molecular sequence annotation

Summary

Summary: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.

Top Publications

  1. Cribbin K, Quackenbush C, Taylor K, Arias Rodriguez L, Kelley J. Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. BMC Genomics. 2017;18:283 pubmed publisher
    ..Finally, the transcriptome assembly will open future research avenues on tropical gar development, cell function, environmental resistance, and evolution in the context of other early vertebrates. ..
  2. Skipper M, Dhand R, Campbell P. Presenting ENCODE. Nature. 2012;489:45 pubmed publisher
  3. Mayer K, Waugh R, Brown J, Schulman A, Langridge P, Platzer M, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711-6 pubmed publisher
    ..Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement. ..
  4. Schmid M, Smith J, Burt D, Aken B, Antin P, Archibald A, et al. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res. 2015;145:78-179 pubmed publisher
  5. Moreira D, Buckup P, Furtado C, Val A, Schama R, Parente T. Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics. BMC Genomics. 2017;18:345 pubmed publisher
    ..Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome. ..
  6. Li L, Zhao W, Tao S, Li J, Xu S, Wang J, et al. Comprehensive long non-coding RNA expression profiling reveals their potential roles in systemic lupus erythematosus. Cell Immunol. 2017;319:17-27 pubmed publisher
    ..Differential lncRNAs might also function through their ceRNAs. Our study established that the aberrant expression profiles of lncRNAs may play a role in SLE and thus warrant further investigation. ..
  7. Kulaeva O, Zhernakov A, Afonin A, Boikov S, Sulima A, Tikhonovich I, et al. Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers. PLoS ONE. 2017;12:e0186713 pubmed publisher
    ..All information contained in PMD1 and PMD2 is available at www.peamarker.arriam.ru. ..
  8. Wang Y, Leung H, Yiu S, Chin F. MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning. BMC Genomics. 2014;15 Suppl 1:S12 pubmed publisher
    ..MetaCluster-TA can outperform widely-used MEGAN4 and can annotate more reads with higher accuracy and higher efficiency. It also outperforms MetaCluster 5.0 as a binning tool. ..
  9. Yang X, Huang Y, Lee Y, Gardeux V, Achour I, Regan K, et al. In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment. BMC Med Genomics. 2014;7 Suppl 1:S2 pubmed publisher
    ..These results provide the initial evidence of improved and cost-efficient analytics for the investigation of cancer cell microenvironment, using species-specificity arrays specifically designed for xenografts models. ..

More Information

Publications108 found, 100 shown here

  1. Zhang Y, Iaffaldano B, Zhuang X, Cardina J, Cornish K. Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives. BMC Plant Biol. 2017;17:34 pubmed publisher
  2. Putman T, Lelong S, Burgstaller Muehlbacher S, Waagmeester A, Diesh C, Dunn N, et al. WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. Database (Oxford). 2017;2017: pubmed publisher
    ..WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction...
  3. CUTLER A, Dammer E, Doung D, Seyfried N, Corbett A, Pavlath G. Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell. 2017;16:738-749 pubmed publisher
    ..Our technique will enable future studies into a heretofore underrepresented compartment of skeletal muscle...
  4. Qin J, Tang Z, Ma X, Meng Y. Investigating the regulatory roles of the microRNAs and the Argonaute 1-enriched small RNAs in plant metabolism. Gene. 2017;628:180-189 pubmed publisher
    ..Several functionally conserved subnetworks were identified between the two plant species. Our study provides a basis for studies on metabolism-related sRNAs in plants. ..
  5. de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nat Biotechnol. 2017;35:872-878 pubmed publisher
    ..We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions. ..
  6. Baryshnikova A, Andrews B. Neighboring-gene effect: a genetic uncertainty principle. Nat Methods. 2012;9:341, 343 pubmed publisher
  7. Bowman M, Pulman J, Liu T, Childs K. A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. BMC Bioinformatics. 2017;18:522 pubmed publisher
    ..We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content. ..
  8. Li S, Garrett Bakelman F, Perl A, Luger S, Zhang C, To B, et al. Dynamic evolution of clonal epialleles revealed by methclone. Genome Biol. 2014;15:472 pubmed publisher
    ..Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone. ..
