• ARACNE

  • Referenced in 22 articles [sw17200]
  • demonstrates ARACNE’s ability to infer validated transcriptional targets of the cMYC proto-oncogene ... Conclusion: ARACNE shows promise in identifying direct transcriptional interactions in mammalian cellular networks, a problem...
  • TopHat

  • Referenced in 17 articles [sw17157]
  • identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments...
  • BioOptimizer

  • Referenced in 4 articles [sw17421]
  • approach to motif discovery. Motivation: Transcription factors (TFs) bind directly to short segments ... thousands of base pairs upstream of gene transcription start sites, to regulate gene expression...
  • DWE

  • Referenced in 3 articles [sw29590]
  • based tool for de novo tissue-specific transcription factor binding site discovery using expression information ... expression. We present a direct statistical approach to find overrepresented transcription factor binding sites...
  • FStitch

  • Referenced in 1 article [sw18729]
  • engaged polymerase, providing a direct read-out on bona fide transcription. Most traditional assays, such...
  • MiRFinder

  • Referenced in 3 articles [sw29577]
  • post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches...
  • 13cflux2

  • Referenced in 3 articles [sw11825]
  • genes, transcripts, proteins and metabolites. In vivo fluxes, however, are not directly observable and have...
  • d2_cluster

  • Referenced in 4 articles [sw28788]
  • construction of gene indices where transcripts are partitioned into index classes (or clusters) such that ... positionally cloned or obtained directly through genomic sequencing. We describe d2_cluster, an agglomerative algorithm ... rapidly and accurately partitioning transcript databases into index classes by clustering sequences according to minimal...
  • ECgene

  • Referenced in 4 articles [sw17328]
  • genome-based version of the UniGene algorithm. Transcript assembly is achieved using graph theory that ... exon connectivity in each cluster as a directed acyclic graph (DAG). Distinct paths along exons ... required to reconstruct all exons in the transcript...
  • RNAplex

  • Referenced in 3 articles [sw17143]
  • Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed...
  • ExpEdit

  • Referenced in 2 articles [sw17165]
  • transcript data obtained by RNA-Seq experiments. Mapping data (in SAM/BAM format) or directly sequence...
  • ROAST

  • Referenced in 7 articles [sw17318]
  • ROAST can test for uni- or bi-direction regulation. Probes can also be weighted ... used to test the degree of transcriptional conservation between human and mouse mammary stems. Availability...
  • F-Seq

  • Referenced in 4 articles [sw17297]
  • identify specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions ... meaningful sites whose output can be displayed directly in the UCSC Genome Browser. Availability...
  • Chippeakanno

  • Referenced in 1 article [sw18996]
  • such as most conserved elements and other transcription factor binding sites supplied by users. Starting ... added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing...
  • CLIPZ

  • Referenced in 3 articles [sw29589]
  • binding proteins (RBPs) that find their targets directly or with the help of guide RNAs ... level of the genome and of individual transcripts. Individual users can upload their own sequence...
  • BiRen

  • Referenced in 1 article [sw27676]
  • limited experimentally validated enhancers and deciphering the transcriptional regulatory code encoded in the enhancer sequences ... that BiRen can learn common enhancer patterns directly from the DNA sequence and exhibits superior...
  • STAMP

  • Referenced in 3 articles [sw17264]
  • expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs ... alignments of known binding sites. STAMP also directly accepts the output files from 12 supported...
  • Exogean

  • Referenced in 1 article [sw17149]
  • developed Exogean, a flexible framework based on directed acyclic colored multigraphs (DACMs) that can represent ... into complex objects such as protein coding transcripts. Conclusion: We show here, in the context...
  • BioMet

  • Referenced in 1 article [sw20501]
  • rapid progress of molecular biology tools for directed genetic modifications, accurate quantitative experimental approaches, high ... deletions or detect metabolites around which major transcriptional changes are concentrated. These tools...
  • LANCELOT

  • Referenced in 264 articles [sw00500]
  • LANCELOT. A Fortran package for large-scale nonlinear...