pypi: MACS | Projects | Ecosyste.ms: Papers

10.15252/embj.201695642

Hypoxia enhances antibody‐dependent dengue virus infection
Cited by: 15
Author(s): Esther S. Gan, Wei Fun Cheong, Kap Luk Chan, Eugenia Z. Ong, Xiaoran Chai, Hwee Cheng Tan, Sujoy Ghosh, Markus R. Wenk, Eng Eong Ooi
Software Mentions: 1
Published: over 7 years ago

10.1002/emmm.201201683

LPS resistance of SPRET/Ei mice is mediated by Gilz, encoded by the Tsc22d3 gene on the X chromosome
Cited by: 56
Author(s): Iris Pinheiro, Lien Dejager, Ιωάννα Πέττα, Sofie Vandevyver, Leen Puimège, Tina Mahieu, Marlies Ballegeer, Filip Van Hauwermeiren, Carlo Riccardi, Marnik Vuylsteke, Claude Libert
Software Mentions: 1
Published: over 11 years ago

10.1186/s13100-021-00231-5

Association analysis of repetitive elements and R-loop formation across species
Cited by: 12
Author(s): Chao Zeng, Masahiro Onoguchi, Michiaki Hamada
Software Mentions: 1
Published: almost 4 years ago

10.15252/embr.201540726

Response to interferons and antibacterial innate immunity in the absence of tyrosine‐phosphorylated <scp>STAT</scp> 1
Cited by: 45
Author(s): Andrea Majoros, Ekaterini Platanitis, Daniel Szappanos, HyeonJoo Cheon, Claus Vogl, Priyank Shukla, George Stark Stark, Veronika Sexl, Robert D. Schreiber, Christian Schindler, Mathias Müller, Thomas Decker
Software Mentions: 1
Published: almost 9 years ago

10.3390/microorganisms9020447

Glucose-Binding of Periplasmic Protein GltB Activates GtrS-GltR Two-Component System in Pseudomonas aeruginosa
Cited by: 13
Author(s): Chenchen Xu, Qiao Cao, Lefu Lan
Software Mentions: 1
Published: almost 4 years ago

10.15252/embr.201540467

Selective influence of Sox2 on <scp>POU</scp> transcription factor binding in embryonic and neural stem cells
Cited by: 52
Author(s): Tapan Kumar Mistri, Arun George Devasia, Lee-Thean Chu, Wei Ping Ng, Florian Halbritter, Douglas Colby, Ben Martynoga, Simon R. Tomlinson, Ian Chambers, Paul Robson, Thorsten Wohland
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.16087

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan
Cited by: 28
Author(s): Isabel Guerreiro, Sandra Gitto, Ana Nóvoa, Julien Codourey, Thi Hanh Nguyen Huynh, Federico González, Michel C. Milinkovitch, Bernard Malissen, Denis Duboule
Software Mentions: 1
Published: over 8 years ago

10.15698/mic2018.04.623

Molecular signature of the imprintosome complex at the mating-type locus in fission yeast
Cited by: 5
Author(s): Célia Raimondi, Bernd Jagla, Caroline Proux, Hervé Waxin, Serge Gangloff, Benoı̂t Arcangioli
Software Mentions: 1
Published: over 6 years ago

10.1186/s13072-018-0214-0

Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements
Cited by: 19
Author(s): Laxmi Narayan Mishra, Vasantha Shalini, Nikhil Gupta, Krittika Ghosh, Neeraj Suthar, Utsa Bhaduri, Rao M
Software Mentions: 1
Published: over 6 years ago

10.1186/1756-8935-7-23

G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors
Cited by: 17
Author(s): Dustin E. Schones, Xiaoji Chen, Candi Trac, Ryan L. Setten, Patrick J. Paddison
Software Mentions: 1
Published: about 10 years ago

10.1186/s13072-017-0147-z

Histone 4 lysine 8 acetylation regulates proliferation and host–pathogen interaction in Plasmodium falciparum
Cited by: 24
Author(s): Archana Patkar Gupta, Lei Zhu, Jaishree Tripathi, Michal Kucharski, Alok Patra, Zbynek Bozdech
Software Mentions: 1
Published: over 7 years ago

10.1186/s13072-015-0017-5

lobChIP: from cells to sequencing ready ChIP libraries in a single day
Cited by: 19
Author(s): Ola Wallerman, Helena Nord, Madhusudhan Bysani, Lisa Borghini, Claes Wadelius
Software Mentions: 1
Published: over 9 years ago