  9. Zhang Q, Ye Y. Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics. 2017;18:92 pubmed publisher
    ..We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR-Cas systems. ..
  10. Chen H, Wang L, Liu X, Hu L, Wang S, Cheng X. De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development. BMC Genet. 2017;18:65 pubmed publisher
  11. Poirson J, Biquand E, Straub M, Cassonnet P, Nominé Y, Jones L, et al. Mapping the interactome of HPV E6 and E7 oncoproteins with the ubiquitin-proteasome system. FEBS J. 2017;284:3171-3201 pubmed publisher
    ..This study establishes a strategy for the rapid identification of interactions between host or pathogen proteins and the human ubiquitination system. ..
  12. Lin Y, Zhu J, Wang Y, Li Q, Lin S. Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages. PLoS ONE. 2017;12:e0182602 pubmed publisher
    ..In conclusion, these data may uncover candidate genes having functional roles in regulation of goat muscle development and lipid metabolism during the various growth stages in goats. ..
  13. Lefever S, Anckaert J, Volders P, Luypaert M, Vandesompele J, Mestdagh P. decodeRNA- predicting non-coding RNA functions using guilt-by-association. Database (Oxford). 2017;2017: pubmed publisher
    ..http://www.decoderna.org...
  14. Tian R, Basu M, Capriotti E. Computational methods and resources for the interpretation of genomic variants in cancer. BMC Genomics. 2015;16 Suppl 8:S7 pubmed publisher
    ..Finally, we discuss the future perspectives in cancer genomics focusing on the impact of computational methods and quantitative approaches for defining personalized strategies to improve the diagnosis and treatment of cancer. ..
  15. Walter K, Min J, Huang J, Crooks L, Memari Y, McCarthy S, et al. The UK10K project identifies rare variants in health and disease. Nature. 2015;526:82-90 pubmed publisher
    ..Finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results. ..
  16. Skippington E, Barkman T, Rice D, Palmer J. Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size. BMC Plant Biol. 2017;17:49 pubmed publisher
    ..Both plants should therefore be able to carry out aerobic respiration. Moreover, with respect to size, the V. scurruloideum mitogenome has experienced a greater level of reductive evolution. ..
  17. Hellerstedt S, Nash R, Weng S, Paskov K, Wong E, Karra K, et al. Curated protein information in the Saccharomyces genome database. Database (Oxford). 2017;2017: pubmed publisher
    ..Here we also present the inclusion of new abundance and protein half-life data obtained from high-throughput proteome studies. These new data types have been included with the aim to facilitate cellular biology research...
  18. He Z, Xu B, Lee S, Ionita Laza I. Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-analysis of Noncoding Variation in Metabochip Data. Am J Hum Genet. 2017;101:340-352 pubmed publisher
  19. Balmer P, Bauer A, Pujar S, McGarvey K, Welle M, Galichet A, et al. A curated catalog of canine and equine keratin genes. PLoS ONE. 2017;12:e0180359 pubmed publisher
    ..The updates are now available in the NCBI Gene database (https://www.ncbi.nlm.nih.gov/gene). ..
  20. Ewing A, Ballinger T, Earl D, Harris C, Ding L, Wilson R, et al. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013;14:R22 pubmed publisher
    ..We find that gene retrocopy polymorphisms are a widespread phenomenon, present a multi-species analysis of these events, and provide a method for their ascertainment. ..
  21. Daccord N, Celton J, Linsmith G, Becker C, Choisne N, Schijlen E, et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet. 2017;49:1099-1106 pubmed publisher
    ..Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development. ..
  22. Snyman M, Solofoharivelo M, Souza Richards R, Stephan D, Murray S, Burger J. The use of high-throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma-infection in Vitis vinifera cv. 'Chardonnay'. PLoS ONE. 2017;12:e0182629 pubmed publisher
    ..Our results may assist in understanding the role that miRNA pathways play during plant pathogenesis, and may be crucial in understanding disease symptom development in aster yellows phytoplasma-infected grapevines. ..
