Works matching DE "CIS-regulatory elements (Genetics)"

Results: 589

Cis-regulatory elements used to control gene expression in plants.

Published in:

Plant Cell, Tissue & Organ Culture, 2016, v. 127, n. 2, p. 269, doi. 10.1007/s11240-016-1057-7

By:

Biłas, Róża;
Szafran, Katarzyna;
Hnatuszko-Konka, Katarzyna;
Kononowicz, Andrzej

Publication type:

Article

HALPER facilitates the identification of regulatory element orthologs across species.

Published in:

Bioinformatics, 2020, v. 36, n. 15, p. 4339, doi. 10.1093/bioinformatics/btaa493

By:

Zhang, Xiaoyu;
Kaplow, Irene M;
Wirthlin, Morgan;
Park, Tae Yoon;
Pfenning, Andreas R

Publication type:

Article

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3879, doi. 10.1093/bioinformatics/btaa246

By:

Kuksa, Pavel P;
Lee, Chien-Yueh;
Amlie-Wolf, Alexandre;
Gangadharan, Prabhakaran;
Mlynarski, Elizabeth E;
Chou, Yi-Fan;
Lin, Han-Jen;
Issen, Heather;
Greenfest-Allen, Emily;
Valladares, Otto;
Leung, Yuk Yee;
Wang, Li-San

Publication type:

Article

T-Gene: improved target gene prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3902, doi. 10.1093/bioinformatics/btaa227

By:

O'Connor, Timothy;
Grant, Charles E;
Bodén, Mikael;
Bailey, Timothy L

Publication type:

Article

Quantifying functional impact of non-coding variants with multi-task Bayesian neural network.

Published in:

Bioinformatics, 2020, v. 36, n. 5, p. 1397, doi. 10.1093/bioinformatics/btz767

By:

Xu, Chencheng;
Liu, Qiao;
Zhou, Jianyu;
Xie, Minzhu;
Feng, Jianxing;
Jiang, Tao

Publication type:

Article

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays.

Published in:

Bioinformatics, 2020, v. 36, n. 2, p. 331, doi. 10.1093/bioinformatics/btz545

By:

Majoros, William H;
Kim, Young-Sook;
Barrera, Alejandro;
Li, Fan;
Wang, Xingyan;
Cunningham, Sarah J;
Johnson, Graham D;
Guo, Cong;
Lowe, William L;
Scholtens, Denise M;
Hayes, M Geoffrey;
Reddy, Timothy E;
Allen, Andrew S

Publication type:

Article

Integration of methylation QTL and enhancer–target gene maps with schizophrenia GWAS summary results identifies novel genes.

Published in:

Bioinformatics, 2019, v. 35, n. 19, p. 3576, doi. 10.1093/bioinformatics/btz161

By:

Wu, Chong;
Pan, Wei

Publication type:

Article

atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding.

Published in:

Bioinformatics, 2019, v. 35, n. 15, p. 2657, doi. 10.1093/bioinformatics/bty1010

By:

Shin, Sunyoung;
Hudson, Rebecca;
Harrison, Christopher;
Craven, Mark;
Keleş, Sündüz

Publication type:

Article

Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants.

Published in:

Bioinformatics, 2019, v. 35, n. 15, p. 2610, doi. 10.1093/bioinformatics/bty992

By:

Shi, Wenqiang;
Fornes, Oriol;
Wasserman, Wyeth W

Publication type:

Article

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i108, doi. 10.1093/bioinformatics/btz352

By:

Nair, Surag;
Kim, Daniel S;
Perricone, Jacob;
Kundaje, Anshul

Publication type:

Article

hicGAN infers super resolution Hi-C data with generative adversarial networks.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i99, doi. 10.1093/bioinformatics/btz317

By:

Liu, Qiao;
Lv, Hairong;
Jiang, Rui

Publication type:

Article

A novel method for predicting activity of cis-regulatory modules, based on a diverse training set.

Published in:

Bioinformatics, 2017, v. 33, n. 1, p. 1, doi. 10.1093/bioinformatics/btw552

By:

Wei Yang;
Sinha, Saurabh

Publication type:

Article

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Published in:

Bioinformatics, 2016, v. 32, n. 18, p. 2858, doi. 10.1093/bioinformatics/btw337

By:

Arenillas, David J.;
Wasserman, Wyeth W.;
Mathelier, Anthony;
Forrest, Alistair R. R.;
Kawaji, Hideya;
Lassmann, Timo

Publication type:

Article

INSECT 2.0: a web-server for genome-wide cis-regulatory modules prediction.