10.1111/1751-7915.12819

Escherichiacoli surface display for the selection of nanobodies
Cited by: 53
Author(s): Valencio Salema, Luis A. Fernández
Software Mentions: 1
Published: over 7 years ago

10.1002/mp.13814

Automatic detection of contouring errors using convolutional neural networks
Cited by: 64
Author(s): Dong Joo Rhee, Carlos Cárdenas, Hesham Elhalawani, Rachel McCarroll, Lifei Zhang, Jinzhong Yang, Adam S. Garden, Christine B. Peterson, Beth M. Beadle, Laurence Edward Court
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-13-199

Normalization of ChIP-seq data with control
Cited by: 98
Author(s): Kun Liang, Sündüz Keleş
Software Mentions: 1
Published: over 12 years ago

10.1186/s13072-017-0140-6

Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation
Cited by: 4
Author(s): Theresa Jox, Melanie K. Buxa, Dorte Bohla, Ikram Ullah, Igor Mačinković, Alexander Brehm, Marek Bartkuhn, Rainer Renkawitz
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.10483

Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma
Cited by: 63
Author(s): Andrew R. Conery, Richard C. Centore, Adrianne Neiss, Patricia J. Keller, Shivangi Joshi, Kerry L. Spillane, Péter Sandy, Charlie Hatton, Eneida Pardo, Laura E. Zawadzke, Archana Bommi-Reddy, Karen E. Gascoigne, Barbara M. Bryant, Jennifer A. Mertz, Robert J. Sims
Software Mentions: 1
Published: almost 9 years ago

10.1007/s00262-018-2202-4

CD11c+ MHCIIlo GM-CSF-bone marrow-derived dendritic cells act as antigen donor cells and as antigen presenting cells in neoepitope-elicited tumor immunity against a mouse fibrosarcoma
Cited by: 12
Author(s): Hakimeh Ebrahimi-Nik, William L. Corwin, Tatiana Shcheglova, Alok Das Mohapatra, Ion Măndoiu, Pramod K. Srivastava
Software Mentions: 1
Published: over 6 years ago

10.1186/s12935-020-01554-8

Joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in gastric cancer
Cited by: 20
Author(s): Zhi Lv, Liping Sun, Qian Xu, Chengzhong Xing, Yuan Yuan
Software Mentions: 1
Published: about 4 years ago

10.20892/j.issn.2095-3941.2020.0420

Biomaterial-based platforms for cancer stem cell enrichment and study
Cited by: 2
Author(s): Chao Luo, Zhongjie Ding, Yun Tu, Jiao Tan, Qing Luo, Guanbin Song
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.00205

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands
Cited by: 405
Author(s): Anca M. Farcas, Neil P. Blackledge, Ian Sudbery, Hannah K. Long, Joanna F. McGouran, Nathan R. Rose, Sheena Lee, David Sims, Andrea Cerase, Thomas W. Sheahan, Haruhiko Koseki, Neil Brockdorff, Chris P. Ponting, Benedikt M. Kessler, Robert J. Klose
Software Mentions: 1
Published: almost 12 years ago

10.1186/1756-8935-7-10

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements
Cited by: 78
Author(s): Petros Kolovos, Harmen J.G. van de Werken, Nick Kepper, Jessica Zuin, Rutger W. W. Brouwer, Christel Kockx, Kerstin S. Wendt, Wilfred F. J. van IJcken, Frank Grosveld, Tobias Knoch
Software Mentions: 1
Published: over 10 years ago

10.1042/BSR20160028

Homeobox genes gain trimethylation of histone H3 lysine 4 in glioblastoma tissue
Cited by: 3
Author(s): Kun Luo, Da Luo, Hao Wen
Software Mentions: 1
Published: over 8 years ago

10.1186/s13072-016-0063-7

The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing
Cited by: 10
Author(s): Cary Stelloh, Michael Reimer, Kirthi Pulakanti, Steven Blinka, Jonathan Peterson, Luca Pinello, Jia Song, S. A. Rumyantsev, Martin J. Hessner, Samuel Milanovich, Guo‐Cheng Yuan, Sridhar Rao
Software Mentions: 1
Published: over 8 years ago