  23. Gymrek M, Willems T, Reich D, Erlich Y. Interpreting short tandem repeat variations in humans using mutational constraint. Nat Genet. 2017;49:1495-1501 pubmed publisher
    ..Constraint scores identified known pathogenic variants with early-onset effects. Our metric will provide a valuable tool for prioritizing pathogenic STRs in medical genetics studies. ..
  24. Hubstenberger A, Courel M, Bénard M, Souquere S, Ernoult Lange M, Chouaib R, et al. P-Body Purification Reveals the Condensation of Repressed mRNA Regulons. Mol Cell. 2017;68:144-157.e5 pubmed publisher
    ..Thus, we uncovered how P-bodies, by condensing and segregating repressed mRNAs, provide a physical substrate for the coordinated regulation of posttranscriptional mRNA regulons...
  25. Ecker J, Bickmore W, Barroso I, Pritchard J, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012;489:52-5 pubmed publisher
  26. Barh D, Jain N, Tiwari S, Field J, Padin Iruegas E, Ruibal A, et al. A novel in silico reverse-transcriptomics-based identification and blood-based validation of a panel of sub-type specific biomarkers in lung cancer. BMC Genomics. 2013;14 Suppl 6:S5 pubmed publisher
    ..The strategy developed in this work is applicable to any other cancer or disease and can assist in the identification of potential biomarkers. ..
  27. Wang V, Xi L, Enayetallah A, Fauman E, Ziemek D. GeneTopics--interpretation of gene sets via literature-driven topic models. BMC Syst Biol. 2013;7 Suppl 5:S10 pubmed publisher
  28. Zaru R, Magrane M, O Donovan C. From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. Biochem J. 2017;474:493-515 pubmed publisher
    ..elegans kinome is composed of 438 kinases and almost half of them have been functionally characterized, highlighting that C. elegans is a valuable and versatile model organism to understand the role of kinases in biological processes. ..
  29. Evangelista D, Tripathi K, Guarracino M. An Atlas of annotations of Hydra vulgaris transcriptome. BMC Bioinformatics. 2016;17:360 pubmed publisher
    ..WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas . ..
  30. Dhingra P, Fu Y, Gerstein M, Khurana E. Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization. Curr Protoc Bioinformatics. 2017;57:15.11.1-15.11.17 pubmed publisher
    ..This unit provides guidelines for installing and running FunSeq2 to (a) annotate and prioritize variants, (b) incorporate user-defined annotations, and (c) detect differential gene expression. © 2017 by John Wiley & Sons, Inc. ..
  31. Diroma M, Calabrese C, Simone D, Santorsola M, Calabrese F, Gasparre G, et al. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics. 2014;15 Suppl 3:S2 pubmed publisher
    ..To the best of our knowledge, this is likely the most extended population-scale mitochondrial genotyping in humans enriched with the estimation of heteroplasmies. ..
  32. Monies D, Abouelhoda M, AlSayed M, Alhassnan Z, Alotaibi M, Kayyali H, et al. The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes. Hum Genet. 2017;136:921-939 pubmed publisher
  33. Ezura K, Ji Seong K, Mori K, Suzuki Y, Kuhara S, Ariizumi T, et al. Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum). PLoS ONE. 2017;12:e0180003 pubmed publisher
    ..This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set. ..
  34. Sierro N, Battey J, Ouadi S, Bovet L, Goepfert S, Bakaher N, et al. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol. 2013;14:R60 pubmed publisher
  35. Spokevicius A, Tibbits J, Rigault P, Nolin M, Muller C, Merchant A. Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin. BMC Genomics. 2017;18:284 pubmed publisher
  36. Phillips A, Berry J, Wilson M, Vijayaraghavan A, Burke J, Bunn J, et al. Genomics-enabled analysis of the emergent disease cotton bacterial blight. PLoS Genet. 2017;13:e1007003 pubmed publisher
    ..These data reveal important insights into the Xcm-G. hirsutum disease complex and strategies for future development of resistant cultivars. ..
  37. Shang Y, Hao H, Wu J, Lin H. Learning to rank-based gene summary extraction. BMC Bioinformatics. 2014;15 Suppl 12:S10 pubmed publisher
    ..The application of learning to rank can facilitate the further expansion of features for measuring the significance of sentences. ..
