Found 1274 results
Wang Y, Janssen H, Milne CB, Magis AT, Jin Y-S, Price ND, Blaschek HP.  2014.  136. Understanding Fundamental Aspects of Butanol Production by Clostridium beijerinckii. 2014 Genomic Science Contractor-Grantee Meeting XII. :234.
Li H, Glusman G, Huff C., Caballero J, Roach JC.  2014.  Accurate and robust prediction of genetic relationship from whole-genome sequences. PloS one. 9:e85437.
Laczny C.C, Pinel N, Vlassis N., Wilmes P.  2014.  Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction. Scientific reports. 4:4516.
Kang S, Kahan S, McDermott J, Flann N, Shmulevich I.  2014.  Biocellion: accelerating computer simulation of multicellular biological system models.. Bioinformatics.
Vialas V., Sun Z, Y. Loureiro PCV, Carrascal M., Abian J., Monteoliva L., Deutsch EW, Aebersold R, Moritz RL, Gil C..  2014.  A Candida albicans PeptideAtlas. Journal of proteomics. 97:62-8.
Liu Y, Patel L, Mills GB, Lu KH, Sood AK, Ding L, Kucherlapati R, Mardis ER, Levine DA, Shmulevich I et al..  2014.  Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma.. J Natl Cancer Inst. 106(9)
Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D et al..  2014.  Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.. Front Microbiol. 5:392.
Cancer Genome Atlas Research Network.  2014.  Comprehensive molecular characterization of gastric adenocarcinoma.. Nature. 513(7517):202-9.
Kemp CJ, Moore J.M, Moser R., Bernard B, Teater M., Smith L.E, Rabaia N.A, Gurley K.E, Guinney J., Busch S.E et al..  2014.  CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer. Cell reports.
Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran J-M.  2014.  Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.. Yeast.
Hood L, Price ND.  2014.  Demystifying disease, democratizing health care. Science translational medicine. 6:225ed5.
Craig TA, Zhang Y, Magis AT, Funk CC, Price ND, Ekker SC, Kumar, iv R.  2014.  Detection of 1,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing.. Zebrafish.
Lehman A, Stittrich A-B, Glusman G, Zong Z, Li H, Eydoux P, Senger C, Lyons C, Roach JC, Patel M.  2014.  Diffuse angiopathy in Adams-Oliver syndrome associated with truncating DOCK6 mutations.. Am J Med Genet A. 164A(10):2656-62.
Shaw S, Bourne T., Meier C., Carrington B., Gelinas R, Henry A., Popplewell A., Adams R., Baker T., Rapecki S. et al..  2014.  Discovery and characterization of olokizumab: A humanized antibody targeting interleukin-6 and neutralizing gp130-signaling. mAbs. 6:773-81.
Powell S., Forslund K., Szklarczyk D., Trachana K., Roth A., Huerta-Cepas J., Gabaldon T., Rattei T., Creevey C., Kuhn M. et al..  2014.  eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids research. 42:D231-9.
Labhsetwar P, Cole J, Price N, Luthey-Schulten Z.  2014.  Elucidating Metabolic Variability in Isogenic Microbial Populations Arising due to Noise in Protein Expression. Biophysical Journal. 106:644a.
Lindner SE, Sartain MJ, Hayes K, Harupa A, Moritz RL, Kappe SHI, Vaughan AM.  2014.  Enzymes involved in plastid-targeted phosphatidic acid synthesis are essential for Plasmodium yoelii liver-stage development.. Mol Microbiol. 91(4):679-93.
Chiang J-H, Cheng W-S, Hood L, Tian Q.  2014.  An Epigenetic Biomarker Panel for Glioblastoma Multiforme Personalized Medicine through DNA Methylation Analysis of Human Embryonic Stem Cell-like Signature. Omics: a journal of integrative biology.
Bundgaard L, Jacobsen S, Sørensen MAamand, Sun Z, Deutsch EW, Moritz RL, Bendixen E.  2014.  The Equine PeptideAtlas–a resource for developing proteomics‐based veterinary research. Proteomics.
Hillesland K.L, Lim S, Flowers J.J, Turkarslan S, Pinel N, Zane G.M, Elliott N., Qin Y., Wu L., Baliga NS et al..  2014.  Erosion of functional independence early in the evolution of a microbial mutualism. Proceedings of the National Academy of Sciences of the United States of America.
Wurtmann EJ, Ratushny AV, Pan M, Beer K.D, Aitchison JD, Baliga NS.  2014.  An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular microbiology. 92:369-82.
Mast FD, Barlow L.D, Rachubinski RA, Dacks J.B.  2014.  Evolutionary mechanisms for establishing eukaryotic cellular complexity. Trends in cell biology.
