pypi: deepTools | Projects | Ecosyste.ms: Papers

10.1016/j.celrep.2021.109671

Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription
Cited by: 3
Author(s): Dong-Hyuk Heo, Krzysztof Kuś, Pawel Grzechnik, Sue Mei Tan-Wong, Adrien Birot, Tea Kecman, Søren Nielsen, Nikolay Zenkin, Lidia Vasiljeva
Software Mentions: 3
Published: about 3 years ago

10.3389/fgene.2014.00277

Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae
Cited by: 14
Author(s): Elena Gómez-Díaz, Ana Rivero, Fabrice Chandre, Victor G. Corcés
Software Mentions: 3
Published: about 10 years ago

10.1186/s13072-020-00358-4

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes
Cited by: 11
Author(s): Parna Saha, Divya Tej Sowpati, Mamilla Soujanya, Ishanee Srivastava, Rakesh K. Mishra
Software Mentions: 3
Published: about 4 years ago

10.3390/genes11010003

Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq
Cited by: 28
Author(s): Nicole B. Kingsley, Colin Kern, Catherine Creppe, Erin N. Hales, Huaijun Zhou, Theodore S. Kalbfleisch, James N. MacLeod, Jessica L Petersen, Carrie J. Finno, Rebecca R. Bellone
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41418-021-00747-6

Deletion of the mitochondria-shaping protein Opa1 during early thymocyte maturation impacts mature memory T cell metabolism
Cited by: 16
Author(s): Mauro Corrado, Dijana Samardžić, Marta Giacomello, Nisha Rana, Erika L. Pearce, Luca Scorrano
Software Mentions: 3
Published: over 3 years ago

10.1016/j.jbc.2021.100374

The elevated transcription of ADAM19 by the oncohistone H2BE76K contributes to oncogenic properties in breast cancer
Cited by: 14
Author(s): Tze Zhen Evangeline Kang, Lina Zhu, Yang Du, Dongbo Ding, Xiaoxuan Zhu, Yi Ching Esther Wan, Jiaxian Liu, Saravanan Ramakrishnan, Landon L. Chan, Siu Yuen Chan, Xin Wang, Haiyun Gan, Junhong Han, Toyotaka Ishibashi, Qing Li, Kui Ming Chan
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41419-021-03897-0

G-protein-coupled receptor GPR17 inhibits glioma development by increasing polycomb repressive complex 1-mediated ROS production
Cited by: 10
Author(s): Huiqing Liu, Rui Xing, Zhimin Ou, Jintong Zhao, Guolin Hong, Tong‐Jin Zhao, Han Ying, Ying Chen
Software Mentions: 3
Published: over 3 years ago

10.1111/jcmm.15323

The proteasome activator PA200 regulates expression of genes involved in cell survival upon selective mitochondrial inhibition in neuroblastoma cells
Cited by: 5
Author(s): Abdennour Douida, Frank Batista, Agnieszka Robaszkiewicz, Pál Botó, Azzam Aladdin, Mónika Szenykiv, Rita Czinege, László Virág, Krisztina Tar
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1006664

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells
Cited by: 23
Author(s): Laura V. Glaser, Simone Rieger, Sybille Thumann, Sophie Beer, Cornelia Kuklik-Roos, Dietmar E. Martin, Kerstin Maier, Marie L. Harth-Hertle, Björn Grüning, Rolf Backofen, Stefan Krebs, Helmut Blum, Ralf Zimmer, Florian Erhard, Bettina Kempkes
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1009529

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters
Cited by: 8
Author(s): Moustafa M. Saleh, Célia Jeronimo, François Robert, Gabriel E. Zentner
Software Mentions: 3
Published: about 3 years ago

10.1534/genetics.118.301674

MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans
Cited by: 30
Author(s): Martina Hajdůšková, Gülkız Baytek, Ena Kolundžić, Alexander Gosdschan, Marlon Kazmierczak, Andreas Ofenbauer, Maria Lena Beato del Rosal, Sergej Herzog, Nida Fatima, Philipp Mertins, Stefanie Müthel, Baris Tursun
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22083982

