pypi: deepTools | Projects | Ecosyste.ms: Papers

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: over 3 years ago

10.1074/jbc.RA120.015876

Elongin A regulates transcription in vivo through enhanced RNA polymerase processivity
Cited by: 5
Author(s): Yating Wang, Liming Hou, M. Behfar Ardehali, Robert E. Kingston, Brian David Dynlacht
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.ppat.1009272

Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms
Cited by: 10
Author(s): Alex Ranieri Jerônimo Lima, Christiane B. de Araujo, Saloê Bispo, José Salvatore Leister Patané, Ariel Mariano Silber, Maria Carolina Elias, Júlia Pinheiro Chagas da Cunha
Software Mentions: 4
Published: almost 4 years ago

10.1007/s13238-020-00728-4

SIRT7 antagonizes human stem cell aging as a heterochromatin stabilizer
Cited by: 69
Author(s): Shijia Bi, Zunpeng Liu, Zeming Wu, Zehua Wang, Xiaoqian Liu, Si Wang, Jie Ren, Yan Yao, Weiqi Zhang, Moshi Song, Guanghui Liu, Jing Qu
Software Mentions: 4
Published: over 4 years ago

10.1126/sciadv.abe3516

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor
Cited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: almost 4 years ago

10.1126/sciadv.abf7346

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome
Cited by: 4
Author(s): Seung Kyoon Kim, Xihui Liu, Jong-Min Park, Dahun Um, Gokhul Kilaru, Cheng Ming Chiang, Min-Hee Kang, Kimberly M. Huber, Keunsoo Kang, Tae Kyung Kim
Software Mentions: 4
Published: over 3 years ago

10.1038/s41597-020-00713-w

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq
Cited by: 2
Author(s): Xiaomeng Zhao, Long Su, Weilin Xu, Sarah Schaack, Cheng Sun
Software Mentions: 4
Published: about 4 years ago

10.1038/srep25864

Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events
Cited by: 19
Author(s): Graham D. Johnson, Meritxell Jodar, Roger Piqué-Regi, Stephen A. Krawetz
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-48979-4

Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken
Cited by: 22
Author(s): Satoshi Yamashita, Kensuke Kataoka, Hiroto Yamamoto, Tomoko Kato, Satoshi Hara, Katsushi Yamaguchi, Claire Renard-Guillet, Yuki Katou, Katsuhiko Shirahige, Haruki Ochi, Hitoshi Ogino, Tatsuo Uchida, Masafumi Inui, Shuji Takada, Shuji Shigenobu, Hiroshi Asahara
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-61678-9

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues
Cited by: 23
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ganrea Chanthavixay, Y. Wang, Mary E. Delany, Huaijun Zhou, Pablo J. Ross
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-97909-w

Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation
Cited by: 7
Author(s): Siv Anita Hegre, Helle Samdal, Antonin Klima, Endre Bakken Stovner, Kristin G. Nørsett, Nina Beate Liabakk, Lene Christin Olsen, Konika Chawla, Per Arne, Pål Sætrom
Software Mentions: 4
Published: about 3 years ago

10.1186/s13287-021-02601-5

Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias
Cited by: 0
Author(s): Gajendra W. Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, Yoojin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P. Presson, Dong-Sung An, Irvin S. Y. Chen
Software Mentions: 4
Published: about 3 years ago

10.1084/jem.20150907

Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells
Cited by: 76
Author(s): Alejandro V. Villarino, Giuseppe Sciumè, Fred P. Davis, S. Iwata, Beatrice Zitti, Gertraud W. Robinson, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: about 7 years ago

10.4049/jimmunol.2000450

Exhausted CD4+ T Cells during Malaria Exhibit Reduced mTORc1 Activity Correlated with Loss of T-bet Expression
Cited by: 9
Author(s): Ana Villegas-Méndez, Garima Khandelwal, Lucy M McGowan, Rebecca S Dookie, Michael Haley, Charlotte George, David Sims, Graham Lord, Linda V. Sinclair, Richard G. Jenner, Kevin N. Couper
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.27024

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Cited by: 113
Author(s): Jason C. Bell, David Jukam, Nicole A Teran, Viviana I. Risca, Owen K. Smith, Whitney L. Johnson, Jan M. Skotheim, William J. Greenleaf, Aaron F. Straight
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.60498