He Y, Zeng K, Zhang X, Chen Q, Wu J, Li H, Zhou Y, Glusman G, Roach J, Etheridge A et al..  2014.  A Gain-of-Function Mutation in TRPV3 Causes Focal Palmoplantar Keratoderma in a Chinese Family.. J Invest Dermatol.
Stolyar S, Liu Z, Thiel V, Tomsho LP, Pinel N, Nelson WC, Lindemann SR, Romine MF, Haruta S, Schuster SC et al..  2014.  Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.. Genome Announc. 2(1)
Peterson EJR, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJR, Sherman DR, Baliga NS.  2014.  A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.. Nucleic Acids Res.
Cary G.A, Yoon SH, C. Torres G, Wang K, Hays M., Ludlow C., Goodlett DR, Dudley AM.  2014.  Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae. Yeast. 31:167-78.
Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M.  2014.  Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.. Nucleic Acids Res. 42(3):1474-96.
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN et al..  2014.  An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.. Genome Biol. 15(3):R53.
Ekici S, Turkarslan S, Pawlik G, Dancis A, Baliga NS, Koch H-G, Daldal F.  2014.  Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production. mBio. 5:e01055-13.
Chevillet J.R, Lee I, Briggs H.A, He Y, Wang K.  2014.  Issues and prospects of microRNA-based biomarkers in blood and other body fluids. Molecules. 19:6080-105.
Benedict MN, Henriksen J.R, Metcalf WW, Whitaker R.J, Price ND.  2014.  ITEP: An integrated toolkit for exploration of microbial pan-genomes. BMC genomics. 15:8.
Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR, MacCoss MJ, Moritz RL et al..  2014.  Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex.. Genetics.
Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A.  2014.  Macromolecular networks and intelligence in microorganisms.. Front Microbiol. 5:379.
Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS et al..  2014.  Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.. Genome Biol. 15(11):502.
Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND.  2014.  MediaDB: a database of microbial growth conditions in defined media.. PLoS One. 9(8):e103548.
Christian N., Skupin A., Morante S., Jansen K., Rossi G., Ebenhoh O..  2014.  Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. Journal of theoretical biology. 343:102-12.
Randhawa M., Sangar V, Tucker-Samaras S., Southall M..  2014.  Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway. PLoS ONE. 9:e90367.
Liu G, Sun Y, Ji P, Li X, Cogdell D, Yang D, Kerrigan B.CParker, Shmulevich I, Chen K, Sood AK et al..  2014.  MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer. The Journal of pathology. 233:308-18.
Beer K.D, Wurtmann EJ, Pinel N, Baliga NS.  2014.  Model organisms have memory of complex ecologically-relevant environmental variation. Applied and environmental microbiology.
Ghaffarizadeh A., Podgorski G.J, Flann N.S.  2014.  Modeling and visualizing cell type switching. Computational and mathematical methods in medicine. 2014:293980.
Cho JH, Lee I, Hammamieh R., Wang K, Baxter D, Scherler K., Etheridge A, Kulchenko A., Gautam A., Muhie S. et al..  2014.  Molecular evidence of stress-induced acute heart injury in a mouse model simulating posttraumatic stress disorder. Proceedings of the National Academy of Sciences of the United States of America. 111:3188-93.
Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2014.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic acids research. 42:1442-60.
Ptak C, Aitchison JD, Wozniak RW.  2014.  The multifunctional nuclear pore complex: a platform for controlling gene expression. Current opinion in cell biology. 28C:46-53.
Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AFA, Wessels LFA, Laird PW, Aderem A, Shmulevich I.  2014.  Multiscale representation of genomic signals.. Nature Methods. 11(6):689-94.
Stittrich A-B, Lehman A, Bodian DL, Ashworth J, Zong Z, Li H, Lam P, Khromykh A, Iyer RK, Vockley JG et al..  2014.  Mutations in NOTCH1 cause Adams-Oliver syndrome.. Am J Hum Genet. 95(3):275-84.
Kusebauch U, Ortega C., Ollodart A., Rogers RS, Sherman DR, Moritz RL, Grundner C..  2014.  Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proceedings of the National Academy of Sciences of the United States of America.
Turkarslan S, Wurtmann EJ, Wu W.J, Jiang N., Bare JC, Foley K, Reiss DJ, Novichkov P., Baliga NS.  2014.  Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Res. 42:D184-90.
Holden JM, Koreny L., Obado S., Ratushny AV, Chen WM, Chiang JH, Kelly S., Chait BT, Aitchison JD, Rout MP et al..  2014.  Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular biology of the cell. 25:1421-36.