The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 3
Published: over 3 years ago

10.1186/s13071-020-04139-6

Actin-related protein Arp4 regulates euchromatic gene expression and development through H2A.Z deposition in blood-stage Plasmodium falciparum
Cited by: 6
Author(s): Hui Liu, Xinyu Cui, Dandan Xu, Fei Wang, Lin-Wen Meng, Yuge Zhao, Meng Liu, Shijun Shen, Xiaohong He, Qiang Fang, Zhi‐Yong Tao, Ci-Zong Jiang, Qingfeng Zhang, Liang Gu, Hui Xing
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2020.561804

CYP27B1 Downregulation: A New Molecular Mechanism Regulating EZH2 in Ovarian Cancer Tumorigenicity
Cited by: 7
Author(s): Xiao Huo, Hengzi Sun, Qiuhong Qian, Xiangwen Ma, Peng Peng, Mei Yu, Ying Zhang, Jiaxin Yang, Dongyan Cao, Ting Gui, Keng Shen
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.51754

Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells
Cited by: 20
Author(s): Ana Filipa Domingues, Rashmi Kulkarni, George Giotopoulos, Shikha Gupta, Laura Vinnenberg, Liliana Arede, Elena Foerner, Mitra Khalili, Rita Romano Adao, Ayona Johns, Sophie Tan, Keti Zeka, Brian J. P. Huntly, Sudhakaran Prabakaran, Cristina Pina
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2021.697994

Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs
Cited by: 3
Author(s): Zhimin Zhou, Yaling Zhu, Zhen Zhang, Tao Jiang, Ziqi Ling, Bin Yang, Wanbo Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s13071-020-04476-6

Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture
Cited by: 1
Author(s): Yair D J Prawer, Andreas J. Stroehlein, Neil D. Young, Shilpa Kapoor, Ross S. Hall, Razi Ghazali, Philip Batterham, Robin B. Gasser, Trent Perry, Clare A. Anstead
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2021.649959

“Adopt-a-Tissue” Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare
Cited by: 7
Author(s): Nicole B. Kingsley, Natasha A. Hamilton, Gabriella Lindgren, Ludovic Orlando, Ernest Bailey, Samantha A. Brooks, Molly E. McCue, Theodore S. Kalbfleisch, James N. MacLeod, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.612031

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages
Cited by: 9
Author(s): Alisha T. Massa, Michelle R. Mousel, Maria K. Herndon, David R. Herndon, Brenda M. Murdoch, Stephen N. White
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2021.628849

Characterizing Genetic Regulatory Elements in Ovine Tissues
Cited by: 6
Author(s): Kimberly M Davenport, Alisha T. Massa, Suraj Bhattarai, Stephanie McKay, Michelle R. Mousel, Maria K. Herndon, Stephen N. White, Noelle E. Cockett, Timothy P. L. Smith, Brenda M. Murdoch
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-021-04320-3

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes
Cited by: 6
Author(s): Lélia Polit, Gwenneg Kerdivel, Sebastian Gregoricchio, Michela Esposito, Christel Guillouf, Valentina Boeva
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0225801

Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP
Cited by: 7
Author(s): Tõnis Org, Kati Hensen, Rita Kreevan, Elina Mark, Olav Sarv, Reidar Andreson, Ülle Jaakma, Andres Salumets, Ants Kurg
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0152322

Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments
Cited by: 12
Author(s): Gordon R. McInroy, Dario Beraldi, Eun‐Ang Raiber, Katarzyna Modrzynska, Pieter van Delft, Oliver Billker, Shankar Balasubramanian
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2017.01038

Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response
Cited by: 44
Author(s): Benoı̂t Roux, James A. Heward, Louise E. Donnelly, Simon W. Jones, Mark A. Lindsay
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2020.598692

Bacterial ClpP Protease Is a Potential Target for Methyl Gallate
Cited by: 6
Author(s): Danxing Zheng, Yanan Xu, Gonglin Yuan, Xiaogang Wu, Qiqin Li
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0176190