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments
Cited by: 11
Author(s): Hajnalka Laura Pálinkás, Angéla Békési, Gergely Róna, Lőrinc Sándor Pongor, Gábor Papp, Gergely Tihanyi, Eszter Holub, Ádám Póti, Carolina Gemma, Simak Ali, Michael J. Morten, Eli Rothenberg, Michele Pagano, Dávid Szűts, Balázs Győrffy, Beáta G. Vértessy
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.37892

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
Cited by: 57
Author(s): Amr Nassrallah, Martin Rougée, Clara Bourbousse, Stéphanie Drevensek, Sandra Fonseca, Elisa Iniesto, Ouardia Aït-Mohamed, Anne Flore Deton-Cabanillas, Gérald Zabulon, Ikhlak Ahmed, David Stroebel, Vanessa Masson, Bérangère Lombard, Dominique Eeckhout, Kris Gevaert, Damarys Loew, Auguste Genovesio, Cécile Breyton, Geert De Jaeger, Chris Bowler, Vicente Rubio, Frédy Barneche
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.64204

Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence
Cited by: 5
Author(s): Shou Liu, Wenjian Cao, Yichi Niu, Jiayi Luo, Yanhua Zhao, Zheng Hu, Chenghang Zong
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.62438

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
Cited by: 52
Author(s): Philip P. Adams, Gabriele Baniulyte, Caroline Esnault, Kavya Chegireddy, Navjot Singh, Molly Monge, Ryan Dale, Gisela Storz, Joseph T. Wade
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.08384

Signal transducer and activator of transcription 5 (STAT5) paralog dose governs T cell effector and regulatory functions
Cited by: 69
Author(s): Alejandro V. Villarino, Gertraud W. Robinson, Michael Bonelli, Bárbara Dema, Behdad Afzali, Han-Yu Shih, Hongwei Sun, Stephen R. Brooks, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.62865

Developmental hourglass and heterochronic shifts in fin and limb development
Cited by: 7
Author(s): Koh Onimaru, Kaori Tatsumi, Chiharu Tanegashima, Mitsutaka Kadota, Osamu Nishimura, Shigehiro Kuraku
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.61965

Sustained TNF-α stimulation leads to transcriptional memory that greatly enhances signal sensitivity and robustness
Cited by: 15
Author(s): Zuodong Zhao, Zhuqiang Zhang, Jingjing Li, Qiang Dong, Jun Xiong, Yingfeng Li, Mengying Lan, Gang Li, Bing Zhu
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.60681

SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Cited by: 6
Author(s): Charlotte P Choi, Rebecca J Tay, Margaret R. Starostik, Suhua Feng, James J. Moresco, Brooke E. E. Montgomery, Emily Xu, Maya A Hammonds, Michael C. Schatz, Taiowa A. Montgomery, John R. Yates, Steven E. Jacobsen, John K. Kim
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.43738

Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice
Cited by: 66
Author(s): Mina Kojima, Dirk G. de Rooij, David C. Page
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29391

Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites
Cited by: 25
Author(s): Fabien Sindikubwabo, Shibin Ding, Tahir Hussain, Philippe Ortet, Mohamed Barakat, Sebastian Baumgarten, Dominique Cannella, Andrés Palencia, Alexandre Bougdour, Lucid Belmudes, Yohann Couté, Isabelle Tardieux, Cyrille Y. Botté, Artur Scherf, Mohamed-Ali Hakimi
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.65146

A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide
Cited by: 22
Author(s): Phillip Wulfridge, Kavitha Sarma
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.22039

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq
Cited by: 48
Author(s): Pingzhu Zhou, Fei Gu, Lina Zhang, Brynn N. Akerberg, Qing Ma, Kai Li, Aibin He, Zhiqiang Lin, Sean Stevens, Bin Zhou, William T. Pu
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.40199

Cellular acidosis triggers human MondoA transcriptional activity by driving mitochondrial ATP production
Cited by: 38
Author(s): Blake R. Wilde, Zhizhou Ye, Tian-Yeh Lim
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms22020530

Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes
Cited by: 14
Author(s): Anna Johanna Wiese, Lenka Steinbachová, Ljudmilla Timofejeva, Vojtěch Čermák, Božena Klodová, Ranjani Sri Ganji, Mariana Limones-Méndez, Pavel Bokvaj, Said Hafidh, David Potěšil, David Honys
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms22105066

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22126503

Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-O-glucoside Dietary Intake
Cited by: 5
Author(s): Giuseppe Persico, Francesca Casciaro, Alessandra Marinelli, Chiara Tonelli, Katia Petroni, Marco Giorgio
Software Mentions: 4
Published: over 3 years ago

10.1523/ENEURO.0211-20.2020

Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons
Cited by: 11
Author(s): Anna Noren Rubin, Ruchi Malik, Kathleen K.A. Cho, Kenneth J. Lim, Susan Lindtner, Sarah E. Robinson Schwartz, Daniel Vogt, Vikaas S. Sohal, John L.R. Rubenstein
Software Mentions: 4
Published: about 4 years ago

10.1126/sciadv.abe5357

S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation
Cited by: 24
Author(s): Ruisheng Song, Kevin Struhl
Software Mentions: 3
Published: almost 4 years ago

10.1007/s00401-020-02225-8

C11orf95-RELA reprograms 3D epigenome in supratentorial ependymoma
Cited by: 11
Author(s): Jacqueline Jufen Zhu, Nathaniel Jillette, Xiao Nan Li, Albert W. Cheng, Ching C. Lau
Software Mentions: 3
Published: about 4 years ago

10.1186/s13072-019-0280-y

p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes
Cited by: 22
Author(s): Jing Qu, Guoqiang Yi, Huiqing Zhou
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-020-00365-5

Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequences
Cited by: 23
Author(s): Jingyi Tang, Scott A. Chisholm, Lee M. Yeoh, Paul R. Gilson, Anthony T. Papenfuss, Karen P. Day, Michaela Petter, Michael Duffy
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.55232

Umbilical cord blood-derived ILC1-like cells constitute a novel precursor for mature KIR+NKG2A- NK cells
Cited by: 22
Author(s): Sabrina Bianca Bennstein, Sandra Weinhold, Angela R. Manser, Nadine Scherenschlich, Angela Noll, Katharina Raba, Gesine Kögler, Lutz Walter, Markus Uhrberg
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.740866

Interplay Between BALL and CREB Binding Protein Maintains H3K27 Acetylation on Active Genes in Drosophila
Cited by: 2
Author(s): Ammad Shaukat, Muhammad Haider Farooq Khan, Hina Ahmad, Zain Umer, Muhammad Tariq
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22115802

OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data
Cited by: 3
Author(s): Jiayin Wang, Liubin Chen, Xuanping Zhang, Yao Tong, Tian Zheng
Software Mentions: 3
Published: over 3 years ago

10.1016/j.mcpro.2021.100064

Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner
Cited by: 8
Author(s): Lauriane Vélot, Frédéric Lessard, Félix-Antoine Bérubé-Simard, Christophe Tav, Bertrand Neveu, Valentine Teyssier, Imène Boudaoud, Ugo Dionne, Noémie Lavoie, Steve Bilodeau, Frédéric Pouliot, Nicolas Bisson
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.59464

Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function
Cited by: 18
Author(s): Yinan Li, Anthony Osuma, Edgar Correa, Munachiso A Okebalama, Pauline Dao, Olivia Gaylord, Jihad Aburas, Priota Islam, André Ex Brown, Paschalis Kratsios
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-12335-1

Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts
Cited by: 23
Author(s): Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L. Stitzel
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-13012-z

Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome
Cited by: 30
Author(s): Zhiyuan Chen, Darren E. Hagen, Tieming Ji, Christine G. Elsik
Software Mentions: 3
Published: about 7 years ago

10.1016/j.molcel.2020.03.017

Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment
Cited by: 39
Author(s): Hon Wing Liu, Céline Bouchoux, Mélanie Panarotto, Yasutaka Kakui, Harshil Patel, Frank Uhlmann
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-018-1510-5