10.3390/biom10040544

The Road Not Taken with Pyrrole-Imidazole Polyamides: Off-Target Effects and Genomic Binding
Cited by: 6
Author(s): Jason Lin, Hiroki Nagase
Software Mentions: 1
Published: over 4 years ago

10.1186/s13072-016-0091-3

Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development
Cited by: 6
Author(s): Stéphanie Kaeser-Pebernard, Catherine Pfefferli, Caroline Aschinger, Chantal Wicky
Software Mentions: 1
Published: about 8 years ago

10.1186/s13072-019-0259-8

Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states
Cited by: 9
Author(s): René A.M. Dirks, Guido van Mierlo, Hindrik H. D. Kerstens, Andreia S. Bernardo, Julianna Kobolák, István Bock, Julien Maruotti, Roger A. Pedersen, András Dinnyés, Martijn Huynen, Alice Jouneau, Hendrik Marks
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13072-019-0320-7

Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model
Cited by: 18
Author(s): Sylvia Garza-Manero, Abdulmajeed Sindi, Gokula Mohan, Ohoud Rehbini, Valentine Jeantet, Mariarca Bailo, Faeezah Abdul Latif, Maureen West, Ross Gurden, Lauren Finlayson, Silvija Svambaryte, Adam G. West, Katherine L. West
Software Mentions: 1
Published: almost 5 years ago

10.1155/2018/4658024

Altered DNA Methylation of Long Noncoding RNA uc.167 Inhibits Cell Differentiation in Heart Development
Cited by: 6
Author(s): Anwen Yin, Mengwen Feng, Zijie Cheng, Qi‐Jun Zhang, Hua Li, Jia Xu, Hao Zhang, Yun Li, Lei Qian
Software Mentions: 1
Published: over 6 years ago

10.1186/s40001-014-0047-7

Network analysis of ChIP-Seq data reveals key genes in prostate cancer
Cited by: 6
Author(s): Yu Zhang, Zhen Huang, Zhiqiang Zhu, Jianwei Liu, Xin Zheng, Yuhai Zhang
Software Mentions: 1
Published: about 10 years ago

10.1155/2016/7276161

Epigenetic Profiling of H3K4Me3 Reveals Herbal Medicine Jinfukang-Induced Epigenetic Alteration Is Involved in Anti-Lung Cancer Activity
Cited by: 16
Author(s): Jun Lü, Xiaoli Zhang, Tingting Shen, Chi Ma, Jun Wu, Hualei Kong, Jing Tian, Zongshu Shao, Xiaodong Zhao, Ling Xu
Software Mentions: 1
Published: almost 9 years ago

10.1155/2015/852070

Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model
Cited by: 8
Author(s): Yu Chen Zhang, Shao Wu Zhang, Lian Liu, Hui Liu, Lin Zhang, Xiaodong Cui, Yufei Huang, Jia Meng
Software Mentions: 1
Published: almost 10 years ago

10.1242/bio.20136262

Targeted inactivation and identification of targets of the Gli2a transcription factor in the zebrafish
Cited by: 22
Author(s): Xingang Wang, Zhonghua Zhao, Julius Müller, Audrey Iyu, Alexis Jiaying Khng, Ernesto Guccione, Yijun Ruan, Philip W. Ingham
Software Mentions: 1
Published: about 11 years ago

10.1242/bio.023218

A developmental transcriptomic analysis ofPax1andPax9in embryonic intervertebral disc development
Cited by: 45
Author(s): V. Sivakamasundari, Petra Kraus, Wenjie Sun, Xiaoming Hu, Siew Lan Lim, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.04207

The transcription factor FOXL2 mobilizes estrogen signaling to maintain the identity of ovarian granulosa cells
Cited by: 76
Author(s): Adrien Georges, David L’Hôte, Anne‐Laure Todeschini, Aurélie Auguste, Bérangère Legois, Alain Zider, Reiner A. Veitia
Software Mentions: 1
Published: about 10 years ago

10.18632/aging.202383

Comprehensive analysis of lncRNAs N6-methyladenosine modification in colorectal cancer
Cited by: 13
Author(s): Luo Zuo, Hui Su, Qiao Zhang, Weiyu Wu, Yan Zeng, Xuemei Li, Jing Xiong, Chen Lan-fang, Yan Zhou
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13062-016-0148-z

