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A HIGHLY SCALABLE ALGORITHM FOR THE EXTRACTION OF CIS-REGULATORY REGIONS

ALEXANDRA M. CARVALHO, ANA T. FREITAS, ARLINDO L. OLIVEIRA, MARIE-FRANCE SAGOT
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
In this paper we propose a new algorithm for identifying cis-regulatory modules in genomic sequences.  ...  In particular, the algorithm extracts structured motifs, defined as a collection of highly conserved regions with pre-specified sizes and spacings between them.  ...  The main contribution of this work is a new algorithm to identify cis-regulatory modules from a set of promoter regions of co-regulated genes.  ... 
doi:10.1142/9781860947322_0027 fatcat:7c3ruoev5rfe3cqahwcv23oyiq

Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation

Seungbyn Baek, Insuk Lee
2020 Computational and Structural Biotechnology Journal  
Genome-wide maps of open chromatin regions can facilitate functional analysis of cis- and trans-regulatory elements via their connections with trait-associated sequence variants.  ...  However, due to the intrinsic nature of scATAC-seq data, which are highly noisy and sparse, accurate extraction of biological signals and devising effective biological hypothesis are difficult.  ...  Harmony is a fast and scalable algorithm of single-cell data integration based on iterative adjustment of data-specific clusters [42] .  ... 
doi:10.1016/j.csbj.2020.06.012 pmid:32637041 pmcid:PMC7327298 fatcat:vpgqehvbifh55dsujcpixwixhe

Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data

Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma, Yan Wang
2021 Briefings in Bioinformatics  
Four metrics were investigated, including the accuracy of motif finding, the performance of DNA/RNA sequence classification, algorithm scalability and tool usability.  ...  for highly accurate predictions.  ...  TFs possess unique gene expressions it is well known that the aligned TFBSs of the same TF tend to be conserved at the sequence level [3] , which are referred to as a cis-regulatory motif (motif for short  ... 
doi:10.1093/bib/bbab374 pmid:34607350 pmcid:PMC8769700 fatcat:rhw4oihsvfb77jnrl2jp5tamrq

Scalable deep learning to identify brick kilns and aid regulatory capacity

Jihyeon Lee, Nina R Brooks, Fahim Tajwar, Marshall Burke, Stefano Ermon, David B Lobell, Debashish Biswas, Stephen P Luby
2021 Proceedings of the National Academy of Sciences of the United States of America  
We demonstrate a low-cost, scalable approach for locating brick kilns in high-resolution satellite imagery from Bangladesh.  ...  Our approach identifies kilns with 94.2% accuracy and 88.7% precision and extracts the precise GPS coordinates of every brick kiln across Bangladesh.  ...  for research assistance with earlier iterations of this work.  ... 
doi:10.1073/pnas.2018863118 pmid:33888583 pmcid:PMC8092470 fatcat:3kjeim2zhzf4xdvloewykdwroe

Nucleotide variation of regulatory motifs may lead to distinct expression patterns

Liat Segal, Michal Lapidot, Zach Solan, Eytan Ruppin, Yitzhak Pilpel, David Horn
2007 Computer applications in the biosciences : CABIOS  
The extracted motifs are assessed for their likely cis-regulatory function by calculating the expression coherence (EC) of the corresponding genes, across a set of biological conditions.  ...  In order to avoid bias introduced by such assumptions, we apply an unsupervised motif extraction (MEX) algorithm to sequences of promoters.  ...  Y.P. is an incumbent of the Rothstein Career Development Chair in Genetic Diseases. M.L. is a Fellow of the Horowitz Foundation for Complexity Sciences.  ... 
doi:10.1093/bioinformatics/btm183 pmid:17646329 fatcat:iue3i4bx7nf7dgojjgoyviftlu

Motif Discovery and Data Mining in Bioinformatics

Nooruldeen Qader, Hussein Keitan Al-Khafaji
2014 INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY  
We show bridge of the two fields, data mining and Bioinformatics, for successful mining of biological data.  ...  Bioinformatics analyses huge amounts of biological data that demands in-depth understanding. On the other hand, data mining research develops methods for discovering motifs in biosequences.  ...  The locations on the DNA where proteins bind to are called cis-acting elements, also referred to as cis-regulatory elements or cis-elements.  ... 
doi:10.24297/ijct.v13i1.2932 fatcat:3h7j7z35t5b3pd3rjekj7r3gla

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K Shiau, Xinzhu Zhou, Fangming Xie, Eran A Mukamel, Kai Zhang (+4 others)
2021 Nature Communications  
Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity.  ...  Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states.  ...  R.F. is is a Howard Hughes Medical Institute Fellow of the Damon Runyon Cancer Research Foundation (DRG-2433-21). Y.Z was supported by NIH grant no. 1K99CA252020-01.  ... 
doi:10.1038/s41467-021-21583-9 pmid:33637727 fatcat:6n2so76lwvgmjcei5rayyabckq

Fast and Accurate Clustering of Single Cell Epigenomes Reveals Cis-Regulatory Elements in Rare Cell Types [article]

Rongxin Fang, Sebastian Preissl, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K Shiau, Eran A Mukamel, Yanxiao Zhang, M. Margarita Behrens, Joseph Ecker, Bing Ren
2019 bioRxiv   pre-print
These results demonstrate a systematic approach for comprehensive analysis of cis-regulatory sequences in the mammalian genomes.  ...  Identification of cis-regulatory elements responsible for cell-type specific gene expression is essential for understanding the origin of the cellular diversity.  ...  GREAT improves functional interpretation of cis-regulatory regions. 681 Nat. Biotechnol. 28, 495-501 (2010). 682 40. Huang, Z. J. & Paul, A.  ... 
doi:10.1101/615179 fatcat:cuaj5j2smncehhyyshyttoge4i

