Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: MACS

https://packages.ecosyste.ms/registries/pypi.org/packages/MACS

Model Based Analysis for ChIP-Seq data
2 versions
Latest release: almost 11 years ago

Papers Mentioning MACS 1,233

10.3390/molecules24091774
A Novel G-Quadruplex Binding Protein in Yeast—Slx9
Cited by: 16
Author(s): Silvia Götz, Satyaprakash Pandey, Sabrina Bartsch, Stefan Juranek, Katrin Paeschke
Software Mentions: 2
Published: over 5 years ago
10.1038/srep33779
SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster
Cited by: 12
Author(s): Jinumary Mathai, Smriti Mittal, Aftab Alam, Payal Ranade, Devraj Mogare, Sonal Patel, Smita Saxena, Suvankar Ghorai, Abhijeet Kulkarni, Samit Chattopadhyay
Software Mentions: 2
Published: about 8 years ago
10.3390/molecules23051136
Detecting Differential Transcription Factor Activity from ATAC-Seq Data
Cited by: 33
Author(s): Ignacio J. Tripodi, Mary A. Allen, Robin Dowell
Software Mentions: 2
Published: over 6 years ago
10.1186/s12859-014-0412-0
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Cited by: 10
Author(s): Anagha Joshi
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12915-021-00959-9
A brain cyst load-associated antigen is a Toxoplasma gondii biomarker for serodetection of persistent parasites and chronic infection
Cited by: 5
Author(s): Céline Dard, Christopher Swale, Marie-Pierre Brenier-Pinchart, Dayana C Farhat, Valeria Bellini, M Robert, Dominique Cannella, H Pelloux, Isabelle Tardieux, Mohamed‐Ali Hakimi
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0099844
OccuPeak: ChIP-Seq Peak Calling Based on Internal Background Modelling
Cited by: 10
Author(s): Bouke A. de Boer, Karel van Duijvenboden, Malou van den Boogaard, Vincent M. Christoffels, Phil Barnett, Jan M. Ruijter
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2164-14-477
Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq
Cited by: 64
Author(s): Md. Shamimuzzaman, Lila O. Vodkin
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12964-019-0504-6
miR-544 promotes maturity and antioxidation of stem cell-derived endothelial like cells by regulating the YY1/TET2 signalling axis
Cited by: 8
Author(s): Jianming Guo, Xiang Qiu, Xin Yao-jie, Yongyi Huang, Gang Zou, Te Liu
Software Mentions: 2
Published: over 4 years ago
10.3389/fgene.2020.00766
Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice
Cited by: 12
Author(s): Nannan Zhao, Kang Zhang, Chunchao Wang, Hengyu Yan, Yue Liu, Wenying Xu, Zhen Su
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-017-04524-9
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness
Cited by: 16
Author(s): Yue Liu, Wenli Zhang, Kang Zhang, Qi You, Hengyu Yan, Yuannian Jiao, Jiming Jiang, Wenying Xu, Zhen Su
Software Mentions: 2
Published: over 7 years ago
10.1038/cdd.2017.62
Nucleosome eviction along with H3K9ac deposition enhances Sox2 binding during human neuroectodermal commitment
Cited by: 17
Author(s): Yanhua Du, Zhenping Liu, Xi Cao, Xiaolong Chen, Zhenyu Chen, Xiaobai Zhang, Xiaoqing Zhang, Cizhong Jiang
Software Mentions: 2
Published: over 7 years ago
10.1093/bioinformatics/btw336
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
Cited by: 12
Author(s): Pol Cuscó, Guillaume J. Filion
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-017-07539-4
Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity
Cited by: 9
Author(s): Roderick A. P. M. van Eijl, Teun van den Brand, Luan N. Nguyen, Klaas W. Mulder