Computational inference of a genomic pluripotency signature in human and mouse stem cells
Cited by: 5
Author(s): Esra Kürüm, Bérénice A. Benayoun, Ankit Malhotra, Joshy George, Duygu Ucar
Software Mentions: 1
Published: about 8 years ago

10.1093/bioinformatics/btt524

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data
Cited by: 43
Author(s): Haitham Ashoor, Aurélie Hérault, Aurélie Kamoun, François Radvanyi, Vladimir B. Bajic, Emmanuel Barillot, Valentina Boeva
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-11-369

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
Cited by: 96
Author(s): Zhaohui S. Qin, Jianjun Yu, Jincheng Shen, Christopher A. Maher, Ming Hu, Shanker Kalyana-Sundaram, Jindan Yu, Arul M. Chinnaiyan
Software Mentions: 1
Published: over 14 years ago

10.18632/oncotarget.20229

Beta-catenin represses protein kinase D1 gene expression by non-canonical pathway through MYC/MAX transcription complex in prostate cancer
Cited by: 11
Author(s): Bita Nickkholgh, Sivanandane Sittadjody, Michael B. Rothberg, Xiaolan Fang, Kunzhao Li, Jeff W. Chou, Gregory A. Hawkins, K.C. Balaji
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-016-1042-5

Identifying peaks in *-seq data using shape information
Cited by: 13
Author(s): Francesco Strino, Michael Lappé
Software Mentions: 1
Published: over 8 years ago

10.3389/fcell.2021.737498

The RNA N6-Methyladenosine Methyltransferase METTL3 Promotes the Progression of Kidney Cancer via N6-Methyladenosine-Dependent Translational Enhancement of ABCD1
Cited by: 17
Author(s): Yue Shi, Yanliang Dou, Jianye Zhang, Jie Qi, Zijuan Xin, Mingxin Zhang, Yu Xiao, Weimin Ci
Software Mentions: 1
Published: about 3 years ago

10.3389/fcell.2021.590468

Profiling of RNA N6-Methyladenosine Methylation Reveals the Critical Role of m6A in Chicken Adipose Deposition
Cited by: 16
Author(s): Baoping Cheng, Li Leng, Ziwei Li, Weijia Wang, Jing Yang, Yudong Li, Ning Wang, Hui Li, Shouzhi Wang
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-015-0787-6

Peak shape clustering reveals biological insights
Cited by: 20
Author(s): Marzia A. Cremona, Laura M. Sangalli, Simone Vantini, Gaetano Ivan Dellino, Pier Giuseppe Pelicci, Piercesare Secchi, Laura Riva
Software Mentions: 1
Published: about 9 years ago

10.1093/bioinformatics/btz150

RECAP reveals the true statistical significance of ChIP-seq peak calls
Cited by: 5
Author(s): Justin G. Chitpin, Aseel Awdeh, Theodore J. Perkins
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.686000

Epitranscriptomic Analysis of m6A Methylome After Peripheral Nerve Injury
Cited by: 9
Author(s): Lei Zhang, Dingyu Hao, Pengyi Ma, Boyuan Ma, Jia Qin, Guangyuan Tian, Zihao Liu, Xianhu Zhou
Software Mentions: 1
Published: over 3 years ago

10.1523/ENEURO.0255-16.2017

NEUROD2 RegulatesStim1Expression and Store-Operated Calcium Entry in Cortical Neurons
Cited by: 19
Author(s): Gökhan Güner, Gizem Guzelsoy, Fatma Sadife Isleyen, Gulcan Semra Sahin, Cansu Akkaya, Efil Bayam, Eser Ilgin Kotan, Alkan Kabakçıoğlu, Gulayse Ince-Dunn
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2020.584460

Integrated Analysis of m6A Methylome in Cisplatin-Induced Acute Kidney Injury and Berberine Alleviation in Mouse
Cited by: 20
Author(s): Jianxiao Shen, Wanpeng Wang, Xinghua Shao, Jinlong Wu, Shu Li, Xiajing Che, Zhaohui Ni
Software Mentions: 1
Published: about 4 years ago

10.1093/bioinformatics/btt001

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
Cited by: 27
Author(s): Parameswaran Ramachandran, Gareth Palidwor, Christopher J. Porter, Theodore J. Perkins
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-14-280

Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
Cited by: 12
Author(s): Marcin Kruczyk, Husen M. Umer, Stefan Enroth, Jan Komorowski
Software Mentions: 1
Published: about 11 years ago

