Ecosyste.ms: Papers

10.1186/s13072-015-0027-3

Tissue-specific expression of histone H3 variants diversified after species separation
Cited by: 46
Author(s): Kazuhira Maehara, Akihito Harada, Yuko Sato, Masaki Matsumoto, Keiichi I. Nakayama, Hiroshi Kimurâ, Yasuyuki Ohkawa
Software Mentions: 2
Published: about 9 years ago

10.1186/1756-8935-8-7

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer
Cited by: 33
Author(s): Joseph D. Fleming, Paul G. Giresi, Marianne Lindahl-Allen, Elizabeth A. Krall, Jason D. Lieb, Kevin Struhl
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pcbi.1003342

Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
Cited by: 57
Author(s): Weronika Sikora-Wohlfeld, Marit Ackermann, Eleni G. Christodoulou, Kalaimathy Singaravelu, Andreas Beyer
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0054359

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data
Cited by: 37
Author(s): Анна Герасимова, Lukas Chávez, Bin Li, Grégory Seumois, Jason A. Greenbaum, Anjana Rao, Pandurangan Vijayanand, Bjoern Peters
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13072-017-0115-7

SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation
Cited by: 44
Author(s): Benjamin L. Kidder, Gangqing Hu, Kairong Cui, Keji Zhao
Software Mentions: 2
Published: over 7 years ago

10.26508/lsa.201800117

CARM1 methylates MED12 to regulate its RNA-binding ability
Cited by: 39
Author(s): Donghang Cheng, Vidyasiri Vemulapalli, Yue Lu, Jianjun Shen, Sakae Aoyagi, Christopher J. Fry, Yanzhong Yang, Charles E. Foulds, Fabio Stossi, Lindsey S. Treviño, Michael A. Mancini, Bert W. O’Malley, Cheryl L. Walker, Thomas G. Boyer, Mark T. Bedford
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0045486

WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets
Cited by: 10
Author(s): Apratim Mitra, Jiuzhou Song
Software Mentions: 2
Published: about 12 years ago

10.7554/eLife.50654

Alterations in the amplitude and burst rate of beta oscillations impair reward-dependent motor learning in anxiety
Cited by: 25
Author(s): Sebastian Sporn, Thomas Hein, María Herrojo Ruiz
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0097849

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) Analysis Uncovers Broad Changes in Chromatin Structure Resulting from Hexavalent Chromium Exposure
Cited by: 9
Author(s): Jerald L. Ovesen, Yunxia Fan, Xiang Zhang, Jing Chen, Mario Medvedovic, Ying Xia, Alvaro Puga
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0221270

Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data
Cited by: 3
Author(s): Nazifa Ahmed Moumi, Badhan Das, Zarin Tasnim Promi, Nishat Anjum Bristy, Md. Shamsuzzoha Bayzid
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pbio.1002449

Structural and Molecular Mechanism of CdpR Involved in Quorum-Sensing and Bacterial Virulence in Pseudomonas aeruginosa
Cited by: 41
Author(s): Jingru Zhao, Xiang Yu, Miao Zhu, Huaping Kang, Jinbiao Ma, Min Wu, Jianhua Gan, Xin Deng, Haihua Liang
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-018-1524-z

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation
Cited by: 15
Author(s): Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki, Kenta Nakai
Software Mentions: 2
Published: about 6 years ago

10.1186/s13059-018-1533-y

Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence
Cited by: 70
Author(s): Yue Lu, Qiutao Xu, Yuan Liu, Yue Yu, Zhongyi Cheng, Yu Zhao, Dao‐Xiu Zhou
Software Mentions: 2
Published: about 6 years ago

10.1080/21505594.2021.1936768

A novel transcription factor UvCGBP1 regulates development and virulence of rice false smut fungus <i>Ustilaginoidea virens</i>
Cited by: 11
Author(s): Xiaoyang Chen, Pingping Li, Hao Líu, Xiaolin Chen, Junbin Huang, Chaoxi Luo, Guotian Li, Tom Hsiang, David B. Collinge, Lu Zheng
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-019-1698-z

VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer
Cited by: 22
Author(s): Andrew N Holding, Federico M. Giorgi, Amanda Donnelly, Amy E Cullen, Sankari Nagarajan, Luke A. Selth, Florian Markowetz
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0061654

Genetic, Functional and Molecular Features of Glucocorticoid Receptor Binding
Cited by: 22
Author(s): Francesca Luca, Joseph C. Maranville, Allison L. Richards, David B. Witonsky, Matthew Stephens, Anna Di Rienzo
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0141066

An Orthologous Epigenetic Gene Expression Signature Derived from Differentiating Embryonic Stem Cells Identifies Regulators of Cardiogenesis
Cited by: 5
Author(s): Brian W. Busser, Yongshun Lin, Yanqin Yang, Jun Zhu, Guokai Chen, Alan M. Michelson
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-019-1746-8

The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements
Cited by: 80
Author(s): Zijuan Li, Meiyue Wang, Kande Lin, Yilin Xie, Jingyu Guo, Luhuan Ye, Yili Zhuang, Wan Teng, Xiaojuan Ran, Yiping Tong, Yongbiao Xue, Wenli Zhang, Yijing Zhang
Software Mentions: 2
Published: over 5 years ago

10.1016/j.celrep.2018.07.009

Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer
Cited by: 68
Author(s): Jonathan T. Lei, Jieya Shao, Jin Zhang, Michael D. Iglesia, Doug W. Chan, Jin Cao, Meenakshi Anurag, Purba Singh, Xiaping He, Yoshimasa Kosaka, Ryoichi Matsunuma, Robert J. Crowder, Jeremy Hoog, Chanpheng Phommaly, Rodrigo Gonçalves, Susana Ramalho, Raquel Mary Rodrigues Peres, Nindo Punturi, Cecilia Schmidt, Alex Bartram, Eric Jou, Vaishnavi Devarakonda, Kimberly Holloway, Weiyi Lai, Oliver A. Hampton, Anna Rogers, Ethan Tobias, Poojan A. Parikh, Sherri R. Davies, Shunqiang Li, X. Cynthia, Vera J. Suman, Kelly K. Hunt, Mark A. Watson, Katherine A. Hoadley, E. Aubrey Thompson, Xi Chen, Shyam M. Kavuri, Chad J. Creighton, Christopher A. Maher, Charles M. Perou, Svasti Haricharan, Matthew J. Ellis
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.203230

Integrated analysis of m6A mRNA methylation in rats with monocrotaline-induced pulmonary arterial hypertension
Cited by: 15
Author(s): Yiwei Zeng, Ting Huang, Wanyun Zuo, Dan Wang, Yonghui Xie, Xun Wang, Xiao Zhou, Zhi Chen, Qiming Liu, Na Liu, Yunbin Xiao
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1003494

Universal Count Correction for High-Throughput Sequencing
Cited by: 17
Author(s): Tatsunori Hashimoto, Matthew D. Edwards, David K. Gifford
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.00762

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics
Cited by: 386
Author(s): Nicole A Rapicavoli, Kun Qu, Jiajing Zhang, Megan E. Mikhail, Rémi-Martin Laberge, Howard Y. Chang
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.03737

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition
Cited by: 167
Author(s): Xiaoyong Li, Melissa M. Harrison, Jacqueline E. Villalta, Tommy Kaplan, Michael B. Eisen
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0125156

Identifying TF-MiRNA Regulatory Relationships Using Multiple Features
Cited by: 3
Author(s): Mingyu Shao, Yanni Sun, Shuigeng Zhou
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-16-S5-S4

Direct ChIP-Seq significance analysis improves target prediction
Cited by: 8
Author(s): Mukesh Bansal, Geetu Mendiratta, Santosh Anand, Ritu Kushwaha, Hyunjae R. Kim, Manjunath Kustagi, Archana Iyer, R. S. K. Chaganti, Andrea Califano, Pavel Sumazin
Software Mentions: 2
Published: over 9 years ago