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2164-15-231
An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation
Cited by: 12
Author(s): Mathieu Lajoie, Yu-Chih Hsu, Richard M. Gronostajski, Timothy L. Bailey
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2105-15-269
Study of cell differentiation by phylogenetic analysis using histone modification data
Cited by: 13
Author(s): Nishanth Ulhas Nair, Yongjun Lin, Ana Manasovska, Jelena Antić, Paulina Grnarova, Avinash Sahu, Philipp Bücher, Bernard M. E. Moret
Software Mentions: 2
Published: over 10 years ago
10.7554/eLife.12717
Zeb1 controls neuron differentiation and germinal zone exit by a mesenchymal-epithelial-like transition
Cited by: 58
Author(s): Shalini Singh, Danielle Howell, Niraj Trivedi, Ketty Kessler, Taren Ong, Pedro Rosmaninho, Alexandre A.S.F. Raposo, Giles Robinson, Martine F. Roussel, Diogo S. Castro, David J. Solecki
Software Mentions: 2
Published: over 8 years ago
10.1186/s12859-016-1306-0
DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks
Cited by: 3
Author(s): Saulius Lukauskas, Roberto Visintainer, Guido Sanguinetti, Gabriele Schweikert
Software Mentions: 2
Published: almost 8 years ago
10.1186/1471-2164-15-1022
Genome-wide mapping of matrix attachment regions in Drosophila melanogaster
Cited by: 27
Author(s): Rashmi U. Pathak, Arumugam Srinivasan, Rakesh K. Mishra
Software Mentions: 2
Published: almost 10 years ago
10.5936/csbj.201401002
LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS
Cited by: 54
Author(s): Yong Yang, Justin M. Fear, Jianhong Hu, Irina Haecker, Lei Zhou, Rolf Renne, David C. Bloom, Lauren M. McIntyre
Software Mentions: 2
Published: almost 11 years ago
10.1038/s41419-021-04176-8
USP7 facilitates SMAD3 autoregulation to repress cancer progression in p53-deficient lung cancer
Cited by: 10
Author(s): Yu Huang, An Chieh Cheng, Hui Chi Tang, Guo Cheng Huang, Ling Cai, Ta Hsien Lin, Kou Juey Wu, Ping Hui Tseng, Greg G. Wang, Wei Yi Chen
Software Mentions: 2
Published: about 3 years ago
10.3389/fimmu.2017.01550
Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination
Cited by: 24
Author(s): Louise S. Matheson, Daniel J. Bolland, Peter Chovanec, Felix Krueger, Simon Andrews, Hashem Koohy, Anne E. Corcoran
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-16009-w
The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation
Cited by: 51
Author(s): Daosheng Huang, Guoji Guo, Ping Yuan, Amy Ralston, Luwei Sun, Mikael Huss, Tapan Kumar Mistri, Luca Pinello, Huck Hui Ng, Guo‐Cheng Yuan, Junfeng Ji, Janet Rossant, Paul Robson, Xiaoping Han
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-19494-9
Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing
Cited by: 5
Author(s): Mari Mito, Mitsutaka Kadota, Kaori Tanaka, Yasuhide Furuta, Kuniya Abe, Shigeo Iwasaki, Shinichi Nakagawa
Software Mentions: 2
Published: almost 7 years ago
10.1093/bioinformatics/btab274
Resolving diverse protein–DNA footprints from exonuclease-based ChIP experiments
Cited by: 3
Author(s): Anushua Biswas, Leelavati Narlikar
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-018-21363-4
PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry
Cited by: 18
Author(s): Angela Palmigiano, F. Santaniello, Aurora Cerutti, Dmitry Penkov, Divya Purushothaman, Ekta Makhija, Lucilla Luzi, Fabrizio d’Adda di Fagagna, Pier Giuseppe Pelicci, Viveswara Shivashankar, Gaetano Ivan Dellino, Francesco Blasi
Software Mentions: 2