10.3389/fgene.2014.00308

Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells
Cited by: 14
Author(s): Yanghua He, José A. Carrillo, Juan Luo, Yi Ding, Fei Tian, Irit Davidson, Jiuzhou Song
Software Mentions: 1
Published: about 10 years ago

10.3389/fgene.2016.00194

The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer
Cited by: 22
Author(s): Fabio Tordini, Marco Aldinucci, Luciano Milanesi, Píetro Lió, Ivan Merelli
Software Mentions: 1
Published: about 8 years ago

10.3389/fgene.2020.574167

Dysregulated H3K27 Acetylation Is Implicated in Fatty Liver Hemorrhagic Syndrome in Chickens
Cited by: 6
Author(s): Yaling Zhu, Qiaoying Zeng, Fang Li, Haoshu Fang, Zhimin Zhou, Tao Jiang, Chao Yin, Qing Wei, Yujie Wang, Jiming Ruan, Jingjing Huang
Software Mentions: 1
Published: almost 4 years ago

10.18632/oncotarget.24432

Brd4 regulates the expression of essential autophagy genes and Keap1 in AML cells
Cited by: 12
Author(s): Min Huang, Li Zhu, Jacqueline S. Garcia, Michael X. Li, Andrew J. Gentles, Beverly S. Mitchell
Software Mentions: 1
Published: almost 7 years ago

10.3389/fgene.2020.00545

LITHOPHONE: Improving lncRNA Methylation Site Prediction Using an Ensemble Predictor
Cited by: 16
Author(s): Lian Liu, Xiujuan Lei, Zengqiang Fang, Yujiao Tang, Jia Meng, Zhen Wei
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2019.00928

Microbiota Inhibit Epithelial Pathogen Adherence by Epigenetically Regulating C-Type Lectin Expression
Cited by: 17
Author(s): Vivienne Woo, Emily M. Eshleman, Taylor Rice, Jordan Whitt, Bruce A. Vallance, Theresa Alenghat
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2020.00841

Opposing Roles for the Related ETS-Family Transcription Factors Spi-B and Spi-C in Regulating B Cell Differentiation and Function
Cited by: 13
Author(s): Anne-Sophie Laramée, Hannah L. Raczkowski, Peng Shao, Cesar Vicente Ferreira Batista, Devanshi Shukla, Li Xu, S.M. Mansour Haeryfar, Yodit Tesfagiorgis, Steven M. Kerfoot, Rodney P. DeKoter
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2020.01292

Globular C1q Receptor (gC1qR/p32/HABP1) Suppresses the Tumor-Inhibiting Role of C1q and Promotes Tumor Proliferation in 1q21-Amplified Multiple Myeloma
Cited by: 7
Author(s): Jiadai Xu, Yang Sun, Junkang Jiang, Zu-De Xu, Jing Li, Tianhong Xu, Peng Liu
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2018.00042

Id Proteins Suppress E2A-Driven Invariant Natural Killer T Cell Development prior to TCR Selection
Cited by: 12
Author(s): Sumedha Roy, Amanda J. Moore, Cassandra Love, Anupama Reddy, Deepthi Rajagopalan, Sandeep S. Davé, Leping Li, Cornelis Murre, Yuan Zhuang
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.24918

LSCC SNP variant regulates SOX2 modulation of VDAC3
Cited by: 2
Author(s): Jacqueline Chyr, Dongmin Guo, Xiaobo Zhou
Software Mentions: 1
Published: over 6 years ago

10.3389/fmolb.2021.624061

Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
Cited by: 7
Author(s): Óscar Huertas-Rosales, Manuel Romero, Kok‐Gan Chan, Kar‐Wai Hong, Miguel Cámara, Stephan Heeb, Laura Barrientos‐Moreno, María Antonia Molina‐Henares, María L. Travieso, Marı́a Isabel Ramos-González, Manuel Espinosa‐Urgel
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmolb.2021.707295

CDK13-Mediated Cell Cycle Disorder Promotes Tumorigenesis of High HMGA2 Expression Gastric Cancer
Cited by: 7
Author(s): Zhanwen Wu, Min Wang, Feng Li, Rui Wang, Jianchao Jia, Zongqi Feng, Xue Huo, Jie Yang, Jing Wen, Rina Sa, Wenbin Gao, Lan Yu
Software Mentions: 1
Published: about 3 years ago