Pax7 remodels the chromatin landscape in skeletal muscle stem cells
Cited by: 35
Author(s): Karin Lilja, Nan Zhang, Alessandro Magli, Volkan Gündüz, Christopher J. Bowman, Robert W. Arpke, Radbod Darabi, Michael Kyba, Rita Perlingeiro, Brian David Dynlacht
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0214102

Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1
Cited by: 6
Author(s): Stefanie Bauer, Chen Jiang, Stefan U. Åström
Software Mentions: 2
Published: over 5 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

10.7554/eLife.22194

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity
Cited by: 48
Author(s): Federico Gaiti, Katia Jindrich, Selene L. Fernández-Valverde, Kathrein E. Roper, Bernard M. Degnan, Miloš Tanurdžić
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2021.634679

Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag
Cited by: 16
Author(s): Weizhi Ouyang, Xiwen Zhang, Yong Peng, Qing Zhang, Zhilin Cao, Guoliang Li, Xingwang Li
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1004716

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria
Cited by: 179
Author(s): Aziz El Hage, Shaun Webb, Alastair Kerr, David Tollervey
Software Mentions: 2
Published: about 10 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

10.3390/genes10040280

The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1
Cited by: 11
Author(s): João Fernando Lourenço de Almeida, Ricardo Zorzetto Nicoliello Vêncio, Alan Péricles Rodrigues Lorenzetti, Felipe Ten Caten, José Vicente Gomes-Filho, Tie Koide
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12040541

Genomic Imprinting at the Porcine PLAGL1 Locus and the Orthologous Locus in the Human
Cited by: 2
Author(s): Jinsoo Ahn, In-Sul Hwang, Mi-Ryung Park, Seongsoo Hwang, Kichoon Lee
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-015-0835-6

Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2
Cited by: 30
Author(s): Young Chae Kim, Sangwon Byun, Yang Zhang, Sunmi Seok, Byron Kemper, Jian Ma, Jongsook Kim Kemper
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13059-017-1150-1

Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania
Cited by: 47
Author(s): Fumiko Kawasaki, Dario Beraldi, Robyn Hardisty, Gordon R. McInroy, Pieter van Delft, Shankar Balasubramanian
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-017-1316-x

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Cited by: 25
Author(s): Dina Hafez, Aslihan Karabacak, Sabrina Krueger, Yi‐Ting Hwang, Li-San Wang, Robert P. Zinzen, Uwe Ohler
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1654-y

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling
Cited by: 68
Author(s): Aslihan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1009185

Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum
Cited by: 20
Author(s): Hang Jiang, Aliang Xia, Meng Ye, Jingyi Ren, Dongao Li, Huiquan Liu, Qinhu Wang, Ping Lü, Chunlan Wu, Jin‐Rong Xu, Cong Jiang
Software Mentions: 2
Published: about 4 years ago

10.1186/s13059-019-1859-0

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize
Cited by: 61
Author(s): Jing Xu, Chao-Yu Guo, Peter J. Hermanson, Qiang Xu, Changshuo Sun, Wenqing Chen, Qiuxin Kan, Minqi Li, Peter A. Crisp, Jianbing Yan, Li Lin, Nathan M. Springer, Qing Li
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1009263

Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation
Cited by: 13
Author(s): Xiuye Wang, Liang Liu, Adam W. Whisnant, Thomas Hennig, Lara Djaković, Nabila Haque, Cindy Bach, Rozanne M. Sandri‐Goldin, Florian Erhard, Caroline C. Friedel, Lars Dölken, Yongsheng Shi
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-020-1927-5

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana
Cited by: 28
Author(s): Hainan Zhao, Wenli Zhang, Tao Zhang, Yuan Lin, Yaodong Hu, Chao Fang, Jiming Jiang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-020-03952-1

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
Cited by: 33
Author(s): Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler
Software Mentions: 2
Published: almost 4 years ago