Published: almost 7 years ago
10.3389/fimmu.2018.00425
Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci
Cited by: 24
Author(s): Salvatore Loguercio, E. Mauricio Barajas-Mora, Han-Yu Shih, Michael S. Krangel, Ann J. Feeney
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-25530-5
Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
Cited by: 32
Author(s): Megan E. Forrest, Alina Saiakhova, Lydia Beard, David A. Buchner, Peter C. Scacheri, Thomas LaFramboise, Sanford D. Markowitz, Ahmad M. Khalil
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-23276-8
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
Cited by: 1,223
Author(s): Ziad Al Bkhetan, Dariusz Plewczynski
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-28670-w
Gestational exposure to chlordecone promotes transgenerational changes in the murine reproductive system of males
Cited by: 20
Author(s): Aurore Gély-Pernot, Chunxiang Hao, Louis Legoff, Luc Multigner, Shereen Cynthia D’Cruz, Christine Kervarrec, Bernard Jégou, Sergei G. Tevosian, Fátima Smagulova
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2164-13-372
Cell-type specificity of ChIP-predicted transcription factor binding sites
Cited by: 16
Author(s): Tony Håndstad, Morten Rye, Rok Močnik, Finn Drabløs, Pål Sætrom
Software Mentions: 2
Published: over 12 years ago
10.1016/j.csbj.2018.02.003
Computational Methods for Assessing Chromatin Hierarchy
Cited by: 20
Author(s): Pearl Chang, Moloya Gohain, Ming‐Ren Yen, Pao‐Yang Chen
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2020.591778
Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins
Cited by: 5
Author(s): Rishikesh Lotke, Ulrike Schneeweiß, Marcel Pietrek, Thomas Guenther, Adam Grundhoff, Magdalena Weidner-Glunde, Thomas F. Schulz
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2021.667637
ChIP-seq Analysis of the Global Regulator Vfr Reveals Novel Insights Into the Biocontrol Agent Pseudomonas protegens FD6
Cited by: 2
Author(s): Qingxia Zhang, Chenglin Xing, Xiangwei Kong, Cheng Wang, Xijun Chen
Software Mentions: 2
Published: over 3 years ago
10.7554/eLife.02439
Distinct and separable roles for EZH2 in neurogenic astroglia
Cited by: 57
Author(s): William W. Hwang, Ryan Salinas, Jason J. Siu, Kevin W. Kelley, Ryan N. Delgado, Mercedes F. Paredes, Arturo Alvarez-Buylla, Michael C. Oldham, Daniel A. Lim
Software Mentions: 2
Published: over 10 years ago
10.1093/dnares/dsz021
The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L.
Cited by: 22
Author(s): Ayasha Akter, Satoshi Takahashi, Wei‐Wei Deng, Daniel J. Shea, Etsuko Itabashi, Mitsuru Shimizu, Noriaki Miyaji, Kenji Osabe, Namiko Nishida, Yutaka Suzuki, Chris A. Helliwell, Motoaki Seki, W. James Peacock, Elizabeth S. Dennis, Ryo Fujimoto
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-019-38809-y
Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells
Cited by: 8
Author(s): Shinichi Hiramatsu, Koichi Watanabe, Sonia Zeggar, Yosuke Asano, Yoshia Miyawaki, Yuriko Yamamura, Eri Katsuyama, Takayuki Katsuyama, Hirotaka Watanabe, Mariko Takano-Narazaki, Yoshinori Matsumoto, Tomoko Kawabata, Ken Ei Sada, Jun Wada
Software Mentions: 2
Published: over 5 years ago
10.1186/1471-2164-13-S1-S1
Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information
Cited by: 5
Author(s): Hatice U. Osmanbeyoglu, Ryan J. Hartmaier, Steffi Oesterreich, Xinghua Lu
Software Mentions: 2
Published: almost 13 years ago
10.1038/s41419-021-04016-9