10.1186/s12915-014-0101-5

The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage
Cited by: 60
Author(s): Nasim Sabouri, John A. Capra, Virginia A. Zakian
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0026054

Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations
Cited by: 11
Author(s): Melissa J. Fullwood, Joanne Lee, Lei Lin, Guoliang Li, Mikael Huss, Patrick Ng, Wing-Kin Sung, Shirish Shenolikar
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0019470

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
Cited by: 110
Author(s): Anja Nitzsche, Maciej Paszkowski‐Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, Ingrid de Vries, Li Ding, Norbert Huebner, Matthias Mann, Hendrik G. Stunnenberg, Frank Buchholz
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-12-15

Shape-based peak identification for ChIP-Seq
Cited by: 45
Author(s): Valerie Hower, Steven N. Evans, Lior Pachter
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0039573

ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries
Cited by: 32
Author(s): Nishanth Ulhas Nair, Avinash Sahu, Philipp Bücher, Bernard M. E. Moret
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0040399

Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes
Cited by: 56
Author(s): Falak Sher, Erik Boddeke, Marta Olah, Sjef Copray
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-018-4533-0

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes
Cited by: 56
Author(s): Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y.R. Dent
Software Mentions: 2
Published: almost 7 years ago

10.1111/acel.13315

ATF3 drives senescence by reconstructing accessible chromatin profiles
Cited by: 29
Author(s): Chao Zhang, Xuebin Zhang, Li Huang, Yiting Guan, Xiaoke Huang, Xiao-Li Tian, Lijun Zhang, Wei Tao
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0138030

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding
Cited by: 37
Author(s): Anil Raj, Heejung Shim, Yoav Gilad, Jonathan K. Pritchard, Matthew Stephens
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-14-4

Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules
Cited by: 61
Author(s): Keunsoo Kang, Gertraud W. Robinson, Lothar Hennighausen
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13072-016-0090-4

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia
Cited by: 20
Author(s): Michiel E. Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, V.E.H. Dahlmans, Lars Eijssen, Timothy A. Beck, Bradly G. Wouters, Jan Willem Voncken, Chris T. Evelo
Software Mentions: 2
Published: about 8 years ago

10.1186/bcr3664

VAV3 mediates resistance to breast cancer endocrine therapy
Cited by: 27
Author(s): Helena Aguilar, Ander Urruticoechea, Pasi Halonen, Kazuma Kiyotani, Taisei Mushiroda, Xavier Barril, Jordi Serra-Musach, Abul B.M.M.K. Islam, Livia Caizzi, Luciano Di Croce, Ekaterina Nevedomskaya, Wilbert Zwart, Josefine Bostner, Elin Karlsson, Gizeh Pérez Tenorio, Tommy Fornander, Dennis Sgroi, Rafael Garcı́a-Mata, Maurice P.H.M. Jansen, Nadia García, Núria Bonifaci, Fina Climent, María Teresa Soler, Alejo Rodríguez‐Vida, Miguel Ángel Cobos Gil, Joan Brunet, Griselda Martrat, Laia Gómez-Baldó, Ana I. Extremera, Agnés Figueras, J. Balart, Robert Clarke, Kerry L. Burnstein, Kathryn E. Carlson, John A. Katzenellenbogen, Miguel Vizoso, Manel Esteller, Alberto Villanueva, Ana B. Rodríguez-Peña, Xosé R. Bustelo, Yusuke Nakamura, Hitoshi Zembutsu, Olle Stål, Roderick L. Beijersbergen, Miguel Ángel Pujana
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0179141

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq
Cited by: 10
Author(s): Dou Liu, Xiaoyun Jia, Hengling Wei, Shuli Fan, Hantao Wang, Yanliang Guo, Shan Duan, Chaoyou Pang, Shuang Yu
Software Mentions: 2
Published: over 7 years ago