10.1128/AEM.02265-19

Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data
Cited by: 35
Author(s): Laura Uelze, Maria Blettner, Carlus Deneke, István Szabó, Jennie Fischer, Simon H. Tausch, Burkhard Malorny
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1006197

Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids
Cited by: 83
Author(s): Dae Kwan Ko, Dominica Rohozinski, Qingxin Song, Samuel H. Taylor, Thomas E. Juenger, Frank G. Harmon, Z Jeffrey Chen
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.69396

Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis
Cited by: 12
Author(s): Ranjith Papareddy, Katalin Páldi, Anna D Smolka, Patrick Hüther, Claude Becker, Michael D. Nodine
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.2005542

Decoding the chromatin proteome of a single genomic locus by DNA sequencing
Cited by: 12
Author(s): Tessy Korthout, Deepani W. Poramba‐Liyanage, Ila van Kruijsbergen, Kitty F. Verzijlbergen, Frank P. A. van Gemert, Tibor van Welsem, Fred van Leeuwen
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.46667

Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells
Cited by: 28
Author(s): Masahiro Oka, Sonoko Mura, Mayumi Otani, Yoichi Miyamoto, Jumpei Nogami, Kazuhira Maehara, Akihito Harada, Taro Tachibana, Yoshihiro Yoneda, Yasuyuki Ohkawa
Software Mentions: 2
Published: almost 5 years ago

10.1111/acel.13042

Demethylation and derepression of genomic retroelements in the skeletal muscles of aged mice
Cited by: 12
Author(s): Byungkuk Min, Kyuheum Jeon, Jung Sun Park, Yong‐Kook Kang
Software Mentions: 2
Published: about 5 years ago

10.1186/s13007-020-00664-8

Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
Cited by: 27
Author(s): Xiaochun Tao, Shouli Feng, Ting Zhao, Xueying Guan
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.ppat.1008835

Downy Mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility
Cited by: 27
Author(s): Sarah Harvey, Priyanka Kumari, Dmitry Lapin, Thomas Griebel, Richard Hickman, Wenbin Guo, Runxuan Zhang, Jane E. Parker, Jim Beynon, Katherine J. Denby, Jens Steinbrenner
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.ppat.1009002

The NS1 protein of the parvovirus MVM Aids in the localization of the viral genome to cellular sites of DNA damage
Cited by: 20
Author(s): Kinjal Majumder, Maria Boftsi, Fawn B. Whittle, Juexin Wang, Matthew S. Fuller, Trupti Joshi, David J. Pintel
Software Mentions: 2
Published: about 4 years ago

10.1073/pnas.2125016118

CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase
Cited by: 33
Author(s): Basudev Ghoshal, Colette L. Picard, Brandon Vong, Suhua Feng, Steven E. Jacobsen
Software Mentions: 2
Published: over 3 years ago

10.3390/jpm11050362

The Usefulness of Cell-Based and Liquid-Based Urine Tests in Clarifying the Diagnosis and Monitoring the Course of Urothelial Carcinoma. Identification of Novel, Potentially Actionable, RB1 and ERBB2 Somatic Mutations
Cited by: 0
Author(s): Tadeusz Kałużewski, Grzegorz K. Przybylski, Michał Bednarek, Sławomir Glazar, Magdalena Grabiec, Adam Jędrzejczyk, Łukasz Kępczyński, Izabela Kubiak, Dorota Kucharska, Agnieszka Morel, Magdalena Owczarek, Marek Rożniecki, Jordan Sałamunia, Dominika Szewczyk, Jarosław Szwalski, Bogdan Kaƚużewski
Software Mentions: 2
Published: over 3 years ago

10.1007/s13238-021-00837-8

Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos
Cited by: 73
Author(s): Chuan Chen, Wenqiang Liu, Jiayin Guo, Yuanyuan Liu, Xuelian Liu, Jun Liu, Xiaoyang Dou, Rongrong Le, Yixin Huang, Chong Li, Lingyue Yang, Xiaochen Kou, Yanhong Zhao, You Wu, Jiayu Chen, Hong Wang, Bin Shen, Yawei Gao, Shaorong Gao
Software Mentions: 2
Published: over 3 years ago