10.3389/fnmol.2019.00214

Genome-Wide Alteration of 5-Hydroxymethylcytosine in Hypoxic-Ischemic Neonatal Rat Model of Cerebral Palsy
Cited by: 7
Author(s): Yunpeng Zhang, Yaodong Zhang, Danmei Chen, Cuiting Wang, Long Chen, Chao Gao, Wei Fan, Jimin Shi, Jihong Zhang, Bing Li
Software Mentions: 1
Published: about 5 years ago

10.3389/fnmol.2018.00285

Nuclear Respiratory Factor 1 (NRF-1) Controls the Activity Dependent Transcription of the GABA-A Receptor Beta 1 Subunit Gene in Neurons
Cited by: 27
Author(s): Zhuting Li, Meaghan Cogswell, Kathryn Hixson, Amy R. Brooks‐Kayal, Shelley J. Russek
Software Mentions: 1
Published: over 6 years ago

10.3389/fnins.2019.00829

The Chromatin Environment Around Interneuron Genes in Oligodendrocyte Precursor Cells and Their Potential for Interneuron Reprograming
Cited by: 11
Author(s): Linda L. Boshans, Daniel C. Factor, Vijender Singh, Jia Liu, Chuntao Zhao, Ion Măndoiu, Qing Lü, Patrizia Casaccia, Paul J. Tesar, Akiko Nishiyama
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-11-377

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
Cited by: 0
Author(s): David B. Burdick, Christopher C. Cavnor, Jeremy Handcock, Sarah Killcoyne, Jake Lin, Bruz Marzolf, Stephen A. Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, John P. Boyle
Software Mentions: 1
Published: over 14 years ago

10.1093/bioinformatics/btt774

PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
Cited by: 27
Author(s): Michael McCarthy, Christopher A. O’Callaghan
Software Mentions: 1
Published: almost 11 years ago

10.7554/eLife.09540

Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes
Cited by: 40
Author(s): Masahiro Oka, Sonoko Mura, Kohji Yamada, Percival Sangel, Saki Hirata, Kazuhira Maehara, Koichi Kawakami, Taro Tachibana, Yasuyuki Ohkawa, Hiroshi Kimurâ, Yoshihiro Yoneda
Software Mentions: 1
Published: almost 9 years ago

10.1093/bioinformatics/btaa920

Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes
Cited by: 6
Author(s): Nan Hao, Huawei Xin, Xiaowei Shi, Jie Xiao, Zhang HaiJuan, Shuntang Guo, Zhen Wang, Chunxiang Hao
Software Mentions: 1
Published: about 4 years ago

10.3389/fphys.2014.00167

Genome-wide (over)view on the actions of vitamin D
Cited by: 109
Author(s): Carsten Carlberg
Software Mentions: 1
Published: over 10 years ago

10.3389/fpls.2019.01031

Dynamic Changes in Genome-Wide Histone3 Lysine27 Trimethylation and Gene Expression of Soybean Roots in Response to Salt Stress
Cited by: 23
Author(s): Lina Sun, Guangshu Song, Weijun Guo, Weixuan Wang, Huabin Zhao, Tingting Gao, Qingxue Lv, Xue Yang, Fan Xu, Yingshan Dong, Li Pu
Software Mentions: 1
Published: about 5 years ago

10.3389/fpls.2021.629069

GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18
Cited by: 2
Author(s): Xue Yang, Yuntong Zhang, Jinming Shan, Jingzhe Sun, Dongmei Li, Xiaoming Zhang, Wenbin Li, Lin Zhao
Software Mentions: 1
Published: over 3 years ago

10.3389/fsoc.2021.601058

Cultivating Health in Martial Arts and Combat Sports Pedagogies: A Theoretical Framework on the Care of the Self
Cited by: 7
Author(s): Lorenzo Pedrini, George Jennings
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.115.017418

Chromatin Mediation of a Transcriptional Memory Effect in Yeast
Cited by: 11
Author(s): Emily Paul, Itay Tirosh, William Lai, Michael Buck, Michael J. Palumbo, Randall H. Morse
Software Mentions: 1
Published: over 9 years ago

10.1534/g3.115.024331

Combinatorial Cis-regulation in Saccharomyces Species
Cited by: 10
Author(s): Aaron Spivak, Gary D. Stormo
Software Mentions: 1
Published: over 8 years ago

