| Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics |
107 |
| InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk |
42 |
| Deciphering the oviductal extracellular vesicles content across the estrous cycle: implications for the gametes-oviduct interactions and the environment of the potential embryo |
32 |
| Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks |
31 |
| Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms |
30 |
| Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing |
29 |
| Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress |
28 |
| Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress |
27 |
| Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes |
27 |
| A Sequel to Sanger: amplicon sequencing that scales |
26 |
| Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle |
26 |
| Evolution and comparative genomics of the most common Trichoderma species |
25 |
| Global accumulation of circRNAs during aging in Caenorhabditis elegans |
24 |
| Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany |
24 |
| DEBrowser: interactive differential expression analysis and visualization tool for count data |
23 |
| A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds |
23 |
| Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure |
23 |
| Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index crosstalk and significantly improve sensitivity of massively parallel sequencing |
22 |
| Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species |
22 |
| Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array |
22 |
| EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
21 |
| Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices |
20 |
| Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce |
20 |
| Refinement of breast cancer molecular classification by miRNA expression profiles |
19 |
| Genetic ancestry, admixture and health determinants in Latin America |
19 |
| Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data |
19 |
| Comparison of normalization methods for the analysis of metagenomic gene abundance data |
18 |
| Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers |
18 |
| A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants |
18 |
| Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species |
18 |
| The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen |
17 |
| Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle |
17 |
| Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources |
16 |
| Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen |
16 |
| Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture |
15 |
| TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees |
15 |
| Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family |
15 |
| Transposable elements generate regulatory novelty in a tissue-specific fashion |
15 |
| Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome |
15 |
| Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-kappa B pathway in porcine intestinal epithelial cell line |
14 |
| Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data |
14 |
| Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures |
14 |
| Prediction of subcellular location of apoptosis proteins by incorporating PsePSSM and DCCA coefficient based on LFDA dimensionality reduction |
14 |
| Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles |
14 |
| Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum) |
14 |
| Transcriptome analysis and identification of genes related to terpenoid biosynthesis in Cinnamomum camphora |
14 |
| MicroRNA-guided regulation of heat stress response in wheat |
14 |
| Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis |
14 |
| ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data |
13 |
| Developing specific molecular biomarkers for thermal stress in salmonids |
13 |