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains
Cited by: 65
Author(s): Abdulrahman Salhab, Karl Nordström, Gilles Gasparoni, Kathrin Kattler, Peter Ebert, Fidel Ramírez, Laura Arrigoni, Fabian Müller, Julia K. Polansky, Cristina Cadenas, Jan G. Hengstler, Thomas Lengauer, Thomas Manke, Jörn Walter
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-41639-7

Hox gene expression determines cell fate of adult periosteal stem/progenitor cells
Cited by: 22
Author(s): Vivian Bradaschia-Corrêa, Kevin Leclerc, Anne Marie Josephson, Sooyeon Lee, Laura Palma, Hannah P. Litwa, Shane S. Neibart, Jason C. Huo, Philipp Leucht
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-42292-w

Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis
Cited by: 19
Author(s): Marina R. Hadjicharalambous, Benoı̂t Roux, Eszter Csomor, Carol Feghali‐Bostwick, Lynne A. Murray, D. S. Clarke, Mark A. Lindsay
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.637873

Kinome-Wide RNAi Screen Uncovers Role of Ballchen in Maintenance of Gene Activation by Trithorax Group in Drosophila
Cited by: 2
Author(s): Muhammad Haider Farooq Khan, Junaid Akhtar, Zain Umer, Najma Shaheen, Ammad Shaukat, Muhammad Shahbaz Munir, Aziz Mithani, Saeed Anwar, Muhammad Tariq
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00342

P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes
Cited by: 9
Author(s): Heeyoun Bunch, Hyeseung Choe, Jong Bum Kim, Doo Sin Jo, Soyeon Jeon, Sang-Hwa Lee, Dong‐Hyung Cho, Keunsoo Kang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-016-0065-5

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells
Cited by: 19
Author(s): Christopher L. Frank, Dinesh Manandhar, Raluca Gordân, Gregory E. Crawford
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-56277-2

ONECUT2 overexpression promotes RAS-driven lung adenocarcinoma progression
Cited by: 20
Author(s): Qingyang Ma, Kai Wu, Hui Li, Huichun Li, Yong Zhu, Guohong Hu, Landian Hu, Xiangyin Kong
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.chom.2019.10.004

An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling
Cited by: 41
Author(s): Alessandro Pagliuso, Tristan Tham, Eric Allemand, Stevens Robertin, Bruno Dupuy, Quentin Bertrand, Christophe Bécavin, Mikael Koutero, Valérie Najburg, Marie–Anne Nahori, Frédéric Tangy, Fabrizia Stavru, Sergey Bessonov, Andréa Dessen, Christian Muchardt, Alice Lebreton, Anastassia V. Komarova, Pascale Cossart
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2020.604785

JNK1 Signaling Downstream of the EGFR Pathway Contributes to Aldara®-Induced Skin Inflammation
Cited by: 3
Author(s): Aurore Le, Abdulkader Azouz, Séverine Thomas, Nicolas Istaces, Muriel Nguyen, Stanislas Goriely
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41422-018-0104-9

Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation
Cited by: 71
Author(s): Shuai Zhao, Lan Cheng, Yifei Gao, Baichao Zhang, Xiangdong Zheng, Liang Wang, Pilong Li, Qianwen Sun, Haitao Li
Software Mentions: 3
Published: about 6 years ago

10.1186/s13148-020-00921-6

Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues
Cited by: 12
Author(s): Hang Gyeong Chin, Zhiyi Sun, Udayakumar S. Vishnu, Pengying Hao, Paloma Cejas, George Spracklin, Pierre‐Olivier Estève, Shuang-yong Xu, Henry W. Long, Sriharsa Pradhan
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.32341

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
Cited by: 60
Author(s): Gabriel Aughey, Alicia Estacio-Gómez, Jamie Thomson, Hang Yin, Tony D. Southall
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-020-07078-9

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Cited by: 36
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ying Wang, Ganrea Chanthavixay, Juan F. Medrano, Alison L. Van Eenennaam, Ian F Korf, Christopher K. Tuggle, Catherine W. Ernst, Huaijun Zhou, Pablo J. Ross
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2019.01333

AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States
Cited by: 34
Author(s): Lingling Da, Yue Liu, Jiaotong Yang, Tian Tian, Jiajie She, Xuelian Ma, Wenying Xu, Zhen Su
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers11121886