10.18632/aging.101193

Age-associated chromatin relaxation is enhanced in Huntington’s disease mice
Cited by: 11
Author(s): Myungsun Park, Byungkuk Min, Kyuheum Jeon, Sunwha Cho, Jung Sun Park, Jisun Kim, Jeha Jeon, Jinhoi Song, Seokho Kim, Sangkyun Jeong, Hyemyung Seo, Yong‐Kook Kang
Software Mentions: 2
Published: over 7 years ago

10.15252/msb.20167279

Subgenic Pol II interactomes identify region‐specific transcription elongation regulators
Cited by: 31
Author(s): Kevin Harlen, L. Stirling Churchman
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.molcel.2018.03.010

Cell-Cycle Modulation of Transcription Termination Factor Sen1
Cited by: 18
Author(s): Hannah E. Mischo, Yujin Chun, Kevin Harlen, Brendan M Smalec, Somdutta Dhir, L. Stirling Churchman, Stephen Buratowski
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-32340-2

Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis
Cited by: 19
Author(s): Nina T. Odermatt, Claudia Sala, Andrej Benjak, Stewart T. Cole
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-44076-8

ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Cited by: 46
Author(s): Madhusudhan Bysani, Rasmus Ågren, Cajsa Davegårdh, Petr Volkov, Tina Rönn, Per Unneberg, Karl Bacos, Charlotte Ling
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.58030

Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication
Cited by: 15
Author(s): Jeziel D. Damasceno, Catarina A. Marques, Dario Beraldi, Kathryn Crouch, Craig Lapsley, Ricardo Obonaga, Luíz Ricardo Orsini Tosi, Richard McCulloch
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.39140

Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila
Cited by: 36
Author(s): Alexander Munden, Zhan Rong, Amanda Sun, Rama Gangula, Simon Mallal, Jared Nordman
Software Mentions: 2
Published: about 6 years ago

10.1016/j.molcel.2020.05.025

Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution
Cited by: 34
Author(s): Pakavarin Louphrasitthiphol, Robert Siddaway, Alessia Loffreda, Vivian Pogenberg, Hans Friedrichsen, Alexander Schepsky, Zhiqiang Zeng, Min Lü, Thomas Strub, Rasmus Freter, Richard J. Lisle, Eda Suer, Benjamin Thomas, Benjamin Schuster-Böckler, P. Filippakopoulos, Mark R. Middleton, Xin Lü, E. Elizabeth Patton, Irwin Davidson, Jean-Philippe Lambert, Matthias Wilmanns, Eirı́kur Steingrı́msson, Davide Mazza, Colin R. Goding
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-79601-7

Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells
Cited by: 10
Author(s): Kylie Hin-Man Mak, Yuk Man Lam, Ray Kit Ng
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-91756-5

Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives
Cited by: 4
Author(s): Mana Iwata, Ana Gutiérrez, Gisela Marques, Grzegorz Sabat, Philip J. Kersten, Daniel Cullen, Jennifer M. Bhatnagar, J. S. Yadav, Anna Lipzen, Yuko Yoshinaga, Aarti Sharma, Catherine Adam, Christopher Daum, Vivian Ng, Igor V. Grigoriev, Chiaki Hori
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-96488-0

Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation
Cited by: 5
Author(s): Nadezhda E. Vorobyeva, Maksim Erokhin, Darya Chetverina, А. Н. Краснов, M. Yu. Mazina
Software Mentions: 2
Published: about 3 years ago

10.1016/j.stemcr.2020.10.007

β-Globin Lentiviral Vectors Have Reduced Titers due to Incomplete Vector RNA Genomes and Lowered Virion Production
Cited by: 11
Author(s): Jiaying Han, Kevin J. Tam, Feiyang Ma, Curtis Tam, Bamidele Aleshe, Xiaoyan Wang, Jason P. Quintos, Marco Morselli, Matteo Pellegrini, Roger P. Hollis, Donald B. Kohn
Software Mentions: 2
Published: almost 4 years ago