  38. Bargsten J, Nap J, Sanchez Perez G, van Dijk A. Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. BMC Plant Biol. 2014;14:330 pubmed publisher
    ..Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation. ..
  39. Ah Fong A, Kim K, Judelson H. RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics. 2017;18:198 pubmed publisher
    ..The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals. ..
  40. Gao R, Li J. Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. BMC Genomics. 2017;18:234 pubmed publisher
    ..Second, our results do not entirely rely on the information of orthologous genes. Interesting results are also observed for fly and worm cassette exon pairs with DNA sequence similarity but not in orthologous gene pairs. ..
  41. Heikkinen L, Kesäniemi J, Knott K. De novo transcriptome assembly and developmental mode specific gene expression of Pygospio elegans. Evol Dev. 2017;19:205-217 pubmed publisher
    ..This comprehensive transcriptome resource for P. elegans adds to the available genomic data for annelids and can be used to uncover mechanisms allowing developmental variation in this and potentially other marine invertebrate species. ..
  42. Rappoport N, Linial N, Linial M. ProtoNet: charting the expanding universe of protein sequences. Nat Biotechnol. 2013;31:290-2 pubmed publisher
  43. Marakhonov A, Sadovskaya N, Antonov I, Baranova A, Skoblov M. Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization. BMC Genomics. 2014;15 Suppl 12:S8 pubmed publisher
    ..The majority of absolute gene expression values collected using Affymetrix microarrays may not be suitable for typical interpretative downstream analysis. ..
  44. Pinoli P, Chicco D, Masseroli M. Computational algorithms to predict Gene Ontology annotations. BMC Bioinformatics. 2015;16 Suppl 6:S4 pubmed publisher
  45. Jarvis D, Ho Y, Lightfoot D, Schmöckel S, Li B, Borm T, et al. The genome of Chenopodium quinoa. Nature. 2017;542:307-312 pubmed publisher
    ..These genomic resources are an important first step towards the genetic improvement of quinoa. ..
  46. Yuan Y, Zhang Q, Zeng S, Gu L, Si W, Zhang X, et al. Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars. BMC Genomics. 2017;18:307 pubmed publisher
    ..Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes. ..
  47. Baruah I, Panda D, M V J, Das D, Acharjee S, Sen P, et al. Bruchid egg induced transcript dynamics in developing seeds of black gram (Vigna mungo). PLoS ONE. 2017;12:e0176337 pubmed publisher
    ..This library would be useful to clone defense related gene(s) such as defensin as represented in our library for crop improvement. ..
  48. Sharma V, Hiller M. Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. Nucleic Acids Res. 2017;45:8369-8377 pubmed publisher
    ..Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. ..
  49. Kakumanu A, Velasco S, Mazzoni E, Mahony S. Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLoS Comput Biol. 2017;13:e1005795 pubmed publisher
    ..Finally, we demonstrate the scalability of SeqUnwinder to discover cell-specific sequence features from over one hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell lines...
  50. Rey J, Deschavanne P, Tuffery P. BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. Database (Oxford). 2014;2014: pubmed publisher
    ..Database URL: http://www.yeastgenome.org/ ..
  51. Pereira C, Denise A, Lespinet O. A meta-approach for improving the prediction and the functional annotation of ortholog groups. BMC Genomics. 2014;15 Suppl 6:S16 pubmed publisher
    ..Since a large number of methods for predicting groups of orthologous genes exist, it is quite conceivable to apply this meta-approach to several combinations of different methods. ..
  52. Stoney R, Ames R, Nenadic G, Robertson D, Schwartz J. Disentangling the multigenic and pleiotropic nature of molecular function. BMC Syst Biol. 2015;9 Suppl 6:S3 pubmed publisher
    ..The pathway network demonstrates the cooperation of multiple pathways to perform biological processes and organises pathways into functionally related clusters with interdependent outcomes. ..
  53. Silberberg Y, Kupiec M, Sharan R. GLADIATOR: a global approach for elucidating disease modules. Genome Med. 2017;9:48 pubmed publisher
    ..The source code for GLADIATOR can be downloaded from http://www.cs.tau.ac.il/~roded/GLADIATOR.zip . ..