The m6A mRNA demethylase FTO in granulosa cells retards FOS-dependent ovarian aging
Cited by: 30
Author(s): Zucheng Jiang, Yining Wang, Zi-Yuan Li, Zhihui Dai, Yi He, Kun Chu, Jiayi Gu, Yixuan Ji, Ning Sun, Li Wen
Software Mentions: 2
Published: over 3 years ago
10.3389/fnmol.2014.00087
Defining the nociceptor transcriptome
Cited by: 102
Author(s): Matthew Thakur, Megan Crow, Natalie Richards, Gareth I. J. Davey, Emma Levine, Jayne H. Kelleher, Chibeza C. Agley, Franziska Denk, Sdr Harridge, Stephen B. McMahon
Software Mentions: 2
Published: about 10 years ago
10.1186/s12974-021-02168-1
Calcitonin gene-related peptide regulates spinal microglial activation through the histone H3 lysine 27 trimethylation via enhancer of zeste homolog-2 in rats with neuropathic pain
Cited by: 19
Author(s): Qi An, Chenyan Sun, Ruidi Li, Shuhui Chen, Xinpei Gu, Shuhong An, Zhaojin Wang
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-14-S5-S3
Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell
Cited by: 9
Author(s): Xing Tang, Mei Hou, Yang Ding, Zhaohui Li, Lixin Ren, Ge Gao
Software Mentions: 2
Published: about 11 years ago
10.1186/s12974-020-01992-1
NFATc2-dependent epigenetic upregulation of CXCL14 is involved in the development of neuropathic pain induced by paclitaxel
Cited by: 13
Author(s): Meng Li, Subo Zhang, Yuxuan Luo, Yanling Yang, Xiangzhong Zhang, Bo Li, Yan Meng, Yuan-Jie Chen, Ruixian Guo, Yang Xiong, Wenjun Xin, Dai Li
Software Mentions: 2
Published: about 4 years ago
10.1038/s41598-020-72822-w
Wnt signaling mediates oncogenic synergy between Akt and Dlx5 in T-cell lymphomagenesis by enhancing cholesterol synthesis
Cited by: 6
Author(s): Yinfei Tan, Eleonora Sementino, Zemin Liu, Kathy Q. Cai, Joseph R. Testa
Software Mentions: 2
Published: about 4 years ago
10.18632/oncotarget.11647
A signaling cascade including ARID1A, GADD45B and DUSP1 induces apoptosis and affects the cell cycle of germ cell cancers after romidepsin treatment
Cited by: 48
Author(s): Daniel Nettersheim, Sina Jostes, Martin H Fabry, Friedemann Honecker, Valérie Schumacher, Jutta Kirfel, Glen Kristiansen, Hubert Schorle
Software Mentions: 2
Published: about 8 years ago
10.1186/1471-2164-13-S8-S18
CTF: a CRF-based transcription factor binding sites finding system
Cited by: 6
Author(s): Yiping He, Yizhe Zhang, Guangyong Zheng, Chaochun Wei
Software Mentions: 2
Published: almost 12 years ago
10.1038/s41598-021-94514-9
Epigenetic regulation of triple negative breast cancer (TNBC) by TGF-β signaling
Cited by: 35
Author(s): Radhakrishnan Vishnubalaji, Nehad M. Alajez
Software Mentions: 2
Published: over 3 years ago
10.1002/pld3.100
Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in<i>Arabidopsis</i>seedlings
Cited by: 62
Author(s): Jie Shu, Chen Chen, Raj Kumar Thapa, Shaomin Bian, Vi Nguyen, Kangfu Yu, Zhongshun Yuan, Jun Li, Susanne E. Kohalmi, Chenlong Li, Yuhai Cui
Software Mentions: 2
Published: almost 6 years ago
10.1093/database/bau009
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
Cited by: 13
Author(s): Margherita Scarpato, Roberta Esposito, Daniela Evangelista, Marianna Aprile, Maria Rosaria Ambrosio, Claudia Angelini, Alfredo Ciccodicola, Valerio Costa
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0179464
Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation
Cited by: 10
Author(s): Huanhuan Cui, V. Bansal, Marcel Grunert, Barbora Malecová, Alessandra Dall’Agnese, Lucia Latella, Sole Gatto, Ryan Tj, Kerstin Schulz, Wei Chen, Cornelia Dorn, Pier Lorenzo Puri, Silke Sperling