10.1534/g3.117.300296

Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins
Cited by: 24
Author(s): Marjan Barazandeh, Samuel A. Lambert, Mihai Albu, Timothy R. Hughes
Software Mentions: 1
Published: almost 7 years ago

10.1186/1756-0500-7-312

A method for generating highly multiplexed ChIP-seq libraries
Cited by: 30
Author(s): Ethan Ford, Chrysa Nikopoulou, Antonis Kokkalis, Dimitris Thanos
Software Mentions: 1
Published: over 10 years ago

10.1534/g3.120.401131

Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A inSaccharomyces cerevisiae
Cited by: 10
Author(s): Jessica R. Eisenstatt, Lars Boeckmann, Wei-Chun Au, Valérie Garcia, Levi Bursch, Josefina Ocampo, Michael Costanzo, Michael Weinreich, Robert A. Sclafani, Anastasia Baryshnikova, Chad L. Myers, Charles Boone, David Clark, Richard E. Baker, Munira A. Basrai
Software Mentions: 1
Published: over 4 years ago

10.3390/genes9040188

UBE2C Is a Transcriptional Target of the Cell Cycle Regulator FOXM1
Cited by: 31
Author(s): Pedro Nicolau-Neto, Antônio Palumbo, Marco De Martino, Francesco Esposito, Tatiana de Almeida Simão, Alfredo Fusco, Luiz Eurico Nasciutti, Nathalia Meireles Da Costa, Luís Felipe Ribeiro Pinto
Software Mentions: 1
Published: over 6 years ago

10.3390/genes10110865

The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook
Cited by: 19
Author(s): Enrique Hernández‐Lemus, Helena Reyes-Gopar, Jesús Espinal-Enríquez, Soledad Ochoa
Software Mentions: 1
Published: about 5 years ago

10.3390/genes11090995

Beyond Trees: Regulons and Regulatory Motif Characterization
Cited by: 2
Author(s): Xuhua Xia
Software Mentions: 1
Published: about 4 years ago

10.3390/genes11101139

Unique and Specific m6A RNA Methylation in Mouse Embryonic and Postnatal Cerebral Cortices
Cited by: 4
Author(s): Longbin Zhang, Kunzhao Du, Jing Wang, Yanzhen Nie, Trevor Lee, Tao Sun
Software Mentions: 1
Published: about 4 years ago

10.18632/genesandcancer.182

Common ELF1 deletion in prostate cancer bolsters oncogenic ETS function, inhibits senescence and promotes docetaxel resistance
Cited by: 15
Author(s): Justin A. Budka, Mary W. Ferris, Matthew J. Capone, Peter C. Hollenhorst
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-019-1677-2

GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max
Cited by: 9
Author(s): Li Song, Wei Chen, Biao Wang, Qiuming Yao, Babu Valliyodan, Ming-Yi Bai, Mingzhe Zhao, Heng Ye, Zhiyong Wang, Henry T. Nguyen
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2377-11-32

Individualized, home-based interactive training of cerebral palsy children delivered through the Internet
Cited by: 70
Author(s): Peder E. Bilde, Mette Kliim-Due, B Rasmussen, Line Z Petersen, Tue Hvass Petersen, Jens Bo Nielsen
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2010-11-12-r126

ArchAlign: Coordinate-free chromatin alignment reveals novel architectures
Cited by: 19
Author(s): William Lai, Michael Buck
Software Mentions: 1
Published: almost 15 years ago

10.1186/gb-2011-12-7-r67

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Cited by: 162
Author(s): Naim U. Rashid, Paul G. Giresi, Joseph G. Ibrahim, Wei Sun, Jason D. Lieb
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12883-015-0334-0

Twenty weeks of home-based interactive training of children with cerebral palsy improves functional abilities
Cited by: 27
Author(s): Jakob Lorentzen, Line Greve, Mette Kliim-Due, B Rasmussen, Peder E. Bilde, Jens Bo Nielsen
Software Mentions: 1
Published: over 9 years ago

10.1186/gb-2012-13-1-r7

Dissecting the regulatory architecture of gene expression QTLs
Cited by: 193
Author(s): Daniel J. Gaffney, Jean‐Baptiste Veyrieras, Jacob F. Degner, Roger Piqué-Regi, Athma A. Pai, Gregory E. Crawford, Matthew Stephens, Yoav Gilad, Jonathan K. Pritchard
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12860-020-00257-2

