(Q43184221)

15 November 2017

Position-dependent motif characterization using non-negative matrix factorization (English)

1 reference

15 November 2017

4

1 reference

15 November 2017

Lucie N Hutchins

1

1 reference

15 November 2017

Sean M Murphy

series ordinal

2

1 reference

15 November 2017

Priyam Singh

series ordinal

3

1 reference

15 November 2017

language of work or name

English

0 references

publication date

13 October 2008

1 reference

15 November 2017

1 reference

15 November 2017

24

1 reference

15 November 2017

23

1 reference

15 November 2017

2684-2690

1 reference

bioNMF: a web-based tool for nonnegative matrix factorization in biology.

15 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

C. elegans sequences that control trans-splicing and operon pre-mRNA processing

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Quantifying similarity between motifs

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

bioNMF: a versatile tool for non-negative matrix factorization in biology

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

The features of Drosophila core promoters revealed by statistical analysis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Analysis of computational approaches for motif discovery

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Assessing computational tools for the discovery of transcription factor binding sites

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

WebLogo: A Sequence Logo Generator

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Metagenes and molecular pattern discovery using matrix factorization

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Subsystem identification through dimensionality reduction of large-scale gene expression data

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Regulatory sequence analysis tools

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Computational analysis of core promoters in the Drosophila genome

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Predictive identification of exonic splicing enhancers in human genes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Learning the parts of objects by non-negative matrix factorization

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Integrating database homology in a probabilistic gene structure model

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Improved splice site detection in Genie

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Sequence logos: a new way to display consensus sequences

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

3' non-coding region sequences in eukaryotic messenger RNA

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Nonsmooth nonnegative matrix factorization (nsNMF).

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

PACdb: PolyA Cleavage Site and 3'-UTR Database.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2639279

Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit beta-globin mRNA 3' end formation

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852176

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTN526

1 reference

journals/bioinformatics/HutchinsMSG08

15 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 November 2017

PubMed publication ID

18852176

1 reference