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, Walter L. Ruzzo
2007 PLoS Computational Biology  
Noncoding RNAs (ncRNAs) are important functional RNAs that do not code for proteins. We present a highly efficient computational pipeline for discovering cis-regulatory ncRNA motifs de novo.  ...  Citation: Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, et al. (2007) A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes.  ...  Moy for help with the ribosomal protein leader analysis and the Yale Life Sciences High Performance Computing Center for great technical assistance and computing resources.  ... 
doi:10.1371/journal.pcbi.0030126 pmid:17616982 pmcid:PMC1913097 fatcat:j524gpu2qzhzxceugg7lqbj42a

DeepReGraph co-clusters temporal gene expression and cis-regulatory elements through heterogeneous graph representation learning

Jesús Fernando Cevallos Moreno, Peyman Zarrineh, Aminael Sánchez-Rodríguez, Massimo Mecella
2022 F1000Research  
This work presents DeepReGraph, a novel method for co-clustering genes and cis-regulatory elements (CREs) into candidate regulatory networks.  ...  We modelled all data sources as a heterogeneous graph and adapted a state-of-the-art representation learning algorithm to produce a low-dimensional and easy-to-cluster embedding of genes and CREs.  ...  Acknowledgements The authors wish to thank Prof. L. Casasús and Dr. Raúl P. Caulier for their valuable insights. References  ... 
doi:10.12688/f1000research.114698.1 fatcat:td5yj4szo5g55heqi3sjpmnv5i

Identification of non-coding RNAs in the hyper thermophilic bacterium Thermotoga maritima MSB8 through comparative genomics and in-silico analyses

2022 Asian Journal of Agriculture and Biology  
A novel pipeline was constructed which involved a combination of various bioinformatics algorithms.  ...  Having a clear understanding of the thermo-tolerance mechanism, the MSB8 can be exploited in the future for the commercial production of thermostable compounds and biohydrogen.  ...  Agric & Biol. 2022(1). composition, using a highly sensitive support vector machine (SVM) build on Rfam and RNAalifold algorithm for structure prediction.  ... 
doi:10.35495/ajab.2021.05.224 fatcat:bpo6yby2sjaqdfnltybxoc3usq

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

Yarui Diao, Rongxin Fang, Bin Li, Zhipeng Meng, Juntao Yu, Yunjiang Qiu, Kimberly C Lin, Hui Huang, Tristin Liu, Ryan J Marina, Inkyung Jung, Yin Shen (+2 others)
2017 Nature Methods  
here we report a high-throughput method, cis-regulatory element scan by tiling-deletion and sequencing (crest-seq), for the unbiased discovery and functional assessment of cis-regulatory sequences in  ...  Articles nAture methods | VOL.14 NO.6 | JUNE 2017 | 629 millions of cis-regulatory elements are predicted to be present in the human genome, but direct evidence for their biological function is scarce.  ...  CREST-seq is a highly scalable tool for the unbiased discovery of cis-regulatory sequences in the human genome.  ... 
doi:10.1038/nmeth.4264 pmid:28417999 pmcid:PMC5490986 fatcat:zfisnlgkyjhwxauphlyccbyp4y

Proteomics Is Not an Island: Multi-omics Integration Is the Key to Understanding Biological Systems

Bing Zhang, Bernhard Kuster
2019 Molecular & Cellular Proteomics  
However, focusing on highly correlated kinases and phosphosites provides a reasonable approach for identifying novel substrates for some kinases. From the ‡Lester and Sue Smith Breast  ...  The updated TCPA provides a comprehensive resource for cancer researchers to test their protein-centric hypotheses using multi-omics data from a broad range of cancer types.  ...  We thank the Molecular and Cellular Proteomics Editors and staff, especially Emily Huff, for their support for the special issue.  ... 
doi:10.1074/mcp.e119.001693 pmid:31399542 pmcid:PMC6692779 fatcat:xyxnuanr2jbrpb3kdis5zpwmbi

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

S. Gelfman, D. Burstein, O. Penn, A. Savchenko, M. Amit, S. Schwartz, T. Pupko, G. Ast
2011 Genome Research  
Experimental validations performed on a selection of these hexamers confirmed their regulatory function.  ...  By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals.  ...  D.B and O.P. are also fellows of the Converging Technologies Program of the Israeli Council for Higher Education.  ... 
doi:10.1101/gr.119834.110 pmid:21974994 pmcid:PMC3246205 fatcat:dgui6t5tmrgohifdal4z6lwaba

Molecular Characterization of UGT94F2 and UGT86C4, Two Glycosyltransferases from Picrorhiza kurrooa: Comparative Structural Insight and Evaluation of Substrate Recognition

Wajid Waheed Bhat, Niha Dhar, Sumeer Razdan, Satiander Rana, Rukmankesh Mehra, Amit Nargotra, Rekha S. Dhar, Nasheeman Ashraf, Ram Vishwakarma, Surrinder K. Lattoo, Vickery Arcus
2013 PLoS ONE  
iridoid-specific transcription factors, upstream regions of each gene were isolated and scanned for putative cis-regulatory elements.  ...  Interestingly, the presence of cis-regulatory elements within the promoter regions of each gene correlated positively with their expression profiles in response to different phytohormones.  ...  To have a better understanding into the regulation of these UGTs, promoter regions of both UGT86C4 and UGT94F2 were isolated and the key cis-regulatory elements including those involved in MeJA, SA and  ... 
doi:10.1371/journal.pone.0073804 pmid:24066073 pmcid:PMC3774767 fatcat:g7ulqhqt2zdozlf6hsu6d2rpbq
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