Cancer Is Associated with Alterations in the Three-Dimensional Organization of the Genome
Cited by: 13
Author(s): Lifei Li, Nicolai K H Barth, Christian Pilarsky, Leila Taher
Software Mentions: 3
Published: almost 5 years ago

10.1111/jpi.12673

Resource: A multi‐species multi‐timepoint transcriptome database and webpage for the pineal gland and retina
Cited by: 12
Author(s): Eric Terry Wang Wei-Chiao Chang, Cong Fu, Steven L. Coon, Shahar Alon, Marjan Bozinoski, Matthew Breymaier, Diego Martín Bustos, Samuel Clokie, Yoav Gothilf, Caroline Esnault, P. Michael Iuvone, Christopher E. Mason, Margaret J. Ochocinska, Adi Tovin, Charles Wang, Pin-Xian Xu, Jiaquan Zhu, Ryan Dale, David C. Klein
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-019-0718-6

Monocytes undergo multi-step differentiation in mice during oral infection by Toxoplasma gondii
Cited by: 8
Author(s): Aurélie Detavernier, Abdulkader Azouz, Hussein Shehade, Marion Splittgerber, Laurye Van Maele, Muriel Nguyen, Séverine Thomas, Younès Achouri, David Švec, Emilie Calonne, François Fuks, Guillaume Oldenhove, Stanislas Goriely
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1009828

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II
Cited by: 11
Author(s): Mohammad S. Baig, Yimo Dou, Benjamin G. Bergey, Russell Bahar, Justin M. Burgener, Marjan Moallem, J B McNeil, Akhi Akhter, Giovanni L Burke, Veroni S. Sri Theivakadadcham, Patricia Richard, Damien D’Amours, Emanuel Rosonina
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22137090

DNA G-Quadruplexes Contribute to CTCF Recruitment
Cited by: 11
Author(s): Polina Tikhonova, Iulia Pavlova, Ekaterina Isaakova, В. Б. Цветков, Alexandra N. Bogomazova, Tatiana Vedekhina, Artem V. Luzhin, Rinat Sultanov, V. V. Severov, Ksenia M. Klimina, Omar L. Kantidze, Г. Е. Позмогова, Maria A. Lagarkova, Anna M. Varizhuk
Software Mentions: 3
Published: over 3 years ago

10.26508/lsa.202000654

A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition
Cited by: 4
Author(s): Mario Cocco, Matthew A. Care, Amel Saadi, Muna Al-Maskari, Gina M. Doody, Reuben Tooze
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.01399-18

Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification
Cited by: 76
Author(s): Giovanni Bussotti, Evi Gouzelou, Mariana Côrtes Boité, Ihcene Kherachi Djenad, Zoubir Harrat, Naouel Eddaikra, Jeremy C. Mottram, Μαρία Αντωνίου, Vasiliki Christodoulou, Aymen Bali, Fatma Z. Guerfali, Dhafer Laouini, M. Shahid Mukhtar, Franck Dumetz, Jean‐Claude Dujardin, Despina Smirlis, Pierre Lechat, Pascale Pescher, Adil El Hamouchi, Meryem Lemrani, Carmen Chicharro, Ivonne Pamela Llanes-Acevedo, Laura Botana, Israel Cruz, Javier Moreno, Fakhri Jeddi, Abdul Karim, A. Bouratbine, Elisa Cupolillo, Gérald F. Späth
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1006224

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters
Cited by: 16
Author(s): Christopher A. Lavender, Kimberly R. Cannady, Jackson A. Hoffman, Kevin W. Trotter, Daniel A. Gilchrist, Brian D. Bennett, Adam Burkholder, Craig J. Burd, David C. Fargo, Trevor Archer
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms22052282

The RNAi Mechanism Regulates a New Exonuclease Gene Involved in the Virulence of Mucorales
Cited by: 8
Author(s): Carlos Pèrez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.03533-20

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
Cited by: 23
Author(s): Carl J. Yeoman, Christopher J. Fields, Pascale Lepercq, Philippe Ruiz, Evelyne Forano, Bryan A. White, Pascale Mosoni
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0136314