10.1098/rsob.170166

Region-specific RNA m ⁶ A methylation represents a new layer of control in the gene regulatory network in the mouse brain
Cited by: 117
Author(s): Mengqi Chang, Hongyi Lv, Weilong Zhang, Chunhui Ma, Xue He, Shuaiyang Zhao, Zhi Wei Zhang, Yi‐Xin Zeng, Shuhui Song, Yamei Niu, Wei Tong
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2407-14-276

Differential regulation of MMPs by E2F1, Sp1 and NF-kappa B controls the small cell lung cancer invasive phenotype
Cited by: 42
Author(s): Zunling Li, Yanxia Guo, Hanming Jiang, Tingguo Zhang, Can Jin, Charles Y.F. Young, Huipin Yuan
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1002368

PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer
Cited by: 171
Author(s): Luca Magnani, Elizabeth B. Ballantyne, Xiaoyang Zhang, Mathieu Lupien
Software Mentions: 1
Published: about 13 years ago

10.1038/s41388-018-0468-9

Role of SUMOylation in differential ERα transcriptional repression by tamoxifen and fulvestrant in breast cancer cells
Cited by: 26
Author(s): Tatiana Traboulsi, Mohamed El Ezzy, Vanessa Dumeaux, Éric Audemard, Sylvie Mader
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1003433

Coordinated Cell Type–Specific Epigenetic Remodeling in Prefrontal Cortex Begins before Birth and Continues into Early Adulthood
Cited by: 64
Author(s): Hennady P. Shulha, Iris Cheung, Yin Guo, Schahram Akbarian, Zhiping Weng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1002649

Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis
Cited by: 103
Author(s): Huasheng Hong, Douglas S. Kim, Bernward Klocke, Kory R. Johnson, Kairong Cui, Noriko Gotoh, Chongzhi Zang, Janina Gregorski, Linn Gieser, Weiqun Peng, Yang C. Fann, Martin Seifert, Keji Zhao, Anand Swaroop
Software Mentions: 1
Published: over 12 years ago

10.1038/s41388-019-0723-8

Cyclin D1 integrates G9a-mediated histone methylation
Cited by: 17
Author(s): Zhiping Li, Xuanmao Jiao, Gabriele Di Sante, Adam Ertel, Mathew C. Casimiro, Min Wang, Sanjay Katiyar, Xiaoming Ju, D. V. Klopfenstein, Aydın Tözeren, William Dampier, Iouri Chepelev, Albert Jeltsch, Richard G. Pestell
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1008129

Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1
Cited by: 23
Author(s): Masato Sorida, Takahiro Hirauchi, Hiroaki Ishizaki, Wataru Kaito, Atsushi Shimada, Chie Mori, Yuji Chikashige, Yasushi Hiraoka, Yutaka Suzuki, Yasuyuki Ohkawa, Hiroaki Kato, Shinya Takahata, Yota Murakami
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1005337

Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins
Cited by: 90
Author(s): Nora Marín-de la Rosa, Anne Pfeiffer, Kristine Hill, Antonella Locascio, Rishikesh P. Bhalerao, Pál Miskolczi, Anne Lentz Grønlund, Aakriti Wanchoo-Kohli, Stephen G. Thomas, Malcolm J. Bennett, Jan U. Lohmann, Miguel Á. Blázquez, David Alabadı́
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.10647

Lysosome-associated membrane glycoprotein 1 predicts fratricide amongst T cell receptor transgenic CD8+ T cells directed against tumor-associated antigens
Cited by: 7
Author(s): A. Kirschner, Melanie Thiede, Franziska Blaeschke, Günther Richter, Julia S. Gerke, Michaela C. Baldauf, Thomas G.P. Grünewald, Dirk H. Busch, Stefan Burdach, Uwe Thiel
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005512

Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots
Cited by: 46
Author(s): Christopher L. Baker, Pavlina Petkova, Michael Walker, Petr Flachs, Ondřej Mihola, Zdeněk Trachtulec, Petko M. Petkov, Kenneth Paigen
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1002154

