• iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • proteome analysis of various human diseases and epigenetic inheritance. One of the most important PTMs...
  • BSmooth

  • Referenced in 11 articles [sw23483]
  • methylated regions. DNA methylation is an important epigenetic modification involved in gene regulation, which...
  • IMA

  • Referenced in 5 articles [sw23822]
  • level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray...
  • HMM-DM

  • Referenced in 4 articles [sw23510]
  • hidden Markov model. DNA methylation is an epigenetic modification involved in organism development and cellular...
  • EpimiR

  • Referenced in 1 article [sw29358]
  • curated mutual regulation between miRNAs and epigenetic modifications. As two kinds of important gene expression ... regulators, both epigenetic modification and microRNA (miRNA) can play significant roles in a wide range ... diseases. Recently, many studies have demonstrated that epigenetics and miRNA can affect each other ... collects 1974 regulations between 19 kinds of epigenetic modifications (such as DNA methylation, histone acetylation...
  • piRBase

  • Referenced in 1 article [sw23006]
  • reveal the functions of piRNAs in the epigenetic and post-transcriptional regulation of transposons ... elements, have been given particular attention. Furthermore, epigenetic data and reported piRNA targets were also ... first piRNA database that systematically integrates epigenetic and post-transcriptional regulation data to support piRNA...
  • SDM6A

  • Referenced in 1 article [sw37445]
  • adenine methylation (6mA) is an epigenetic modification in prokaryotes and eukaryotes. Identifying 6mA sites ... rice genome is important in rice epigenetics and breeding, but non-random distribution and biological ... prediction accuracy, which limits their usability in epigenetic research. Here, we developed a novel computational...
  • MEDIPS

  • Referenced in 2 articles [sw17294]
  • applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these...
  • GtRNAdb

  • Referenced in 2 articles [sw23001]
  • from other sources includes tRNA modification data, epigenetic data, single nucleotide polymorphisms, gene expression...
  • iDNA4mC

  • Referenced in 2 articles [sw34190]
  • Motivation: DNA N4-methylcytosine (4mC) is an epigenetic modification. The knowledge about the distribution...
  • DeepChrome

  • Referenced in 1 article [sw15813]
  • regulation. This knowledge can help in developing ’epigenetic drugs’ for diseases like cancer. Previous studies ... This provides an intuitive description of underlying epigenetic mechanisms that regulate genes. Results: We show...
  • metilene

  • Referenced in 1 article [sw28768]
  • necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify ... versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology...
  • ThIEF

  • Referenced in 1 article [sw33129]
  • ThIEF: finding genome-wide trajectories of epigenetics marks. We address the problem of comparing multiple ... present a tool called ThIEF (TrackIng of Epigenetic Features) that can efficiently compute these trajectories...
  • SegCorr

  • Referenced in 1 article [sw21050]
  • such as copy number variation (CNV) or epigenetic alterations as factors that may significantly alter...
  • WaveSeq

  • Referenced in 1 article [sw22384]
  • that can be used to detect various epigenetic phenomena such as, transcription factor binding sites...
  • ModHMM

  • Referenced in 1 article [sw29057]
  • valuable alternative to study the epigenetic and regulatory landscape across and within cell types...
  • RnBeads

  • Referenced in 1 article [sw29564]
  • analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts...
  • MLML

  • Referenced in 1 article [sw30173]
  • methylation and hydroxymethylation. Motivation: The two major epigenetic modifications of cytosines, 5-methylcytosine...
  • MrTADFinder

  • Referenced in 1 article [sw34259]
  • further explore the interplay between TADs and epigenetic marks, as tumor mutational burden is known...
  • Meta-i6mA

  • Referenced in 1 article [sw37446]
  • framework. DNA N6-methyladenine (6mA) represents important epigenetic modifications, which are responsible for various cellular...