Lalli MA, Cox HC, Arcila ML, Cadavid L, Moreno S, Garcia G, Madrigal L, Reiman EM, Arcos-Burgos M, Bedoya G et al..  2014.  Origin of the PSEN1 E280A mutation causing early-onset Alzheimer's disease.. Alzheimers Dement. 10(5 Suppl):S277-S283.e10.
Schoggins J.W, Macduff D.A, Imanaka N., Gainey M.D, Shrestha B., Eitson J.L, Mar K.B, Richardson R.B, Ratushny AV, Litvak V et al..  2014.  Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature. 505:691-5.
Wu X., Hasan M.A, Chen J.Y.  2014.  Pathway and network analysis in proteomics. Journal of theoretical biology.
Omenn GS.  2014.  Plasma proteomics, the human proteome project, and cancer-associated alternative splice variant proteins. Biochimica et biophysica acta. 1844:866-73.
Guo F, Kerrigan BCParker, Yang D, Hu L, Shmulevich I, Sood AK, Xue F, Zhang W.  2014.  Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions.. J Hematol Oncol. 7:19.
Silva R.R, Jourdan F., Salvanha D.M, Letisse F., Jamin E.L, Guidetti-Gonzalez S., Labate C.A, Vencio RZ.  2014.  ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. Bioinformatics.
Kauffman SA.  2014.  Prolegomenon to patterns in evolution. Bio Systems.
Sun B, Hood L.  2014.  Protein-Centric N-Glycoproteomics Analysis of Membrane and Plasma Membrane Proteins.. J Proteome Res.
Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D., Dianes J.A, Sun Z, Farrah T, Bandeira N. et al..  2014.  ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature biotechnology. 32:223-6.
Ruusuvuori P, Lin J, Scott A.C, Tan Z., Sorsa S., Kallio A., Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.  2014.  Quantitative analysis of colony morphology in yeast. BioTechniques. 56:18-27.
Hu Z, Lausted C, Yoo H, Yan X, Brightman A, Chen J, Wang W, Bu X., Hood L.  2014.  Quantitative liver-specific protein fingerprint in blood: a signature for hepatotoxicity. Theranostics. 4:215-28.
Carpp L.N, Rogers RS, Moritz RL, Aitchison JD.  2014.  Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection. Molecular & cellular proteomics : MCP.
Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND.  2014.  Quantitative Proteomic Analysis Reveals Effects of Epidermal Growth Factor Receptor (EGFR) on Invasion-promoting Proteins Secreted by Glioblastoma Cells.. Mol Cell Proteomics. 13(10):2618-31.
Daugherty M.D, Young J.M, Kerns J.A, Malik H.S.  2014.  Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts. PLoS genetics. 10:e1004403.
Caballero J, Smit AFA, Hood L, Glusman G.  2014.  Realistic artificial DNA sequences as negative controls for computational genomics.. Nucleic Acids Res. 42(12):e99.
Li H, Glusman G, Hu H, , Caballero J, Hubley R, Witherspoon D., Guthery S.L, Mauldin DE, Jorde LB et al..  2014.  Relationship estimation from whole-genome sequence data. PLoS genetics. 10:e1004144.
Rosenberger G, Koh CChiek, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A et al..  2014.  A repository of assays to quantify 10,000 human proteins by SWATH-MS. SCIENTIFIC DATA. 1
Thyme S.B, Boissel S.J, S. Quadri A, Nolan T., Baker D.A, Park R.U, Kusak L., Ashworth J, Baker D..  2014.  Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic acids research. 42:2564-76.
Goldberg R., Kauffman S, Topol E.J.  2014.  Study design and the drug development process. JAMA : the journal of the American Medical Association. 311:2023.
Cermelli S, Jang ISock, Bernard B, Grandori C.  2014.  Synthetic lethal screens as a means to understand and treat MYC-driven cancers.. Cold Spring Harb Perspect Med. 4(3)
Hao D., Wang G., Yin Z, Li C., Cui Y., Zhou M.  2014.  Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. European journal of human genetics : EJHG.
Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2014.  Systems approach to neurodegenerative disease biomarker discovery. Annual review of pharmacology and toxicology. 54:457-81.
Bai JPF, Fontana RJ, Price ND, Sangar V.  2014.  Systems pharmacology modeling: an approach to improving drug safety. Biopharmaceutics & drug disposition. 35:1-14.
Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, uumlttenhain R, Koomen JM.  2014.  Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach. Molecular & Cellular Proteomics. :mcp.M113.036095.
Lopes M., Kutlu B, Miani M., Bang-Berthelsen C.H, Storling J., Pociot F., Goodman N, Hood L, Welsh N, Bontempi G. et al..  2014.  Temporal profiling of cytokine-induced genes in pancreatic beta-cells by meta-analysis and network inference. Genomics.
