmann, B, Capella-Gutierrez, S, Dalquen, DA, DeLuca, T, Forslund, K, Huerta-Cepas, J, Linard, B, Pereira, C, Pryszcz, LP, Schreiber, F, Da Silva, AS, Szklarczyk, D, Train, CM, Bork, P, Lecompte, O, Von Mering, C, Xenarios, I, Sjölander, K, Jensen, LJ, Martin, MJ, Muffato, M, Quest for Orthologs consortium, ., Gabaldón, T, Lewis, SE, Thomas, PD, Sonnhammer, E, Dessimoz, C
المصدر: Nature Methods , 13 (5) pp. 425-430. (2016)
مصطلحات موضوعية: Phylogeny, Protein function predictions, Sequence annotation, Standards
وصف الملف: text
Relation: https://discovery.ucl.ac.uk/id/eprint/1478137/1/Dessimoz_nmeth.3830.pdf; https://discovery.ucl.ac.uk/id/eprint/1478137/
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17Academic Journal
المؤلفون: Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M.C., Rattei, T., Mende, D.R., Sunagawa, S., Kuhn, M., Jensen, L.J., von Mering, C., Bork, P.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/15201/1/15201oa.pdf; eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Huerta-Cepas, J. and Szklarczyk, D. and Forslund, K. and Cook, H. and Heller, D. and Walter, M.C. and Rattei, T. and Mende, D.R. and Sunagawa, S. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P. Nucleic Acids Research 44 (D1): D286-D293. 4 January 2016
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18Academic Journal
المؤلفون: Szklarczyk, D., Santos, A., von Mering, C., Jensen, L.J., Bork, P., Kuhn, M.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/15199/1/15199oa.pdf; STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Szklarczyk, D. and Santos, A. and von Mering, C. and Jensen, L.J. and Bork, P. and Kuhn, M. Nucleic Acids Research 44 (D1): D380-D384. 4 January 2016
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19Academic Journal
المؤلفون: Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., Kuhn, M., Bork, P., Jensen, L.J., von Mering, C.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/17325/1/17325oa.pdf; STRING v10: protein-protein interaction networks, integrated over the tree of life. Szklarczyk, D. and Franceschini, A. and Wyder, S. and Forslund, K. and Heller, D. and Huerta-Cepas, J. and Simonovic, M. and Roth, A. and Santos, A. and Tsafou, K.P. and Kuhn, M. and Bork, P. and Jensen, L.J. and von Mering, C. Nucleic Acids Research 43 (D1): D447-D452. January 2015
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20Academic Journal
المؤلفون: Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J., von Mering, C., Bork, P.
مصطلحات موضوعية: Cardiovascular and Metabolic Diseases
وصف الملف: application/pdf
Relation: http://edoc.mdc-berlin.de/13712/1/13712oa.pdf; eggNOG v4.0: nested orthology inference across 3686 organisms. Powell, S. and Forslund, K. and Szklarczyk, D. and Trachana, K. and Roth, A. and Huerta-Cepas, J. and Gabaldon, T. and Rattei, T. and Creevey, C. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P. Nucleic Acids Research 42 (1): D231-D239. 1 January 2014