10.1128/mBio.01127-19

The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in Acinetobacter baumannii: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
Cited by: 27
Author(s): Edward Geisinger, Germán Vargas-Cuebas, Nadav J. Mortman, Sapna Syal, Yunfei Dai, Elizabeth L. Wainwright, David W. Lazinski, Stephen Wood, Zeyu Zhu, Jon Anthony, Tim van Opijnen, Ralph R. Isberg
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201900536

Virus-induced transposable element expression up-regulation in human and mouse host cells
Cited by: 35
Author(s): Marissa Macchietto, Ryan A. Langlois, Steven S. Shen
Software Mentions: 2
Published: almost 5 years ago

10.1128/mBio.01067-21

Methyltransferase-like 3 Modulates Severe Acute Respiratory Syndrome Coronavirus-2 RNA N6-Methyladenosine Modification and Replication
Cited by: 43
Author(s): Xueyan Zhang, Haojie Hao, Li Ma, Yecheng Zhang, Xiao Hu, Zhe Chen, Di Liu, Jun Yuan, Zhangli Hu, Wuxiang Guan
Software Mentions: 2
Published: about 3 years ago

10.1186/s40478-018-0573-6

Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA
Cited by: 15
Author(s): Jorge Mata-Garrido, Olga Tapia, Íñigo Casafont, Marı́a T. Berciano, Ana Cuadrado, Miguel Lafarga
Software Mentions: 2
Published: over 6 years ago

10.26508/lsa.201900516

Endogenous epitope-tagging of Tet1, Tet2 and Tet3 identifies TET2 as a naïve pluripotency marker
Cited by: 13
Author(s): Raphaël Pantier, Tülin Tatar, Douglas Colby, Ian Chambers
Software Mentions: 2
Published: about 5 years ago

10.1002/advs.202004635

The Dual Function of KDM5C in Both Gene Transcriptional Activation and Repression Promotes Breast Cancer Cell Growth and Tumorigenesis
Cited by: 23
Author(s): Hai‐feng Shen, Wen‐juan Zhang, Ying Huang, Yaohui He, Guo-Sheng Hu, Lei Wang, Bing‐ling Peng, Yi Jia, Ting‐ting Li, Rui Rong, Xiao‐yan Chen, Jun‐yi Liu, Wenjuan Li, Kenny Ohgi, Shaowei Li, Michael G. Rosenfeld, Wen Li
Software Mentions: 2
Published: over 3 years ago

10.1093/bib/bbab021

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis
Cited by: 11
Author(s): Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Software Mentions: 2
Published: over 3 years ago

10.1186/s12860-020-00296-9

Differential contribution of p300 and CBP to regulatory element acetylation in mESCs
Cited by: 37
Author(s): Sara Matarazzo, Jennifer P. Nguyen, Aishwarya Sundaresan, Laura A. Banaszynski
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.25637

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases
Cited by: 49
Author(s): Sofia Battaglia, Michael Lidschreiber, Carlo Baejen, Phillipp Torkler, Seychelle M. Vos, Patrick Cramer
Software Mentions: 2
Published: over 7 years ago

10.1111/apha.13496

Exercise‐dependent increases in protein synthesis are accompanied by chromatin modifications and increased MRTF‐SRF signalling
Cited by: 23
Author(s): Francesca Solagna, Leonardo Nogara, Kenneth A. Dyar, Franziska Greulich, Ashfaq Ali Mir, Clara Türk, Theresa Bock, Alessia Geremia, Martina Baraldo, Roberta Sartori, Jean Farup, N. Henriette Uhlenhaut, Kristian Vissing, Marcus Krüger, Bert Blaauw
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-020-07165-x

HiCHap: a package to correct and analyze the diploid Hi-C data
Cited by: 4
Author(s): Han Luo, Xinxin Li, Haitao Fu, Cheng Peng
Software Mentions: 2
Published: about 4 years ago

