Published in Bioinformatics on May 03, 2012
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics (2013) 1.64
Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions. Nucleic Acids Res (2014) 0.98
Objective and comprehensive evaluation of bisulfite short read mapping tools. Adv Bioinformatics (2014) 0.92
Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2. BMC Bioinformatics (2016) 0.91
A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet (2013) 0.91
MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. BMC Bioinformatics (2013) 0.89
Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation. EMBO J (2014) 0.89
Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis. Epigenomics (2015) 0.86
High-throughput sequencing of cytosine methylation in plant DNA. Plant Methods (2013) 0.84
MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data. F1000Res (2013) 0.84
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. BMC Bioinformatics (2013) 0.82
Neurospora importin α is required for normal heterochromatic formation and DNA methylation. PLoS Genet (2015) 0.81
BS-SNPer: SNP calling in bisulfite-seq data. Bioinformatics (2015) 0.80
Profiling genome-wide DNA methylation. Epigenetics Chromatin (2016) 0.79
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. Int J Mol Sci (2013) 0.78
HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples. Cancer Inform (2015) 0.77
GPU-BSM: a GPU-based tool to map bisulfite-treated reads. PLoS One (2014) 0.77
A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics (2015) 0.77
SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing. Gigascience (2015) 0.76
SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis. Nucleic Acids Res (2016) 0.76
DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines. Cancer Inform (2016) 0.75
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. Brief Bioinform (2015) 0.75
The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat Plants (2016) 0.75
Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. BMC Genomics (2016) 0.75
Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci U S A (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A (1992) 29.51
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics (2011) 9.79
BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics (2010) 4.66
BRAT: bisulfite-treated reads analysis tool. Bioinformatics (2009) 1.81
Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics (2009) 4.23
Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility. Nat Chem Biol (2008) 3.23
Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet (2008) 3.13
The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol (2005) 3.02
Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival. Proc Natl Acad Sci U S A (2009) 2.32
A probabilistic method for small RNA flowgram matching. Pac Symp Biocomput (2008) 2.03
BRAT: bisulfite-treated reads analysis tool. Bioinformatics (2009) 1.81
Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol (2008) 1.73
Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res (2010) 1.70
Marine actinomycetes: a new source of compounds against the human malaria parasite. PLoS One (2008) 1.67
Assignment of orthologous genes via genome rearrangement. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.66
Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics (2007) 1.64
Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science (2002) 1.52
A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling. Genome Res (2004) 1.49
In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics (2008) 1.48
In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins. J Infect Dis (2005) 1.46
Accurate construction of consensus genetic maps via integer linear programming. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.43
Data mining in bioinformatics: selected papers from BIOKDD. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.39
On the accurate construction of consensus genetic maps. Comput Syst Bioinformatics Conf (2008) 1.36
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BMC Bioinformatics (2006) 1.28
Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biol (2013) 1.18
Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence. PLoS One (2008) 1.18
NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model. Bioinformatics (2012) 1.09
Efficient selection of unique and popular oligos for large EST databases. Bioinformatics (2004) 1.09
Monotony of surprise and large-scale quest for unusual words. J Comput Biol (2003) 1.06
Recent advances in malaria drug discovery. Bioorg Med Chem Lett (2013) 1.04
Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics (2011) 1.02
Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence? Infect Genet Evol (2010) 0.98
Post-translational modifications in Plasmodium: more than you think! Mol Biochem Parasitol (2009) 0.97
Unraveling the ubiquitome of the human malaria parasite. J Biol Chem (2011) 0.95
In vivo transcriptional profiling of Plasmodium falciparum. Malar J (2004) 0.94
A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. Int J Data Min Bioinform (2007) 0.93
FHAST: FPGA-Based Acceleration of Bowtie in Hardware. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.90
Targeting the Plasmodium ubiquitin/proteasome system with anti-malarial compounds: promises for the future. Infect Disord Drug Targets (2010) 0.89
Graphlet kernels for prediction of functional residues in protein structures. J Comput Biol (2010) 0.88
The E3 ubiquitin ligase XIAP restricts Anaplasma phagocytophilum colonization of Ixodes scapularis ticks. J Infect Dis (2013) 0.87
High-content live cell imaging with RNA probes: advancements in high-throughput antimalarial drug discovery. BMC Cell Biol (2009) 0.87
Characterization of the ubiquitylating components of the human malaria parasite's protein degradation pathway. PLoS One (2012) 0.86
DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum. BMC Genomics (2014) 0.86
An apicoplast localized ubiquitylation system is required for the import of nuclear-encoded plastid proteins. PLoS Pathog (2013) 0.86
Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Mol Plant (2013) 0.86
Coupling of transcriptional response to oxidative stress and secondary metabolism regulation in filamentous fungi. Crit Rev Microbiol (2013) 0.85
Length-based encoding of binary data in DNA. Langmuir (2008) 0.85
The ubiquitin system: an essential component to unlocking the secrets of malaria parasite biology. Mol Biosyst (2014) 0.85
Deconvoluting BAC-gene relationships using a physical map. J Bioinform Comput Biol (2008) 0.84
Efficient algorithms for genome-wide tagSNP selection across populations via the linkage disequilibrium criterion. Comput Syst Bioinformatics Conf (2007) 0.81
Efficient genome-wide TagSNP selection across populations via the linkage disequilibrium criterion. J Comput Biol (2010) 0.78
PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinformatics (2014) 0.78
Strand-specific RNA-seq applied to malaria samples. Methods Mol Biol (2012) 0.78
Storage and transmission of microarray images. Drug Discov Today (2005) 0.78
Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite. BMC Genomics (2011) 0.77
Structures and bioactivities of dihydrochalcones from Metrodorea stipularis. J Nat Prod (2014) 0.77
Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites. BMC Genomics (2014) 0.77
A compartmentalized approach to the assembly of physical maps. BMC Bioinformatics (2009) 0.77
Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp]. BMC Genomics (2014) 0.77
High content live cell imaging for the discovery of new antimalarial marine natural products. BMC Infect Dis (2012) 0.77
A graph-theoretical approach to the selection of the minimum tiling path from a physical map. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.77
Bioguided isolation, characterization, and biotransformation by Fusarium verticillioides of maize kernel compounds that inhibit fumonisin production. Mol Plant Microbe Interact (2014) 0.76
A linear-time algorithm for predicting functional annotations from PPI networks. J Bioinform Comput Biol (2008) 0.76
Deconvoluting the BAC-gene relationships using a physical map. Comput Syst Bioinformatics Conf (2007) 0.75
23 Genome-wide and positional homopolymeric tract enrichment at promoter-exon boundaries and exclusion of nucleosomes in Plasmodium spp. and related parasites. J Biomol Struct Dyn (2015) 0.75