Published in:

Bioinformatics, 2016, v. 32, n. 8, p. 1229, doi. 10.1093/bioinformatics/btv726

By:

Parra, R. Gonzalo;
Rohr, Cristian O.;
Koile, Daniel;
Perez-Castro, Carolina;
Yankilevich, Patricio

Publication type:

Article

LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1091, doi. 10.1093/bioinformatics/btv705

By:

Seyres, Denis;
Darbo, Elodie;
Perrin, Laurent;
Herrmann, Carl;
González, Aitor

Publication type:

Article

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

Published in:

Bioinformatics, 2015, v. 31, n. 23, p. 3758, doi. 10.1093/bioinformatics/btv466

By:

De Witte, Dieter;
Van de Velde, Jan;
Decap, Dries;
Van Bel, Michiel;
Audenaert, Pieter;
Demeester, Piet;
Dhoedt, Bart;
Vandepoele, Klaas;
Fostier, Jan

Publication type:

Article

Effects of Water Stress on Cotton (Gossypium spp.) Plants and Productivity.

Published in:

Egyptian Journal of Agronomy, 2021, v. 43, n. 3, p. 307, doi. 10.21608/agro.2021.89343.1272

By:

Rehman, Mashal;
Bakhsh, Ali;
Zubair, Muhammad;
Rehmani, Muhammad Ishaq Asif;
Shahzad, Aqeel;
Nayab, Syeda Fiza;
Khan, Madiha Mobeen;
Anum, Wajiha;
Akhta, Rubina;
Kanwal, Natasha;
Manzoor, Nadia;
Ali, Imtiaz

Publication type:

Article

EFFECT OF MUTATION RESULTED FROM ERROR PRONE PCR ON THE STRENGTH OF PROMOTER ACTIVITY.

Published in:

Journal of Experimental Zoology India, 2019, v. 22, n. 2, p. 981

By:

Priyadarsini, Swagatika;
Nikhil, K. C.;
Ratta, Barkha;
Pashupathi, M.;
Behera, Parthasarathi;
Kumar, Ajay

Publication type:

Article

CHARACTERIZING AND DESIGNING PROMOTER OF GENE ZmDREB2.7 INTO PLANT EXPRESSION VECTOR.

Published in:

Journal of Biology / TẠp chí Sinh HỌc, 2022, v. 44, n. 1, p. 83, doi. 10.15625/2615-9023/15941

By:

Huynh Thi Thu Hue;
Dao Quang Ha;
Nguyen Thuy Duong

Publication type:

Article

The ODC 3'-Untranslated Region and 5'-Untranslated Region Contain cis-Regulatory Elements: Implications for Carcinogenesis.

Published in:

Medical Sciences, 2018, v. 6, n. 1, p. 2, doi. 10.3390/medsci6010002

By:

Nowotarski, Shannon L.;
Shantz, Lisa M.

Publication type:

Article

Global identification and characterization of soybean TPR genes with expression analysis under photoperiod variations.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-10368-5

By:

Yu, Song;
Ren, Wenwen;
Song, Chengyang;
Wang, Yuxuan;
Fang, Yisheng;
Huang, Can;
Liu, Xiulin;
Zhang, Yifei;
Luo, Xiao

Publication type:

Article

Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat (Triticum aestivum L.).

Published in:

Life (2075-1729), 2022, v. 12, n. 7, p. 941, doi. 10.3390/life12070941

By:

Shumayla;
Mendu, Venugopal;
Singh, Kashmir;
Upadhyay, Santosh Kumar

Publication type:

Article

Role of Transposable Elements in Gene Regulation in the Human Genome.

Published in:

Life (2075-1729), 2021, v. 11, n. 2, p. 118, doi. 10.3390/life11020118

By:

Ali, Arsala;
Han, Kyudong;
Liang, Ping;
Makalowska, Izabela

Publication type:

Article

Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability.

Published in:

Life (2075-1729), 2020, v. 10, n. 11, p. 300, doi. 10.3390/life10110300

By:

Fraser, Leyland;
Paukszto, Łukasz;
Mańkowska, Anna;
Brym, Paweł;
Gilun, Przemysław;
Jastrzębski, Jan P.;
Pareek, Chandra S.;
Kumar, Dibyendu;
Pierzchała, Mariusz

Publication type:

Article

Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica.

Published in:

Frontiers in Plant Science, 2023, p. 01, doi. 10.3389/fpls.2023.1243806

By:

Luping Gong;
Bingbing Li;
Tao Zhu;
Baoping Xue

Publication type:

Article

Systematic analysis of the effects of genetic variants on chromatin accessibility to decipher functional variants in non-coding regions.

Published in:

Frontiers in Oncology, 2022, v. 12, p. 1, doi. 10.3389/fonc.2022.1035855

By:

Dongyang Wang;
Xiaohong Wu;
Guanghui Jiang;
Jianye Yang;
Zhanhui Yu;
Yanbo Yang;
Wenqian Yang;
Xiaohui Niu;
Ke Tang;
Jing Gong

Publication type:

Article

To bind or not to bind: Cistromic reprogramming in prostate cancer.