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells
Cited by: 255
Author(s): Keith E. Szulwach, Xuekun Li, Yujing Li, Chun-Xiao Song, Ji Yun Han, Sangsung Kim, Sandeep Namburi, Karen Hermetz, Julie J Kim, M. Katharine Rudd, Young-sup Yoon, Bing Ren, Chuanchuan He, Peng-Peng Jin
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1002933

H4K20me1 Contributes to Downregulation of X-Linked Genes for C. elegans Dosage Compensation
Cited by: 69
Author(s): Anne Vielle, Jackie Lang, Dong Yan, Sevinç Ercan, Chitra V. Kotwaliwale, Andreas Rechtsteiner, Alex Appert, Q. Brent Chen, Andréa C. Dosé, Thea A. Egelhofer, Hiroshi Kimurâ, Przemyslaw Stempor, Abby F. Dernburg, Jason D. Lieb, Susan Strome, Julie Ahringer
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1006966

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells
Cited by: 30
Author(s): Krzysztof Poterlowicz, Joanne L. Yarker, Igor Malashchuk, Brian R. Lajoie, Andrei N. Mardaryev, Michal R. Gdula, Andrey A. Sharov, Terumi Kohwi‐Shigematsu, Vladimir A. Botchkarev, Michael Y. Fessing
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1004944

The Arabidopsis SWI2/SNF2 Chromatin Remodeler BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene SVP
Cited by: 90
Author(s): Chenlong Li, Chen Chen, Lei Gao, Shi-Nine Yang, Vi Nguyen, Xuejiang Shi, Katherine A. Siminovitch, Susanne E. Kohalmi, Shangzhi Huang, Keqiang Wu, Xuemei Chen, Yuhai Cui
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1002610

Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo
Cited by: 56
Author(s): Michael J. Guertin, André L. Martins, Adam Siepel, John T. Lis
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1005102

Zinc Finger Independent Genome-Wide Binding of Sp2 Potentiates Recruitment of Histone-Fold Protein Nf-y Distinguishing It from Sp1 and Sp3
Cited by: 49
Author(s): Sara Völkel, Bastian Stielow, Florian Finkernagel, Thorsten Stiewe, Andrea Nist, Guntram Suske
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1001065

Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus
Cited by: 167
Author(s): Evelyn N. Kouwenhoven, Simon J. van Heeringen, Juan J. Tena, Martin Oti, Bas E. Dutilh, M. Eva Alonso, Elisa de la Calle‐Mustienes, Leonie Smeenk, Tuula Rinne, Lilian Parsaulian, Emine Bolat, Rasa Jurgelenaite, Martijn A. Huynen, Alexander Hoischen, Joris A. Veltman, Han G. Brunner, Tony Roscioli, Emily C. Oates, Meredith Wilson, Miguel Manzanares, José Luis Gómez‐Skarmeta, Hendrik G. Stunnenberg, Marion Lohrum, Hans van Bokhoven, Huiqing Zhou
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1006200

Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements
Cited by: 40
Author(s): Sandip De, Apratim Mitra, Yuzhong Cheng, Karl Pfeifer, Judith A. Kassis
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1007908

Estimating recent migration and population-size surfaces
Cited by: 63
Author(s): Hussein Al-Asadi, Desislava Petkova, Matthew Stephens, John Novembre
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1007193

MGA, L3MBTL2 and E2F6 determine genomic binding of the non-canonical Polycomb repressive complex PRC1.6
Cited by: 90
Author(s): Bastian Stielow, Florian Finkernagel, Thorsten Stiewe, Andrea Nist, Guntram Suske
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.06535

Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism
Cited by: 100
Author(s): Huasong Lu, Yuahua Xue, Guoying Karen Yu, Carolina Arias, Julie Lin, Susan Fong, M Faure, Ben Weisburd, Xiaodong Ji, Alexandre Mercier, James Sutton, Kunxin Luo, Zhenhai Gao, Qiang Zhou
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1005845

MEF2C and EBF1 Co-regulate B Cell-Specific Transcription
Cited by: 29
Author(s): Nikki R. Kong, Matthew D. Davis, Li Chai, Astar Winoto, Robert Tjian
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1004404

