TY - JOUR AU - Yaseen, A. AU - Li, Y. PY - 2014 DA - 2014// TI - Context-based features enhance protein secondary structure prediction accuracy JO - J Chem Inf Model VL - 54 UR - https://doi.org/10.1021/ci400647u DO - 10.1021/ci400647u ID - Yaseen2014 ER - TY - JOUR AU - Mirabello, C. AU - Pollastri, G. PY - 2013 DA - 2013// TI - Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt344 DO - 10.1093/bioinformatics/btt344 ID - Mirabello2013 ER - TY - JOUR AU - Ghouila, A. AU - Florent, I. AU - Guerfali, F. Z. AU - Terrapon, N. PY - 2014 DA - 2014// TI - Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0095275 DO - 10.1371/journal.pone.0095275 ID - Ghouila2014 ER - TY - STD TI - Aganezov S, Alekseyev MA. On pairwise distances and median score of three genomes under DCJ. BMC Bioinformatics 2012;13 Suppl 19:S1. ID - ref4 ER - TY - JOUR AU - Krylov, D. M. AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Koonin, E. V. PY - 2003 DA - 2003// TI - Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1589103 DO - 10.1101/gr.1589103 ID - Krylov2003 ER - TY - JOUR AU - Borenstein, E. AU - Shlomi, T. AU - Ruppin, E. AU - Sharan, R. PY - 2007 DA - 2007// TI - Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl792 DO - 10.1093/nar/gkl792 ID - Borenstein2007 ER - TY - JOUR AU - Song, T. AU - Gu, H. PY - 2015 DA - 2015// TI - Discovering short linear protein motif based on selective training of profile hidden Markov models JO - J Theor Biol VL - 377 UR - https://doi.org/10.1016/j.jtbi.2015.03.010 DO - 10.1016/j.jtbi.2015.03.010 ID - Song2015 ER - TY - STD TI - Kalkatawi M, Alam I, Bajic VB. BEACON: automated tool for bacterial GEnome annotation ComparisON. BMC Genomics 2015;16:616. ID - ref8 ER - TY - JOUR AU - Nazarian, A. AU - Gezan, S. A. PY - 2016 DA - 2016// TI - GenoMatrix: a software package for pedigree-based and genomic prediction analyses on complex traits JO - J Hered VL - 107 UR - https://doi.org/10.1093/jhered/esw020 DO - 10.1093/jhered/esw020 ID - Nazarian2016 ER - TY - STD TI - Glass K, Girvan M. Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets. Sci. Rep. 2014;4:srep04191. ID - ref10 ER - TY - JOUR AU - Lawrence, M. AU - Huber, W. AU - Pagès, H. AU - Aboyoun, P. PY - 2013 DA - 2013// TI - Software for computing and annotating genomic ranges JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003118 DO - 10.1371/journal.pcbi.1003118 ID - Lawrence2013 ER - TY - JOUR AU - Riddell, N. AU - Crewther, S. G. PY - 2017 DA - 2017// TI - Integrated Comparison Of GWAS, transcriptome, and proteomics studies highlights similarities in the biological basis of animal and human MyopiaIntegrated comparison of myopia omics studies JO - Invest Ophthalmol Vis Sci VL - 58 UR - https://doi.org/10.1167/iovs.16-20618 DO - 10.1167/iovs.16-20618 ID - Riddell2017 ER - TY - JOUR AU - Shen, L. AU - Shao, N. -. Y. AU - Liu, X. AU - Maze, I. PY - 2013 DA - 2013// TI - diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0065598 DO - 10.1371/journal.pone.0065598 ID - Shen2013 ER - TY - JOUR AU - Quinlan, A. R. PY - 2014 DA - 2014// TI - BEDTools: the Swiss-Army tool for genome feature analysis JO - Curr Protoc Bioinforma VL - 47 UR - https://doi.org/10.1002/0471250953.bi1112s47 DO - 10.1002/0471250953.bi1112s47 ID - Quinlan2014 ER - TY - STD TI - Daniel WW, Cross CL. Biostatistics. A Foundation For analysis in Health Sciences 2013;p.22–23. ID - ref15 ER - TY - JOUR AU - Baker, G. M. AU - Trivedi, P. K. PY - 1985 DA - 1985// TI - Estimation of unemployment duration from grouped data: a comparative study JO - J Labor Econ VL - 3 UR - https://doi.org/10.1086/298050 DO - 10.1086/298050 ID - Baker1985 ER - TY - JOUR AU - Prytuliak, R. AU - Volkmer, M. AU - Meier, M. AU - Habermann, B. H. PY - 2017 DA - 2017// TI - HH-MOTiF: de novo detection of short linear motifs in proteins by hidden Markov model comparisons JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkx341 DO - 10.1093/nar/gkx341 ID - Prytuliak2017 ER - TY - JOUR AU - Doğruel, M. AU - Down, T. A. AU - Hubbard, T. J. PY - 2008 DA - 2008// TI - NestedMICA as an ab initio protein motif discovery tool JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-19 DO - 10.1186/1471-2105-9-19 ID - Doğruel2008 ER - TY - JOUR AU - Dinkel, H. AU - Van Roey, K. AU - Michael, S. AU - Kumar, M. PY - 2016 DA - 2016// TI - ELM 2016--data update and new functionality of the eukaryotic linear motif resource JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1291 DO - 10.1093/nar/gkv1291 ID - Dinkel2016 ER - TY - JOUR AU - Falb, M. AU - Pfeiffer, F. AU - Palm, P. AU - Rodewald, K. PY - 2005 DA - 2005// TI - Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3952905 DO - 10.1101/gr.3952905 ID - Falb2005 ER - TY - JOUR AU - Pfeiffer, F. AU - Oesterhelt, D. PY - 2015 DA - 2015// TI - A manual curation strategy to improve genome annotation: application to a set of Haloarchael genomes JO - Life VL - 5 UR - https://doi.org/10.3390/life5021427 DO - 10.3390/life5021427 ID - Pfeiffer2015 ER - TY - STD TI - Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res 2016;44:D67–D72. ID - ref22 ER - TY - JOUR AU - O’Leary, N. A. AU - Wright, M. W. AU - Brister, J. R. AU - Ciufo, S. PY - 2016 DA - 2016// TI - Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1189 DO - 10.1093/nar/gkv1189 ID - O’Leary2016 ER - TY - JOUR AU - Coordinators, N. C. B. I. R. PY - 2014 DA - 2014// TI - Database resources of the National Center for biotechnology information JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1146 DO - 10.1093/nar/gkt1146 ID - Coordinators2014 ER - TY - JOUR AU - dos Santos, G. AU - Schroeder, A. J. AU - Goodman, J. L. AU - Strelets, V. B. PY - 2015 DA - 2015// TI - FlyBase: introduction of the Drosophila Melanogaster release 6 reference genome assembly and large-scale migration of genome annotations JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1099 DO - 10.1093/nar/gku1099 ID - dos Santos2015 ER - TY - JOUR AU - Nunes, B. AU - Natário, I. AU - Carvalho, M. L. PY - 2011 DA - 2011// TI - Time series methods for obtaining excess mortality attributable to influenza epidemics JO - Stat Methods Med Res VL - 20 UR - https://doi.org/10.1177/0962280209340201 DO - 10.1177/0962280209340201 ID - Nunes2011 ER - TY - JOUR AU - Nielsen, M. B. AU - Birkeland, M. S. AU - Hansen, M. B. AU - Knardahl, S. PY - 2017 DA - 2017// TI - Victimization from workplace bullying after a traumatic event: time-lagged relationships with symptoms of posttraumatic stress JO - Int Arch Occup Environ Health VL - 90 UR - https://doi.org/10.1007/s00420-017-1204-4 DO - 10.1007/s00420-017-1204-4 ID - Nielsen2017 ER - TY - JOUR PY - 2017 DA - 2017// TI - UniProt: the universal protein knowledgebase JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1099 DO - 10.1093/nar/gkw1099 ID - ref28 ER - TY - JOUR AU - Edwards, R. J. AU - Davey, N. E. AU - Shields, D. C. PY - 2007 DA - 2007// TI - SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins JO - PLoS One VL - 2 UR - https://doi.org/10.1371/journal.pone.0000967 DO - 10.1371/journal.pone.0000967 ID - Edwards2007 ER - TY - JOUR AU - Bailey, T. L. AU - Williams, N. AU - Misleh, C. AU - Li, W. W. PY - 2006 DA - 2006// TI - MEME: discovering and analyzing DNA and protein sequence motifs JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl198 DO - 10.1093/nar/gkl198 ID - Bailey2006 ER -