Software Mentions: 2
Published: over 7 years ago
10.3389/fnins.2017.00307
Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
Cited by: 23
Author(s): Akiko Sakai, Ryuichiro Nakato, Yiwei Ling, Xubin Hou, Norikazu Hara, Tomoya Iijima, Yuchio Yanagawa, Ryozo Kuwano, Shujiro Okuda, Katsuhiko Shirahige, Sayaka Sugiyama
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pcbi.1003884
Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain
Cited by: 12
Author(s): Jinhua Liu, Xuelong Wang, Juan Li, Haifang Wang, Gang Wei, Jun Yan
Software Mentions: 2
Published: about 10 years ago
10.1038/s41419-021-03982-4
The long noncoding RNA HOTAIRM1 controlled by AML1 enhances glucocorticoid resistance by activating RHOA/ROCK1 pathway through suppressing ARHGAP18
Cited by: 7
Author(s): Liang Liang, Wenbin Gu, Meng Li, Ran Gao, Xin Zhang, Chongye Guo, Shuangli Mi
Software Mentions: 2
Published: over 3 years ago
10.4172/2157-7633.S10-009
Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells
Cited by: 5
Author(s): Satyabrata Das, Snehalata Jena, Eun‐Mi Kim, Nicholas Zavazava, Dana N. Levasseur
Software Mentions: 2
Published: almost 13 years ago
10.3389/fonc.2020.526866
IL-37 Confers Anti-Tumor Activity by Regulation of m6A Methylation
Cited by: 12
Author(s): Xiaofeng Mu, Qi Zhao, Wen Chen, Yuxiang Zhao, Qing Guo Yan, Rui Peng, Jie Zhu, Chunrui Yang, Ketao Lan, Xiaosong Gu, Ye Wang
Software Mentions: 2
Published: almost 4 years ago
10.18632/oncotarget.7513
Pre-neoplastic epigenetic disruption of transcriptional enhancers in chronic inflammation
Cited by: 22
Author(s): Aline Cristiane Planello, Rajat Singhania, Ken J. Kron, Swneke D. Bailey, David Roulois, Mathieu Lupien, Sérgio Roberto Peres Line, Ana Paula de Souza, Daniel D. De Carvalho
Software Mentions: 2
Published: almost 9 years ago
10.1093/bioinformatics/btt756
CGAT: computational genomics analysis toolkit
Cited by: 61
Author(s): David Sims, Nicholas E. Ilott, Stephen N. Sansom, Ian Sudbery, Jethro Johnson, Katherine A. Fawcett, Antonio J. Berlanga‐Taylor, Sebastián Luna-Valero, Chris P. Ponting, Andreas Heger
Software Mentions: 2
Published: almost 11 years ago
10.1016/j.ydbio.2012.03.024
The transcriptional programme controlled by Runx1 during early embryonic blood development
Cited by: 41
Author(s): Yosuke Tanaka, Anagha Joshi, Nicola K. Wilson, Sarah Kinston, Shin‐Ichi Nishikawa, Berthold Göttgens
Software Mentions: 2
Published: over 12 years ago
10.7554/eLife.11627
Loss of the transcription factor Meis1 prevents sympathetic neurons target-field innervation and increases susceptibility to sudden cardiac death
Cited by: 22
Author(s): Fabrice Bouilloux, Jérôme Thireau, Stéphanie Venteo, Charlotte Farah, Sarah Arangurem Karam, Yves Dauvilliers, Jean Valmier, Neal G. Copeland, Nancy A. Jenkins, Sylvain Richard, Frédéric Marmigère
Software Mentions: 2
Published: almost 9 years ago
10.1186/1471-2105-16-S1-S2
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
Cited by: 44
Author(s): Yun Lung Li, Jui Cheng Weng, Chiung Chih Hsiao, Min Te Chou, Chin Wen Tseng, Jui-Hung Hung
Software Mentions: 2
Published: almost 10 years ago
10.3389/fpls.2016.02044
The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana
Cited by: 4
Author(s): Elena V. Zemlyanskaya, Victor G. Levitsky, Dmitry Oshchepkov, Ivo Große, В. В. Миронова
Software Mentions: 2
Published: almost 8 years ago
10.3389/fpls.2021.659634
Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.