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells
Cited by: 46
Author(s): Xinli Hu, Hyun Kim, Towfique Raj, Patrick J. Brennan, Gosia Trynka, Nikola C. Teslovich, Kamil Slowikowski, Wei Min Chen, Suna Önengüt, Clare Baecher-Allan, Philip L. De Jager, Stephen S. Rich, Barbara Elaine Stranger, Michael B. Brenner, Soumya Raychaudhuri
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1007657

CXXC1 is not essential for normal DNA double-strand break formation and meiotic recombination in mouse
Cited by: 21
Author(s): Hui Tian, Timothy Billings, Petko M. Petkov
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.00726

DNA methylation presents distinct binding sites for human transcription factors
Cited by: 291
Author(s): Shaohui Hu, Jun Wan, Yijing Su, Qifeng Song, Yue Zeng, Ha Nam Nguyen, Jaehoon Shin, Eric Cox, Hee Sool Rho, Crystal Woodard, Shuli Xia, Shuang Liu, Huibin Lyu, Guo Li Ming, Herschel Wade, Hongjun Song, Jiang Qian, Heng Zhu
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0142924

Characterization of FGF23-Dependent Egr-1 Cistrome in the Mouse Renal Proximal Tubule
Cited by: 23
Author(s): Anthony A. Portale, Martin Y. H. Zhang, Véronique David, Aline Martin, Yan Jiao, Weikuan Gu, Farzana Perwad
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0011425

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites
Cited by: 47
Author(s): Christoph D. Schmid, Philipp Bücher
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0074745

An Innovative Cascade System for Simultaneous Separation of Multiple Cell Types
Cited by: 17
Author(s): Arkadiusz Pierzchalski, Anja Mittag, József Bocsi, Attila Tárnok
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0180568

Biophysical induction of cell release for minimally manipulative cell enrichment strategies
Cited by: 2
Author(s): P. Joly, Thomas E. Schaus, Andrea Saß, Anke Dienelt, Alexander S. Cheung, Georg N. Duda, David J. Mooney
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0127285

PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond
Cited by: 10
Author(s): Paul W. Bible, Yuka Kanno, Lai Wei, Stephen R. Brooks, John J. O’Shea, María I. Morasso, Rasiah Loganantharaj, Hongwei Sun
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.10520

Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer
Cited by: 38
Author(s): Hong Jin, Su-Young Jung, Auditi DebRoy, Ramana V. Davuluri
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1007270

Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space
Cited by: 39
Author(s): Amanda O. Veri, Zhengqiang Miao, Rebecca Shapiro, Faïza Tebbji, Teresa R. O’Meara, Sang Hu Kim, Juan M. Colazo, Kaeling Tan, Valmik K. Vyas, Malcolm Whiteway, Nicole Robbins, Koon Ho Wong, Leah E. Cowen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0047366

Elongation Factor 1 alpha1 and Genes Associated with Usher Syndromes Are Downstream Targets of GBX2
Cited by: 14
Author(s): David A. Roeseler, Shrikesh Sachdev, Desirè M. Buckley, Trupti Joshi, Doris K. Wu, Dong Xu, Mark Hannink, Samuel T. Waters
Software Mentions: 1
Published: about 12 years ago

10.7554/eLife.06857

Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells
Cited by: 141
Author(s): Patrick Laurette, Thomas Strub, Dana Koludrović, Céline Keime, Stéphanie Le Gras, Hannah Seberg, Eric Van Otterloo, Hana Imrichová, Robert Siddaway, Stein Aerts, Robert A. Cornell, Gabrielle Mengus, Irwin Davidson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1005523

An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster
Cited by: 16
Author(s): Andrea B. Eberle, Antonio Jordán-Pla, Antoni Gàñez-Zapater, Viktoria Hessle, Gilad Silberberg, Anne von Euler, Rebecca A. Silverstein, Neus Visa
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0180147

Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs
Cited by: 37
Author(s): Michael Allevato, Eugene Bolotin, Mark H. Grossman, Daniel Mané-Padrós, Frances M. Sladek, Ernest Martinez
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0205983

Ehrlichia chaffeensis TRP47 enters the nucleus via a MYND-binding domain-dependent mechanism and predominantly binds enhancers of host genes associated with signal transduction, cytoskeletal organization, and immune response
Cited by: 14
Author(s): Clayton E. Kibler, Sarah Milligan, Tierra R. Farris, Bing Zhu, Shubhajit Mitra, Jere W. McBride
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0042483

Novel Nuclear Localization and Potential Function of Insulin-Like Growth Factor-1 Receptor/Insulin Receptor Hybrid in Corneal Epithelial Cells
Cited by: 29
Author(s): Yu Chieh Wu, Meifang Zhu, Danielle M. Robertson
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0088933

Myc and Max Genome-Wide Binding Sites Analysis Links the Myc Regulatory Network with the Polycomb and the Core Pluripotency Networks in Mouse Embryonic Stem Cells
Cited by: 28
Author(s): Anna Krepelova, Francesco Neri, Mara Maldotti, Stefania Rapelli, Salvatore Oliviero
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0245863

Primary and secondary supportive partnerships among HIV-positive and HIV-negative middle-aged and older gay men
Cited by: 4
Author(s): Matthew Statz, Deanna Ware, Nicholas S. Perry, David M. Huebner, Christopher Cox, Brown Ae, Steven Meanley, Sabina Haberlen, James E. Egan, Mark Brennan, Linda A. Teplin, Robert Bolan, M. Reuel Friedman, Michael Plankey
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0028272

CATCHprofiles: Clustering and Alignment Tool for ChIP Profiles
Cited by: 11
Author(s): Fiona Nielsen, Kasper Markus, Rune Møllegaard Friborg, Lene M. Favrholdt, Hendrik G. Stunnenberg, Martijn A. Huynen
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0087301

Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis
Cited by: 10
Author(s): Matloob Khushi, Christopher Liddle, Christine L. Clarke, J. Dinny Graham
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12885-020-06762-z

CHD4 mediates proliferation and migration of non-small cell lung cancer via the RhoA/ROCK pathway by regulating PHF5A
Cited by: 24
Author(s): Nuo Xu, Fanglei Liu, Shengdi Wu, Maosong Ye, Heng Ge, Meiling Zhang, Yuanlin Song, Tongyu Lin, Jian Zhou, Chunxue Bai
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1004271

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
Cited by: 69
Author(s): Manu Setty, Christina Leslie
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0035175

Methylcap-Seq Reveals Novel DNA Methylation Markers for the Diagnosis and Recurrence Prediction of Bladder Cancer in a Chinese Population
Cited by: 58
Author(s): Yiwei Zhao, Shicheng Guo, Jinfeng Sun, Zhaohui Huang, Tongyu Zhu, Hongyu Zhang, Jun Gu, Yinghua He, Wei Wang, Kelong Ma, Jina Wang, Jian Yu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0096303

A Comparison of Peak Callers Used for DNase-Seq Data
Cited by: 68
Author(s): Hashem Koohy, Thomas A. Down, Mikhail Spivakov, Tim Hubbard
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0017574

Role of p53 Serine 46 in p53 Target Gene Regulation
Cited by: 151
Author(s): Leonie Smeenk, Simon J. van Heeringen, Max Koeppel, Bianca Gilbert, Eva M. Janssen-Megens, Hendrik G. Stunnenberg, Marion Lohrum
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0251660

Dynamics of SAS-I mediated H4 K16 acetylation during DNA replication in yeast
Cited by: 1
Author(s): Mark Boltengagen, Anke Samel-Pommerencke, David Fechtig, Ann E. Ehrenhofer‐Murray
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0153767

Chemical Inhibition of Histone Deacetylases 1 and 2 Induces Fetal Hemoglobin through Activation of GATA2
Cited by: 29
Author(s): Jeffrey R. Shearstone, Olga Golonzhka, Apurva Chonkar, David Tamang, John H. van Duzer, Simon Jones, Matthew Jarpe
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.12115