10.1093/database/baab030

Integration of 1:1 orthology maps and updated datasets into Echinobase
Cited by: 8
Author(s): Saoirse Foley, Carolyn J Ku, Brad Arshinoff, Vaneet Lotay, Kamran Karimi, Peter D. Vize, Veronica F. Hinman
Software Mentions: 2
Published: almost 4 years ago

10.15252/embj.201798219

The long non‐coding <scp>RNA</scp> Paupar promotes <scp>KAP</scp> 1‐dependent chromatin changes and regulates olfactory bulb neurogenesis
Cited by: 43
Author(s): Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil R. Clark, Tamara Sirey, Sheena Lee, Dan J. Woodcock, Chris P. Ponting, Francis G. Szele, Keith W. Vance
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-020-1043-9

Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation
Cited by: 5
Author(s): Saadia Khilji, Munerah Hamed, Jihong Chen, Qiao Li
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-020-01456-5

Lysine demethylase 7a regulates murine anterior-posterior development by modulating the transcription of Hox gene cluster
Cited by: 5
Author(s): Yoshiki Higashijima, Naomi Nagai, Masamichi Yamamoto, Takatoshi Kitazawa, Yuuki Kawamura, Azuma Taguchi, Natsuko Nakada, Masaomi Nangaku, Tetsushi Furukawa, Hiroyuki Aburatani, Hiroki Kurihara, Youichiro Wada, Yasuharu Kanki
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.25776

CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Cited by: 446
Author(s): Anders S. Hansen, Iryna Pustova, Claudia Cattoglio, Robert Tjian, Xavier Darzacq
Software Mentions: 2
Published: over 7 years ago

10.1093/eep/dvz007

Mature sperm small-RNA profile in the sparrow: implications for transgenerational effects of age on fitness
Cited by: 7
Author(s): Wayo Matsushima, Kristiana Brink, Julia Schroeder, Eric A. Miska, Katharina Gapp
Software Mentions: 2
Published: over 5 years ago

10.3390/cells9040984

Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model
Cited by: 4
Author(s): Maciej Jerzy Smialek, Erkut Ilaslan, Marcin Sajek, Aleksandra Świercz, Damian Mikolaj Janecki, Kamila Kusz-Zamelczyk, Tomasz Woźniak, Maciej Kotecki, Luiza Handschuh, Marek Figlerowicz, Jadwiga Jaruzelska
Software Mentions: 2
Published: over 4 years ago

10.1186/s12863-020-00894-8

CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity
Cited by: 8
Author(s): Manthan Patel, Divyesh Patel, Subhamoy Datta, Uma Singh
Software Mentions: 2
Published: over 4 years ago

10.1186/s13072-018-0204-2

Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx
Cited by: 22
Author(s): Kai O. Hensel, Franziska Cantner, Felix Bangert, Stéfan Wirth, Jan Postberg
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21218100

Genotypic and Phenotypic Changes in Candida albicans as a Result of Cold Plasma Treatment
Cited by: 5
Author(s): Ewa Tyczkowska-Sieroń, Tadeusz Kałużewski, Magdalena Grabiec, Bogdan Kaƚużewski, J. Tyczkowski
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms21239052

Impact of AHR Ligand TCDD on Human Embryonic Stem Cells and Early Differentiation
Cited by: 4
Author(s): Indrek Teino, Antti Matvere, Martin Pook, Inge Varik, Laura Pajusaar, Keyt Uudeküll, Helen Vaher, Annika Trei, Arnold Kristjuhan, Tõnis Org, Toivo Maimets
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-021-04272-8

A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns
Cited by: 0
Author(s): Wan Kin Au Yeung, Osamu Maruyama, Hidetada Sasaki
Software Mentions: 2
Published: over 3 years ago