Molecular effects of dADD1 misexpression in chromatin organization and transcription
Cited by: 3
Author(s): Silvia Meyer-Nava, Amada Torres, Mario Zurita, Viviana Valadéz-Graham
Software Mentions: 1
Published: over 4 years ago

10.1186/gb-2013-14-6-r57

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids
Cited by: 94
Author(s): Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2013-14-9-r105

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
Cited by: 275
Author(s): Jessica Nordlund, Christofer Bäcklin, Per Wahlberg, Stephan Busche, Eva Berglund, Maija‐Leena Eloranta, Trond Flægstad, Erik Forestier, Britt‐Marie Frost, Arja Harila‐Saari, Mats Heyman, Ólafur G. Jónsson, Rolf Larsson, Josefine Palle, Lars Rönnblom, Kjeld Schmiegelow, Daniel Sinnett, Stefan Söderhäll, Tomi Pastinen, Mats Gustafsson, Gudmar Lönnerholm, Ann‐Christine Syvänen
Software Mentions: 1
Published: almost 12 years ago

10.1186/gb-2013-14-10-r108

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development
Cited by: 182
Author(s): Yi-An Ko, Davoud Mohtat, Masako Suzuki, Ae Seo Deok Park, María C. Izquierdo, Sang Youb Han, Hyun Mi Kang, Han Si, Thomas H. Hostetter, James Pullman, Melissa Fazzari, Amit Verma, Deyou Zheng, John M. Greally, Katalin Suszták
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2199-15-3

Spdef deletion rescues the crypt cell proliferation defect in conditional Gata6 null mouse small intestine
Cited by: 7
Author(s): Boaz E. Aronson, Kelly A. Stapleton, Laurens A. T. M. Vissers, Eva Stokhuijzen, Hanneke Bruijnzeel, Stephen D. Krasinski
Software Mentions: 1
Published: almost 11 years ago

10.1186/gb-2013-14-12-r144

Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition
Cited by: 76
Author(s): Gabriel G. Malouf, Joseph H. Taube, Yue Lu, Tapasree Roysarkar, Shoghag Panjarian, Marcos R.H. Estécio, Jaroslav Jelı́nek, Jumpei Yamazaki, Noël J.-M. Raynal, Hai Long, Tomomitsu Tahara, Agata A. Tinnirello, Priyanka P. Ramachandran, Xiu Ying Zhang, Shoudan Liang, Sendurai A. Mani, Jean–Pierre J. Issa
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12920-019-0520-9

Integrated high-throughput analysis identifies super enhancers associated with chemoresistance in SCLC
Cited by: 13
Author(s): Jingjing Bao, Man Li, Shu‐Chuan Liang, Yunchu Yang, Jing Wu, Qianli Zou, Shun Fang, Size Chen, Linlang Guo
Software Mentions: 1
Published: over 5 years ago

10.1186/gb-2013-14-8-r91

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells
Cited by: 147
Author(s): Francesco Neri, Danny Incarnato, Anna Krepelova, Stefania Rapelli, Andrea Pagnani, Riccardo Zecchina, Caterina Parlato, Salvatore Oliviero
Software Mentions: 1
Published: almost 12 years ago

10.1186/gb-2013-14-7-r81

Experimental characterization of the human non-sequence-specific nucleic acid interactome
Cited by: 5
Author(s): Gerhard Dürnberger, Tilmann Bürckstümmer, Kilian Huber, Roberto Giambruno, Tobias Doerks, Evren Karayel, Thomas R Burkard, Ines Kaupe, André C. Müller, Andreas Schönegger, Gerhard F. Ecker, Hans Lohninger, Peer Bork, Keiryn L. Bennett, Giulio Superti‐Furga, Jacques Colinge
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-015-1311-0

Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor
Cited by: 18
Author(s): Jinu Kim, Yu‐Jin Jeong, Ji-Sun Yoo, Jung‐Hye Roe, Byung-Kwan Cho, Byung‐Gee Kim
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-834

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution
Cited by: 16
Author(s): Marco Antonio Mendoza-Parra, Małgorzata Nowicka, Wouter Van Gool, Hinrich Gronemeyer
Software Mentions: 1
Published: almost 12 years ago

Projects: pypi: MACS

Papers Mentioning MACS 1,233