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species
Cited by: 62
Author(s): Eric T. Domyan, Zev Kronenberg, Carlos R. Infante, Anna I. Vickrey, Sydney A. Stringham, Rebecca Bruders, Michael W Guernsey, Sungdae Park, Jerry A. Payne, Robert B. Beckstead, Gabrielle Kardon, Douglas B. Menke, Mark Yandell, Michael D. Shapiro
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0023691

Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling
Cited by: 49
Author(s): Bin Tang, Pietro Di Lena, Lana Schaffer, Steven R. Head, Pierre Baldi, Elizabeth A. Thomas
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0019428

Genome-Wide Mapping of DNA Methylation in Chicken
Cited by: 113
Author(s): Qinghe Li, Ning Li, Xiaoxiang Hu, Jinxiu Li, Zhuo Du, Li Chen, Guangliang Yin, Jinjie Duan, Haichao Zhang, Yaofeng Zhao, Jun Wang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1002304

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development
Cited by: 50
Author(s): Jonathan Göke, Myung-Hwan Jung, Sarah Behrens, Lukas Chávez, Sean O’Keeffe, Bernd Timmermann, Hans Lehrach, James Adjaye, Martin Vingron
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0146709

Multi-Objective Ant Colony Optimization Based on the Physarum-Inspired Mathematical Model for Bi-Objective Traveling Salesman Problems
Cited by: 17
Author(s): Zili Zhou, Chao Gao, Yuxiao Lu, Yuxin Liu, Mingxin Liang
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0094735

Generation and Characterization of Induced Pluripotent Stem Cells from Aid-Deficient Mice
Cited by: 18
Author(s): Ren Shimamoto, Naoki Amano, Tomoko Ichisaka, Akira Watanabe, Shinya Yamanaka, Keisuke Okita
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0196223

Mice lacking the transcriptional regulator Bhlhe40 have enhanced neuronal excitability and impaired synaptic plasticity in the hippocampus
Cited by: 16
Author(s): Kelly Hamilton, Yue Wang, Sophia M. Raefsky, Sean T. Berkowitz, Ryan D. Spangler, Caitlin N. Suire, Simonetta Camandola, Robert H. Lipsky, Mark P. Mattson
Software Mentions: 1
Published: over 6 years ago

10.1002/advs.201903185

MACS: Rapid Aqueous Clearing System for 3D Mapping of Intact Organs
Cited by: 46
Author(s): Jingtan Zhu, Tingting Yu, Yusha Li, Jianyi Xu, Yisong Qi, Yingtao Yao, Yilin Ma, Peng Wan, Zhilong Chen, Xiangning Li, Hui Gong, Qingming Luo, Dan Zhu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0071538

Sexually Dimorphic Genome-Wide Binding of Retinoid X Receptor alpha (RXRα) Determines Male-Female Differences in the Expression of Hepatic Lipid Processing Genes in Mice
Cited by: 20
Author(s): Astrid Kosters, Deqiang Sun, Hao Wu, Feng Tian, Julio C. Felix, Wei Li, Saul J. Karpen
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0047176

Isolation of Osteoprogenitors from Human Jaw Periosteal Cells: A Comparison of Two Magnetic Separation Methods
Cited by: 20
Author(s): Marcus Olbrich, Melanie Rieger, Siegmar Reinert, Dorothea Alexander
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0044869

A p53-Pax2 Pathway in Kidney Development: Implications for Nephrogenesis
Cited by: 36
Author(s): Zubaida Saifudeen, Jiao Liu, Susana Dipp, Yao Xiao, Yuwen Li, Nathan McLaughlin, Karam Aboudehen, Samir S. El‐Dahr
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0111748

Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
Cited by: 8
Author(s): Gamze Günal-Sadık, Maciej Paszkowski‐Rogacz, Kalaimathy Singaravelu, Andreas Beyer, Frank Buchholz, Rolf Jessberger
Software Mentions: 1
Published: about 10 years ago