Published in:

Frontiers in Oncology, 2022, v. 12, p. 1, doi. 10.3389/fonc.2022.963007

By:

Shen, Michelle;
Demers, Léa-Kristine;
Bailey, Swneke D.;
Labbé, David P.

Publication type:

Article

Investigating the Prognostic Significance of Pyroptosis-Related Genes in Gastric Cancer and Their Impact on Cells' Biological Functions.

Published in:

Frontiers in Oncology, 2022, v. 12, p. 1, doi. 10.3389/fonc.2022.861284

By:

Yin, Jie;
Che, Gang;
Wang, Wankun;
Chen, Shitu;
Liu, Jian

Publication type:

Article

Remodeling of the chromatin landscape in peripheral blood cells in patients with severe Delta COVID-19.

Published in:

Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1415317

By:

Akimov, Vasiliy E.;
Tychinin, Dmitriy I.;
Antonova, Olga A.;
Shaymardanov, Abusaid M.;
Voronina, Maria D.;
Deinichenko, Kseniia A.;
Fateev, Oleg D.;
Yudin, Vladimir S.;
Yudin, Sergey M.;
Mukhin, Vladimir E.;
Romanova, Svetlana V.;
Nekrasova, Aleksandra I.;
Zhdanova, Anastasia S.;
Tsypkina, Anastasia V.;
Vladimirov, Ivan S.;
Makhotenko, Antonida V.;
Keskinov, Anton A.;
Kraevoy, Sergey A.;
Snigir, Ekaterina A.;
Svetlichnyy, Dmitry V.

Publication type:

Article

Genome-Wide Analysis of the G2-Like Transcription Factor Genes and Their Expression in Different Senescence Stages of Tobacco (Nicotiana tabacum L.).

Published in:

Frontiers in Genetics, 2021, v. 11, p. 1, doi. 10.3389/fgene.2021.626352

By:

Qin, Mingyue;
Zhang, Binghui;
Gu, Gang;
Yuan, Jiazheng;
Yang, Xuanshong;
Yang, Jiahan;
Xie, Xiaofang

Publication type:

Article

The Chromatin Accessibility Landscape of Adult Rat.

Published in:

Frontiers in Genetics, 2021, v. 11, p. 1, doi. 10.3389/fgene.2021.651604

By:

Yuan, Yue;
Deng, Qiuting;
Wei, Xiaoyu;
Liu, Yang;
Lan, Qing;
Jiang, Yu;
Yu, Yeya;
Guo, Pengcheng;
Xu, Jiangshan;
Yu, Cong;
Han, Lei;
Cheng, Mengnan;
Wu, Peiying;
Zhang, Xiao;
Lai, Yiwei;
Volpe, Giacomo;
Esteban, Miguel A.;
Yang, Huanming;
Liu, Chuanyu;
Liu, Longqi

Publication type:

Article

Integrated lncRNA and mRNA Transcriptome Analyses in the Ovary of Cynoglossus semilaevis Reveal Genes and Pathways Potentially Involved in Reproduction.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.671729

By:

Dong, Yani;
Lyu, Likang;
Zhang, Daiqiang;
Li, Jing;
Wen, Haishen;
Shi, Bao

Publication type:

Article

Bioinformatics and Expression Analysis of IDA-Like Genes Reveal Their Potential Functions in Flower Abscission and Stress Response in Tobacco (Nicotiana tabacum L.).

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.670794

By:

Guo, Cun;
Wang, Qi;
Li, Zhiyuan;
Sun, Jinhao;
Zhang, Zenglin;
Li, Xiaoxu;
Guo, Yongfeng

Publication type:

Article

Functional Interrogation of Enhancer Connectome Prioritizes Candidate Target Genes at Ovarian Cancer Susceptibility Loci.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.646179

By:

Wang, Wei;
Song, Fengju;
Feng, Xiangling;
Chu, Xinlei;
Dai, Hongji;
Tian, Jing;
Fang, Xuan;
Song, Fangfang;
Liu, Ben;
Li, Lian;
Li, Xiangchun;
Zhao, Yanrui;
Zheng, Hong;
Chen, Kexin

Publication type:

Article

Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis).