  54. Fraser T, Shao R, Fountain Jones N, Charleston M, Martin A, Whiteley P, et al. Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials. BMC Evol Biol. 2017;17:233 pubmed publisher
    ..If this is the case, comparable patterns may exist elsewhere in the 'New World'. This work provides a basis for expanded molecular studies into mange epidemiology in humans and animals in Australia and other geographic regions. ..
  55. Moskalev A, Kudryavtseva A, Graphodatsky A, Beklemisheva V, Serdyukova N, Krutovsky K, et al. De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. BMC Evol Biol. 2017;17:258 pubmed publisher
    ..This preliminary study of the gray whale genome and transcriptome provides new data to better understand the whale evolution and the mechanisms of their adaptation to the hypoxic conditions. ..
  56. St Laurent G, Shtokalo D, Dong B, Tackett M, Fan X, Lazorthes S, et al. VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biol. 2013;14:R73 pubmed publisher
    ..This provides additional understanding of transcriptome regulation during the malignant state, and could lead to additional targets and options for its reversal. ..
  57. Alkan N, Meng X, Friedlander G, Reuveni E, Sukno S, Sherman A, et al. Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis. Mol Plant Microbe Interact. 2013;26:1345-58 pubmed publisher
    ..The results suggest a global regulation by pacC of key pathogenicity genes during pH change in alkalinizing and acidifying pathogens. ..
  58. Engchuan W, Dhindsa K, Lionel A, Scherer S, Chan J, Merico D. Performance of case-control rare copy number variation annotation in classification of autism. BMC Med Genomics. 2015;8 Suppl 1:S7 pubmed publisher
    ..The neurally-relevant annotations used in this study could be successfully applied to rare CNV case-control data-sets for other neuropsychiatric disorders. ..
  59. Bárta J, Stone J, Pech J, Sirová D, Adamec L, Campbell M, et al. The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba. BMC Plant Biol. 2015;15:78 pubmed publisher
    ..We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia. ..
  60. Cao Y, Xu W, Niu C, Bo X, Li F. NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks. Biomed Res Int. 2017;2017:7457131 pubmed publisher
    ..The software shows great potential in biological network study. The open source NFP R package is freely available under the GNU General Public License v2.0 at CRAN along with the vignette. ..
  61. Ampattu B, Hagmann L, Liang C, Dittrich M, Schluter A, Blom J, et al. Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC Genomics. 2017;18:282 pubmed publisher
    ..They further highlight the role of regulatory elements for bacterial virulence and the limitations of model strain approaches when studying such genetically diverse species as N. meningitidis. ..
  62. Varshney R, Shi C, Thudi M, Mariac C, Wallace J, Qi P, et al. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol. 2017;35:969-976 pubmed publisher
    ..We believe that these resources should empower researchers and breeders to improve this important staple crop. ..
  63. Johnston J, Biesecker L. Databases of genomic variation and phenotypes: existing resources and future needs. Hum Mol Genet. 2013;22:R27-31 pubmed publisher
    ..Ultimately, we need a dynamic and comprehensive reference database of medically important variants that is easily cross referenced to exome and genome sequence data and allows for an accumulation of expert opinion. ..
  64. Gan R, Chen T, Wu T, Huang P, Lee C, Yeh Y, et al. PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. BMC Bioinformatics. 2016;17:513 pubmed publisher
    ..This strategy will shed lights on the field of comparative genomics for non-model organism. We have implemented PARRoT as a web service which is freely available at http://parrot.cgu.edu.tw . ..
  65. Yang L, Cheng T, Zhao F. Comparative profiling of hepatopancreas transcriptomes in satiated and starving Pomacea canaliculata. BMC Genet. 2017;18:18 pubmed publisher
    ..canaliculata, and this information has the potential to expedite the study of digestive physiology in apple snails. ..
  66. Guo X, Yu C, Luo L, Wan H, Zhen N, Xu T, et al. Transcriptome of the floral transition in Rosa chinensis 'Old Blush'. BMC Genomics. 2017;18:199 pubmed publisher
    ..The DEGs are candidates for functional analyses of genes affecting the floral transition in the rose, which is a precious resource that reveals the molecular mechanism of mediating floral transition in other perennial plants. ..