Liu X, Chen X, Zhong B., Wang A., Wang X, Chu F, Nurieva RI, Yan X, Chen P., van der Flier L.G et al..  2014.  Transcription factor achaete-scute homologue 2 initiates follicular T-helper-cell development. Nature. 507:513-8.
Kash JC, Xiao Y., Davis A.S, Walters KA, Chertow D.S, Easterbrook J.D, Dunfee RL, Sandouk A., Jagger BW, Schwartzman LM et al..  2014.  Treatment with the reactive oxygen species scavenger EUK-207 reduces lung damage and increases survival during 1918 influenza virus infection in mice. Free radical biology & medicine. 67:235-47.
Li X, Liu Y, Granberg K.J, Wang Q, Moore LM, Ji P, Gumin J., Sulman E.P, Calin G.A, Haapasalo H. et al..  2014.  Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene.
Garmendia-Torres C, Skupin A., Michael S.A, Ruusuvuori P, Kuwada N.J, Falconnet D, Cary G.A, Hansen C., Wiggins P.A, Dudley AM.  2014.  Unidirectional P-Body Transport during the Yeast Cell Cycle. PLoS ONE. 9:e99428.
Hu H, Roach JC, Coon H., Guthery S.L, Voelkerding K.V, Margraf R.L, Durtschi J.D, Tavtigian SV, , Wu W. et al..  2014.  A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nature biotechnology.
Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Tavtigian SV, Wu W et al..  2014.  A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.. Nat Biotechnol. 32(7):663-9.
Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL.  2014.  Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. 46:13251-132528.
Huang S.  2014.  When correlation and causation coincide.. Bioessays. 36(1):1-2.
Subramanian N, Natarajan K, Clatworthy MR, Wang Z, Germain RN.  2013.  The adaptor MAVS promotes NLRP3 mitochondrial localization and inflammasome activation.. Cell. 153(2):348-61.
Tan Z., Hays M., Cromie G.A, Jeffery E.W, Scott A.C, Ahyong V., Sirr A., Skupin A., Dudley AM.  2013.  Aneuploidy underlies a multicellular phenotypic switch. Proc Natl Acad Sci U S A. 110:12367-72.
Tjernström M, Leck C, Birch CE, Bottenheim JW, Brooks BJ, Brooks IM, Bäcklin L, Chang RY-W, Granath E, Graus M et al..  2013.  The Arctic Summer Cloud-Ocean Study (ASCOS): 1 Overview and experimental design. Atmospheric Chemsitry and Physics. 13
Earls J.C, Eddy JA, Funk C.C, Ko Y., Magis AT, Price ND.  2013.  AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. BMC bioinformatics. 14:78.
Zheng H, Wang W, Li X, Wang Z, Hood L, Lausted C, Hu Z.  2013.  An automated Teflon microfluidic peptide synthesizer.. Lab Chip. 13(17):3347-50.
Omenn GS.  2013.  On best practices: The Institute of Medicine scheme for developing, validating, and demonstrating clinical utility of omics-based diagnostic and predictive tests. Proteomics Clin Appl. 7:748-55.
Zhou Y, Qin S, Wang K.  2013.  Biomarkers of drug-induced liver injury.. Current Biomarker Findings. 2013:1-9.
Ko Y., Ament SA, Eddy JA, Caballero J, Earls J.C, Hood L, Price ND.  2013.  Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 110:3095-100.
Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C et al..  2013.  A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. Journal of proteome research. 12:45-57.
Glusman G.  2013.  Clinical applications of sequencing take center stage. Genome Biol. 14:303.
Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.  2013.  Combining results of multiple search engines in proteomics. Mol Cell Proteomics. 12:2383-93.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al..  2013.  A community-driven global reconstruction of human metabolism. Nature biotechnology.
Picotti P, Clement-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Rost H, Sun Z, Rinner O, Reiter L et al..  2013.  A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature.
Cancer Genome Atlas Research Network.  2013.  Comprehensive molecular characterization of clear cell renal cell carcinoma.. Nature. 499(7456):43-9.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaino JA, Hermjakob H, Oveillero D, Julian R et al..  2013.  Controlled Vocabularies and Ontologies in Proteomics: Overview, Principles and Practice. Biochimica et biophysica acta.
Hoopmann MR, Moritz RL.  2013.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol. 24:31-8.
Wang Y, Li X, Milne CB, Janssen H, Lin W, Phan G, Hu H, Jin Y-S, Price ND, Blaschek HP.  2013.  Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii.. Appl Environ Microbiol. 79(19):5853-63.
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.  2013.  Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic acids research. 41:D70-82.