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.538733

By:

Nan, Hong;
Ludlow, Richard A.;
Lu, Min;
An, Huaming

Publication type:

Article

Transcriptome Analysis of Long Noncoding RNAs and mRNAs in Granulosa Cells of Jinghai Yellow Chickens Illuminated With Red Light.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.563623

By:

Wang, Ying;
Shi, Huiqiang;
Zhang, Genxi;
Wu, Pengfei;
Chen, Lan;
Shen, Manman;
Li, Tingting;
Lv, Xiaoyang;
Gu, Yunfei;
Wang, Jinyu

Publication type:

Article

Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.606285

By:

Fagny, Maud;
Kuijjer, Marieke Lydia;
Stam, Maike;
Joets, Johann;
Turc, Olivier;
Rozière, Julien;
Pateyron, Stéphanie;
Venon, Anthony;
Vitte, Clémentine

Publication type:

Article

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.612031

By:

Massa, Alisha T.;
Mousel, Michelle R.;
Herndon, Maria K.;
Herndon, David R.;
Murdoch, Brenda M.;
White, Stephen N.

Publication type:

Article

Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.599292

By:

Go, Alwyn C.;
Civetta, Alberto

Publication type:

Article

An Enhancer-Based Analysis Revealed a New Function of Androgen Receptor in Tumor Cell Immune Evasion.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.595550

By:

Wang, Yuan;
Li, Jiajia;
Li, Jingjing;
Li, Peipei;
Wang, Li;
Di, Lijun

Publication type:

Article

Functional Characterization of a Dual Enhancer/Promoter Regulatory Element Leading Human CD69 Expression.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.552949

By:

Redondo-Antón, Jennifer;
Fontela, MG;
Notario, Laura;
Torres-Ruiz, Raúl;
Rodríguez-Perales, Sandra;
Lorente, Elena;
Lauzurica, Pilar

Publication type:

Article

RNA, Genome Output and Input.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.589413

By:

Morf, Jörg;
Basu, Srinjan;
Amaral, Paulo P.

Publication type:

Article

Small Open Reading Frames: How Important Are They for Molecular Evolution?

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.574737

By:

Guerra-Almeida, Diego;
Nunes-da-Fonseca, Rodrigo

Publication type:

Article

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.).

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.570156

By:

Zhang, Zhishuo;
Chen, Juan;
Liang, Chengliang;
Liu, Feng;
Hou, Xilin;
Zou, Xuexiao

Publication type:

Article

Genome-Wide Identification of a Regulatory Mutation in BMP15 Controlling Prolificacy in Sheep.

Published in:

Frontiers in Genetics, 2020, v. 11, p. 1, doi. 10.3389/fgene.2020.00585

By:

Chantepie, Louise;
Bodin, Loys;
Sarry, Julien;
Woloszyn, Florent;
Plisson-Petit, Florence;
Ruesche, Julien;
Drouilhet, Laurence;
Fabre, Stéphane

Publication type:

Article

ΔNp63α is a super enhancer-enriched master factor controlling the basal-to-luminal differentiation transcriptional program and gene regulatory networks in nasopharyngeal carcinoma.

Published in:

Carcinogenesis, 2020, v. 41, n. 9, p. 1282, doi. 10.1093/carcin/bgz203

By:

Cai, Jing;
Chen, Shengnan;
Yi, Mei;
Tan, Yixin;
Peng, Qian;
Ban, Yuanyuan;
Yang, Jianbo;
Li, Xiaoling;
Zeng, Zhaoyang;
Xiong, Wei;
McCarthy, James B;
Li, Guiyuan;
Li, Xiayu;
Xiang, Bo

Publication type:

Article

Genetic variants in the human leukocyte antigen region and survival of Chinese patients with non-small cell lung carcinoma.

Published in:

Carcinogenesis, 2020, v. 41, n. 9, p. 1203, doi. 10.1093/carcin/bgaa066

By:

Cheng, Lei;
Liu, Qi;
Wang, Mengyun;
Gu, Yanzi;
Wang, Jialei;
Wei, Qingyi;
Zhang, Ruoxin

Publication type:

Article

Cis-regulatory evolution of the recently expanded Ly49 gene family.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-48990-y

By:

Fan, Changxu;
Xing, Xiaoyun;
Murphy, Samuel J. H.;
Poursine-Laurent, Jennifer;
Schmidt, Heather;
Parikh, Bijal A.;
Yoon, Jeesang;
Choudhary, Mayank N. K.;
Saligrama, Naresha;
Piersma, Sytse J.;
Yokoyama, Wayne M.;
Wang, Ting

Publication type:

Article

Lipid-lowering drug targets and Parkinson's disease: A sex-specific Mendelian randomization study.

Published in:

Frontiers in Neurology, 2022, v. 13, p. 1, doi. 10.3389/fneur.2022.940118

By:

Yangfan Zhao;
Taliun, Sarah A. Gagliano

Publication type:

Article

Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken.

Published in:

Mobile DNA, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13100-019-0181-4

By:

Li, Jingyi;
Davis, Brian W.;
Jern, Patric;
Dorshorst, Ben. J.;
Siegel, Paul B.;
Andersson, Leif

Publication type:

Article