Cited by: 7
Author(s): Hasan Mehraj, Satoshi Takahashi, Noriaki Miyaji, Ayasha Akter, Yutaka Suzuki, Motoaki Seki, Elizabeth S. Dennis, Ryo Fujimoto
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2021.687826
RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers
Cited by: 17
Author(s): Dandan Yang, Huachao Xu, Yue Liu, Mengzhuo Li, Muhammad Ali, Xiangyang Xu, Gang Lü
Software Mentions: 2
Published: over 3 years ago
10.1093/bioinformatics/btv002
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Cited by: 11
Author(s): Andrew S. Warren, Cristina Aurrecoechea, Brian P. Brunk, Prerak Desai, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Deborah Hix, Daniel Lawson, Dustin Machi, Chunhong Mao, Michael McClelland, Eric K. Nordberg, Maulik Shukla, Leslie B. Vosshall, Alice R. Wattam, Rebecca Will, Hyun Seung Yoo, Bruno W. S. Sobral
Software Mentions: 2
Published: almost 10 years ago
10.1016/j.molcel.2018.09.016
Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci
Cited by: 123
Author(s): Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert
Software Mentions: 2
Published: about 6 years ago
10.1186/1471-2164-16-S4-S2
HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data
Cited by: 15
Author(s): Xiaodong Cui, Jia Meng, Manjeet K. Rao, Yidong Chen, Yufei Huang
Software Mentions: 2
Published: over 9 years ago
10.7554/eLife.09003
A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver
Cited by: 32
Author(s): Miyuki Suzawa, Diego A. Miranda, Karmela A Ramos, Kenny K-H Ang, Emily J. Faivre, Christopher G. Wilson, Laura Caboni, Michelle R. Arkin, Yeong-Sang Kim, Robert J. Fletterick, Aaron A. Diaz, John S. Schneekloth, Holly A. Ingraham
Software Mentions: 2
Published: almost 9 years ago
10.3389/fpls.2017.00607
Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae
Cited by: 30
Author(s): Paweł Mikulski, Olga Komarynets, Fabio Fachinelli, Andreas P.M. Weber, Daniel Schubert
Software Mentions: 2
Published: over 7 years ago
10.1186/s12915-015-0132-6
snoRNAs are a novel class of biologically relevant Myc targets
Cited by: 44
Author(s): Eva K. Herter, Maria Stauch, Maria Gallant, Elmar Wolf, Thomas Raabe, Peter Gallant
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-016-3077-4
Genome-wide identification and characterisation of HOT regions in the human genome
Cited by: 11
Author(s): Hao Li, Feng Liu, Chao Ren, Xiaochen Bo, Wenjie Shu
Software Mentions: 2
Published: about 8 years ago
10.1186/s12859-019-3049-1
AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU
Cited by: 1
Author(s): Chih-Hao Fang, Nawanol Theera-Ampornpunt, Michael Roth, Ananth Grama, Somali Chaterji
Software Mentions: 2
Published: about 5 years ago
10.4172/jpb.1000302
Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis
Cited by: 13
Author(s): Mohammad Heydarian
Software Mentions: 2
Published: almost 11 years ago
10.1534/g3.113.007229
Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing
Cited by: 67
Author(s): Justin T. Page, Mark D. Huynh, Zach S. Liechty, Kara Grupp, David M. Stelly, Amanda M. Hulse, Hamid Ashrafi, Allen Van Deynze, Jonathan F. Wendel, Joshua A. Udall
Software Mentions: 2
Published: about 11 years ago
10.1242/dev.133686
Drosophila Condensin II subunit, Chromosome Associated Protein-D3, regulates cell fate determination through non-cell autonomous signaling
Cited by: 5
Author(s): Lindsey R. Klebanow, Emanuela C. Peshel, Andrew Schuster, Kuntal De, Kavitha Sarvepalli, Madeleine E. Lemieux, Jessica J. Lenoir, Adrian W. Moore, Jocelyn A. McDonald, Michelle S. Longworth
Software Mentions: 2
Published: almost 9 years ago
10.1016/j.bbagrm.2018.06.010
Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells
Cited by: 16
Author(s): Ioanna Pavlaki, Igor Chernukhin, Georgia Kita, Svetlana Gretton, Christopher T. Clarkson, Vladimir B. Teif, Elena Klenova
Software Mentions: 2
Published: over 6 years ago
10.1128/mBio.00924-17
An Alternative STAT Signaling Pathway Acts in Viral Immunity in <i>Caenorhabditis elegans</i>