  67. Chen T, Siddiqui H, Olsen I. In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics. Front Cell Infect Microbiol. 2017;7:28 pubmed publisher
    ..gingivalis strains, when compared to a neighboring species P. asaccharolytica. All the comparative results of this study are available online for download at ftp://www.homd.org/publication_data/20160425/. ..
  68. Zhou A, Ma H, Liu E, Jiang T, Feng S, Gong S, et al. Transcriptome Sequencing of Dianthus spiculifolius and Analysis of the Genes Involved in Responses to Combined Cold and Drought Stress. Int J Mol Sci. 2017;18: pubmed publisher
    ..spiculifolius to the combined stress. Functional characterization of these genes and pathways will provide new targets for enhancement of plant stress tolerance through genetic manipulation. ..
  69. Panda A, De S, Grammatikakis I, Munk R, Yang X, Piao Y, et al. High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs. Nucleic Acids Res. 2017;45:e116 pubmed publisher
    ..In sum, isolating high-purity circRNAs using the RPAD method can enable quantitative and qualitative analyses of circRNA types and sequence composition, paving the way for the elucidation of circRNA functions. ..
  70. Jiao Y, Peluso P, Shi J, Liang T, Stitzer M, Wang B, et al. Improved maize reference genome with single-molecule technologies. Nature. 2017;546:524-527 pubmed publisher
    ..In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes. ..
  71. Singh R, Runthala A, Khan S, Jha P. Quantitative proteomics analysis reveals the tolerance of wheat to salt stress in response to Enterobacter cloacae SBP-8. PLoS ONE. 2017;12:e0183513 pubmed publisher
  72. Stamatoyannopoulos J, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert D, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012;13:418 pubmed publisher
  73. Holliday G, Brown S, Akiva E, Mischel D, Hicks M, Morris J, et al. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017;2017: pubmed publisher
  74. Tsochatzidou M, Malliarou M, Papanikolaou N, Roca J, Nikolaou C. Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae. Nucleic Acids Res. 2017;45:5818-5828 pubmed publisher
  75. Boudellioua I, Mahamad Razali R, Kulmanov M, Hashish Y, Bajic V, Goncalves Serra E, et al. Semantic prioritization of novel causative genomic variants. PLoS Comput Biol. 2017;13:e1005500 pubmed publisher
    ..We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants. ..
  76. Wen F, Wu X, Li T, Jia M, Liu X, Li P, et al. Genome-wide survey of heat shock factors and heat shock protein 70s and their regulatory network under abiotic stresses in Brachypodium distachyon. PLoS ONE. 2017;12:e0180352 pubmed publisher
    ..Our genomics analysis of BdHsfs and BdHsp70s provides important evolutionary and functional characterization for further investigation of the accurate regulatory mechanisms among Hsfs and Hsp70s in herbaceous plants. ..
  77. Lönnstedt I, Caramia F, Li J, Fumagalli D, Salgado R, Rowan A, et al. Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biol. 2014;15:470 pubmed publisher
    ..We show that chromosomal copy numbers can only be estimated from SNP array signals or sequencing depths for subclonal tumor samples with simple subclonal architectures under certain assumptions. ..
  78. Zhu Y, Chen L, Zhang C, Hao P, Jing X, Li X. Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii. BMC Genomics. 2017;18:1042 pubmed publisher
    ..The study offered important insight into the evolution of vascular plants, and the regulation mechanism of vascular development in a non-seed plant. ..
  79. Fernández Pérez J, Nantón A, Ruiz Ruano F, Camacho J, Mendez J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS ONE. 2017;12:e0184464 pubmed publisher
    ..Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource. ..
  80. Pokorn T, Radisek S, Javornik B, Stajner N, Jakse J. Development of hop transcriptome to support research into host-viroid interactions. PLoS ONE. 2017;12:e0184528 pubmed publisher
    ..These results provide a deep transcriptome of hop and the first insights into complex viroid-hop plant interactions. ..
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