10.1111/cpr.13080

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming
Cited by: 4
Author(s): Liying Wang, Zhiliang Xu, Yunlong Wang, Chao Liu, Haixia Wei, Ruidan Zhang, Yinghong Chen, Lina Wang, Wenwen Liu, Shu-Hua Xiao, Wei Li
Software Mentions: 2
Published: over 3 years ago

10.1038/s41421-017-0004-z

Loss of ASXL1 in the bone marrow niche dysregulates hematopoietic stem and progenitor cell fates
Cited by: 21
Author(s): Peng Zhang, Zizhen Chen, Rong Li, Ying Guo, Hui Shi, Jie Bai, Hui Yang, Mengyao Sheng, Zhaomin Li, Zhuo Li, Jianping Li, Shi Chen, Weiping Yuan, Tao Cheng, Mingjiang Xu, Yuan Zhou, Feng Chun Yang
Software Mentions: 2
Published: almost 7 years ago

10.3389/fcell.2021.686737

JFK Is a Hypoxia-Inducible Gene That Functions to Promote Breast Carcinogenesis
Cited by: 1
Author(s): Ziran Yang, Xuehong Zhou, Enrun Zheng, Yizhou Wang, Xinhua Liu, Yue Wang, Yiguang Wang, Zhaofei Liu, Fei Pei, Yue Zhang, Jie Ren, Yunchao Huang, Xianping Lu, Sudun Guan, Sen Qin, Feiya Suo, Jie Shi, Lijing Wang, Lin He, Luyang Sun
Software Mentions: 2
Published: over 3 years ago

10.1038/s41419-020-2341-3

Chromatin accessibility is associated with the changed expression of miRNAs that target members of the Hippo pathway during myoblast differentiation
Cited by: 7
Author(s): Huanhuan Zhou, Yue Xiang, Mingyang Hu, Yongming Xu, Ye Hou, Xiaolong Qi, Liangliang Fu, Yu Luan, Zhangxu Wang, Xinyun Li, Yi‐Fang Zhao, Zhao Song
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.61090

Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones
Cited by: 38
Author(s): Jay F. Sarthy, Michael P. Meers, Derek H. Janssens, Steven Henikoff, Heather Feldman, Patrick J. Paddison, Christina M. Lockwood, Nicholas A. Vitanza, James M. Olson, Kami Ahmad, Steven Henikoff
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-68953-9

Application of next generation sequencing (NGS) for descriptive analysis of 30 genomes of Leishmania infantum isolates in Middle-North Brazil
Cited by: 12
Author(s): Kátia Silene Sousa Carvalho, Wilson José da Silva Júnior, Marcos da Silveira Regueira-Neto, Vladimir Costa Silva, Sérgio de Sá Leitão Paiva Júnior, Valdir Queiroz Balbino, Dorcas Lamounier Costa, Carlos Henrique Nery Costa
Software Mentions: 1
Published: over 4 years ago

10.1186/s13072-017-0148-y

Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize
Cited by: 19
Author(s): Fei‐Man Hsu, Ming‐Ren Yen, Rachel Wang, Chien‐Yu Lin, Pao‐Yang Chen
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-49316-5

Yeast PAF1 complex counters the pol III accumulation and replication stress on the tRNA genes
Cited by: 8
Author(s): Pratibha Bhalla, Avanish Shukla, Dipti Vinayak Vernekar, Aneeshkumar G. Arimbasseri, Kuljeet Singh Sandhu, Poonam Bhargava
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-018-4677-y

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing
Cited by: 13
Author(s): Wells W. Wu, Je-Nie Phue, Chun Ting Lee, Chang-Yi Lin, Lai Xu, Rong Wang, Yaqin Zhang, Rong Shen
Software Mentions: 1
Published: over 6 years ago

10.1038/s41420-021-00555-4

Methyltransferase-like protein 7A (METTL7A) promotes cell survival and osteogenic differentiation under metabolic stress
Cited by: 13
Author(s): Eugene Lee, Ju‐Young Kim, Tae‐Kyung Kim, Seo-Young Park, Gun‐Il Im
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: deepTools

Papers Mentioning deepTools 435