Cited by: 37
Author(s): M. Tanguy, Louise Véron, Przemyslaw Stempor, Julie Ahringer, Peter Sarkies, Eric A. Miska
Software Mentions: 2
Published: about 7 years ago
10.1534/g3.115.023499
Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects
Cited by: 14
Author(s): Karl M. Glastad, Michael A. D. Goodisman, Soojin V. Yi, Brendan G. Hunt
Software Mentions: 2
Published: almost 9 years ago
10.1242/dev.115808
Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells
Cited by: 22
Author(s): Emmanouil Metzakopian, Kamal Bouhali, Matías Alvarez-Saavedra, Jeffrey A. Whitsett, David J. Picketts, Siew‐Lan Ang
Software Mentions: 2
Published: over 9 years ago
10.1128/mBio.00142-20
Merkel Cell Polyomavirus DNA Replication Induces Senescence in Human Dermal Fibroblasts in a Kap1/Trim28-Dependent Manner
Cited by: 15
Author(s): Svenja Siebels, Manja Czech-Sioli, Michael Spohn, Claudia Schmidt, Juliane Theiß, Daniela Indenbirken, Thomas Günther, Adam Grundhoff, Nicole Fischer
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-12-165
Rice-Map: a new-generation rice genome browser
Cited by: 12
Author(s): Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: over 13 years ago
10.1186/s13104-018-3633-x
The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments
Cited by: 3
Author(s): Daniel Wiegreffe, Lydia Müller, Jens Steuck, Dirk Zeckzer, Peter F. Stadler
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2164-15-S1-S1
An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example
Cited by: 17
Author(s): Chia Yang Cheng, Chia Han Chu, Hung Wei Hsu, Fang‐Rong Hsu, Chung Yi Tang, Wen-Ching Wang, Hsing Jien Kung, Pei Ching Chang
Software Mentions: 2
Published: almost 11 years ago
10.1038/emboj.2013.177
Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor
Cited by: 192
Author(s): Graziano Martello, Paul Bertone, Austin Smith
Software Mentions: 2
Published: over 11 years ago
10.1093/hmg/ddy440
Functional characterization of the<i>ZEB2</i>regulatory landscape
Cited by: 12
Author(s): Reut Bar Yaacov, Reut Eshel, Einan Farhi, Fania Shemuluvich, Tommy Kaplan, Ramon Y. Birnbaum
Software Mentions: 2
Published: almost 6 years ago
10.1093/hmg/ddy255
Functional characteristics of novel pancreatic Pax6 regulatory elements
Cited by: 14
Author(s): Adam Buckle, Ryu-Suke Nozawa, Dirk A. Kleinjan, Nick Gilbert
Software Mentions: 2
Published: over 6 years ago
10.1002/humu.22909
Putative Prostate Cancer Risk SNP in an Androgen Receptor‐Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites
Cited by: 34
Author(s): Huajie Bu, Narisu Narisu, Bettina Schlick, Johannes Michael Rainer, Thomas Manke, Georg Schäfer, Lorenza Pasqualini, Peter S. Chines, Michal R. Schweiger, Christian Fuchsberger, Helmut Klocker
Software Mentions: 2
Published: about 9 years ago
10.1038/s41419-021-03948-6
The AML-associated K313 mutation enhances C/EBPα activity by leading to C/EBPα overexpression
Cited by: 0
Author(s): Ian E Gentle, Isabel Moelter, Mohamed Tarek Badr, Konstanze Döhner, Michael Lübbert, Georg Häcker
Software Mentions: 2
Published: over 3 years ago
10.15252/embj.2019102096
Residual apoptotic activity of a tumorigenic p53 mutant improves cancer therapy responses
Cited by: 20
Author(s): Oleg Timofeev, Boris Klimovich, Jean Schneikert, Michael Wanzel, Evangelos Pavlakis, Julia Han Noll, Samet Mutlu, Sabrina Elmshäuser, Andrea Nist, Marco Mernberger, Boris Lamp, Ulrich Wenig, Alexander Brobeil, Stefan Gattenlöhner, Kernt Köhler, Thorsten Stiewe
Software Mentions: 2
Published: about 5 years ago
10.1093/g3journal/jkab101
Effects of sheared chromatin length on ChIP-seq quality and sensitivity
Cited by: 2
Author(s): Cheryl A. Keller, Alexander Q. Wixom, Elisabeth F. Heuston, Belinda Giardine, Chris C.-S. Hsiung, Maria Long, Amber Miller, Stacie M. Anderson, April Cockburn, Gerd A. Blobel, David M. Bodine, R Hardison
Software Mentions: 2
Published: over 3 years ago
10.1084/jem.20170484
JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia
Cited by: 22
Author(s): Marc R. Mansour, Shuning He, Zhaodong Li, Riadh Lobbardi, Brian J. Abraham, Clemens Hug, Sunniyat Rahman, Theresa E. León, Youyi Kuang, Mark W. Zimmerman, Traci M. Blonquist, Evisa Gjini, Alejandro Gutiérrez, Qin Tang, Laura García-Pérez, Karin Pike-Overzet, Lars Anders, Alla Berezovskaya, Yi Zhou, Leonard I. Zon, Donna Neuberg, Adele K. Fielding, Frank J. T. Staal, David M. Langenau, Takaomi Sanda, Richard A. Young, A. Thomas Look
Software Mentions: 2
Published: over 6 years ago
10.18632/oncotarget.10422
MITF depletion elevates expression levels of ERBB3 receptor and its cognate ligand NRG1-beta in melanoma
Cited by: 11
Author(s): Tine Norman Alver, Timothy J. Lavelle, Ane Sager Longva, Geir Frode Øy, Eivind Hovig, Sigurd Leinæs Bøe
Software Mentions: 2
Published: over 8 years ago
10.18632/oncotarget.10637
Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer
Cited by: 25
Author(s): Callie R. Merry, Sandra McMahon, Megan E. Forrest, Cynthia F. Bartels, Alina Saiakhova, Courtney A. Bartel, Peter C. Scacheri, Cheryl L. Thompson, Mark W. Jackson, Lyndsay N. Harris, Ahmad M. Khalil
Software Mentions: 2
Published: over 8 years ago
10.7554/eLife.22474
Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling
Cited by: 40
Author(s): Davide Martino Coda, Tessa Gaarenstroom, Philip East, Harshil Patel, Daniel S. J. Miller, Anna Lobley, Nik Matthews, Aengus Stewart, Caroline S. Hill
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pgen.1004153
A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS
Cited by: 122
Author(s): Jessica Zuin, Vedran Franke, Wilfred F. J. van IJcken, Antoine A.J. van der Sloot, Ian D. Krantz, Michael I.J.A. van der Reijden, Ryuichiro Nakato, Boris Lenhard, Kerstin S. Wendt
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pgen.1002736
The NSL Complex Regulates Housekeeping Genes in Drosophila
Cited by: 82
Author(s): Kin Chung Lam, Friederike Mühlpfordt, Juan M. Vaquerizas, Sunil Jayaramaiah Raja, Heribert Holz, Nicholas M. Luscombe, Thomas Manke, Asifa Akhtar
Software Mentions: 2
Published: over 12 years ago
10.3390/genes10100750
The H3K9 Methylation Writer SETDB1 and its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells
Cited by: 13
Author(s): Paola Cruz‐Tapias, Philippe Robin, Julien Pontis, Laurence Del Maestro, Slimane Ait‐Si‐Ali
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pgen.1005331
Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila
Cited by: 37
Author(s): Qi Zhou, Doris Bachtrog
Software Mentions: 2
Published: over 9 years ago
10.7554/eLife.53447
Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity
Cited by: 25
Author(s): Nicholas Sciascia, Wei Wu, Dali Zong, Yilun Sun, Nancy Wong, Sam John, Darawalee Wangsa, Thomas Ried, Samuel F. Bunting, Yves Pommier, André Nussenzweig
Software Mentions: 2
Published: almost 5 years ago
10.15252/embj.201592532
Sororin actively maintains sister chromatid cohesion
Cited by: 84
Author(s): René Ladurner, Emanuel Kreidl, Miroslav P Ivanov, Heinz Ekker, Maria Helena Idarraga-Amado, Georg A. Busslinger, Gordana Wutz, David A. Cisneros, Jan‐Michael Peters
Software Mentions: 2
Published: almost 9 years ago
10.15252/embj.201488740
<scp>TDP</scp>‐1, the <i><scp>C</scp>aenorhabditis elegans</i> ortholog of <scp>TDP</scp>‐43, limits the accumulation of double‐stranded <scp>RNA</scp>
Cited by: 58
Author(s): Tassa Saldi, Peter E.A. Ash, Gavin Wilson, Patrick Gonzales, Alfonso Garrido-Lecca, Christine M. Roberts, Vishantie Dostal, Tania F. Gendron, Lincoln Stein, Thomas Blumenthal, Leonard Petrucelli, Christopher D. Link
Software Mentions: 2
Published: about 10 years ago
10.3390/genes11111301
PURα Promotes the Transcriptional Activation of PCK2 in Oesophageal Squamous Cell Carcinoma Cells
Cited by: 6
Author(s): Yan Sun, Jiajia Gao, Zongpan Jing, Yan Zhao, Yulin Sun, Xiaohang Zhao
Software Mentions: 2
Published: about 4 years ago