scholarly journals Erratum: Mohammad Shibli Kaysar and Mohammad Ibrahim Khan A Modified Median String Algorithm for Gene Regulatory Motif Classification Symmetry 2020, 12, 8

Symmetry ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1433
Author(s):  
Mohammad Shibli Kaysar ◽  
Mohammad Ibrahim Khan
Keyword(s):  
Regulatory Motif ◽  
String Algorithm ◽  
Gene Regulatory ◽  
Median String

The authors wish to make the following corrections to their paper: [...]

scholarly journals A Modified Median String Algorithm for Gene Regulatory Motif Classification

Symmetry ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 1363
Author(s):  
Mohammad Shibli Kaysar ◽  
Mohammad Ibrahim Khan
Keyword(s):  
Dna Sequence ◽  
Deoxyribonucleic Acid ◽  
Exact Algorithms ◽  
Experimental Result ◽  
Significant Feature ◽  
Regulatory Motif ◽  
String Algorithm ◽  
Np Complete ◽  
Gene Regulatory ◽  
Median String

Consensus string is a significant feature of a deoxyribonucleic acid (DNA) sequence. The median string is one of the most popular exact algorithms to find DNA consensus. A DNA sequence is represented using the alphabet Σ= {a, c, g, t}. The algorithm generates a set of all the 4l possible motifs or l-mers from the alphabet to search a motif of length l. Out of all possible l-mers, it finds the consensus. This algorithm guarantees to return the consensus but this is NP-complete and runtime increases with the increase in l-mer size. Using transitional probability from the Markov chain, the proposed algorithm symmetrically generates four subsets of l-mers. Each of the subsets contains a few l-mers starting with a particular letter. We used these reduced sets of l-mers instead of using 4ll-mers. The experimental result shows that the proposed algorithm produces a much lower number of l-mers and takes less time to execute. In the case of l-mer of length 7, the proposed system is 48 times faster than the median string algorithm. For l-mer of size 7, the proposed algorithm produces only 2.5% l-mer in comparison with the median string algorithm. While compared with the recently proposed voting algorithm, our proposed algorithm is found to be 4.4 times faster for a longer l-mer size like 9.

scholarly journals motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences

2015 ◽  
Vol 8 (4) ◽  
pp. 463-476 ◽  
Author(s):  
Dennis Kostka ◽  
Tara Friedrich ◽  
Alisha K. Holloway ◽  
Katherine S. Pollard
Keyword(s):  
Dna Sequences ◽  
Statistical Significance ◽  
Regulatory Motif ◽  
Gene Regulatory

scholarly journals Homeostasis in a feed forward loop gene regulatory motif

2018 ◽  
Vol 445 ◽  
pp. 103-109 ◽  
Author(s):  
Fernando Antoneli ◽  
Martin Golubitsky ◽  
Ian Stewart
Keyword(s):  
Regulatory Motif ◽  
Feed Forward ◽  
Feed Forward Loop ◽  
Gene Regulatory

The GCGGAA gene-regulatory motif of herpes simplex virus type-1 is also found in hepatitis C virus

Gene ◽  
1995 ◽  
Vol 154 (1) ◽  
pp. 131-132 ◽  
Author(s):  
JoséL. Vizmanos ◽  
Javier I. Jauregui ◽  
Arturo Gullón ◽  
Carlos J. González ◽  
Maria P. Civeira ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Herpes Simplex Virus ◽  
Hepatitis C ◽  
Herpes Simplex ◽  
Virus Type ◽  
Herpes Simplex Virus Type ◽  
Regulatory Motif ◽  
Gene Regulatory ◽  
Simplex Virus

scholarly journals Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM

2009 ◽  
pp. 263-276 ◽  
Author(s):  
Leonardo Mariño-Ramírez ◽  
Kannan Tharakaraman ◽  
John L. Spouge ◽  
David Landsman
Keyword(s):  
Promoter Analysis ◽  
Regulatory Motif ◽  
Motif Identification ◽  
Gene Regulatory

How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

2020 ◽  
Vol 48 (3) ◽  
pp. 1019-1034 ◽  
Author(s):  
Rachel M. Woodhouse ◽  
Alyson Ashe
Keyword(s):  
Histone Modifications ◽  
Molecular Mechanisms ◽  
Epigenetic Inheritance ◽  
Nematode Caenorhabditis Elegans ◽  
Histone Methyltransferases ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Recent Developments ◽  
Gene Regulatory

Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.

Myelin Gene Regulatory Factor Is a Critical Transcriptional Regulator Required for CNS Myelination

2009 ◽  
Vol 138 (1) ◽  
pp. 172-185
Author(s):  
Ben Emery ◽  
Dritan Agalliu ◽  
John D. Cahoy ◽  
Trent A. Watkins ◽  
Jason C. Dugas ◽  
...  
Keyword(s):  
Transcriptional Regulator ◽  
Regulatory Factor ◽  
Gene Regulatory ◽  
Cns Myelination ◽  
Myelin Gene

2061-P: Islet Single Cell Transcriptomes Reveal Cellular and Gene Regulatory Alterations in Type 2 Diabetes Pathogenesis

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 2061-P
Author(s):  
NATHAN LAWLOR ◽  
ROMY KURSAWE ◽  
MICHAEL L. STITZEL
Keyword(s):  
Type 2 Diabetes ◽  
Single Cell ◽  
Gene Regulatory
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