Nucleosome Organization in Human Embryonic Stem Cells
Cited by: 22
Author(s): Puya G. Yazdi, Brian Pedersen, Jared F. Taylor, Omar Khattab, Yuhan Chen, Steven E. Jacobsen, Ping H. Wang
Software Mentions: 3
Published: about 9 years ago

10.1128/mSphere.00305-16

Coordinate Regulation of Antimycin and Candicidin Biosynthesis
Cited by: 34
Author(s): Thomas C McLean, Paul A. Hoskisson, Ryan F. Seipke
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41423-019-0219-z

The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection
Cited by: 32
Author(s): Xiangyu Chen, Guoshuai Cao, Jialin Wu, Xinxin Wang, Zhiwei Pan, Jianbao Gao, Tian Qin, Lifan Xu, Zhirong Li, Yaxing Hao, Qizhao Huang, Pengcheng Wang, Minglu Xiao, Luoyingzi Xie, Shupei Tang, Zhenyu Liu, Li Hu, Jianfang Tang, Ran He, Li Wang, Xinyuan Zhou, Yuzhang Wu, Mengjie Chen, Beicheng Sun, Bo Zhu, Jun Huang, Lilin Ye
Software Mentions: 3
Published: over 5 years ago

10.1016/j.celrep.2020.107742

Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer
Cited by: 29
Author(s): John R. Christin, Chunhui Wang, Chi Yeh Chung, Yu Liu, Christopher Dravis, Wei Tang, Maja H. Oktay, Geoffrey M. Wahl, Wenjun Guo
Software Mentions: 3
Published: over 4 years ago

10.26508/lsa.201900635

Essential role of theCrkfamily-dosage in DiGeorge-like anomaly and metabolic homeostasis
Cited by: 7
Author(s): Akira Imamoto, Sewon Ki, Leiming Li, Kenji Iwamoto, Venkat Maruthamuthu, John Devany, Ocean Lu, Takayuki Kanazawa, Suxiang Zhang, Takuji Yamada, Akiyoshi Hirayama, Shinji Fukuda, Yutaka Suzuki, Mariko Okada
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.cell.2019.06.006

Human Artificial Chromosomes that Bypass Centromeric DNA
Cited by: 71
Author(s): Glennis A. Logsdon, Craig W. Gambogi, Mikhail Liskovykh, Evelyne J. Barrey, Vladimir Larionov, Karen H. Miga, Patrick Heun, Ben E. Black
Software Mentions: 3
Published: over 5 years ago

10.1038/s41388-020-01435-4

The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen
Cited by: 2
Author(s): Shixiong Wang, Venkata S. Somisetty, Baoyan Bai, Igor Chernukhin, Henri Niskanen, Minna U. Kaikkonen, Meritxell Bellet, Jason S. Carroll, Antoni Hurtado
Software Mentions: 3
Published: about 4 years ago

10.1111/jipb.12871

The transcription factor GATA10 regulates fertility conversion of a two‐line hybrid tms5 mutant rice via the modulation of UbL40 expression
Cited by: 15
Author(s): Jing Jin, Songtao Gui, Qian Li, Ying Wāng, Hongyuan Zhang, Zhixuan Zhu, Hao Chen, Yueyang Sun, Yu Zeng, Xingguo Huang, Yi Ding
Software Mentions: 3
Published: about 5 years ago

10.1007/s10911-020-09465-0

Characterization of Organoid Cultures to Study the Effects of Pregnancy Hormones on the Epigenome and Transcriptional Output of Mammary Epithelial Cells
Cited by: 11
Author(s): Michael F. Ciccone, Marygrace C. Trousdell, Camila O. dos Santos
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1008828

Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication
Cited by: 16
Author(s): Jeziel D. Damasceno, João Luís Reis-Cunha, Kathryn Crouch, Dario Beraldi, Craig Lapsley, Luíz Ricardo Orsini Tosi, Daniella Castanheira Bartholomeu, Richard McCulloch
Software Mentions: 3
Published: over 4 years ago

10.15252/embj.2018100788

The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment
Cited by: 41
Author(s): Thomas Burgold, M. Barber, Susan L. Kloet, Julie Cramard, Sarah Gharbi, Robin Floyd, Masaki Kinoshita, Markus Ralser, Michiel Vermeulen, Nicola Reynolds, Sabine Dietmann, Brian Hendrich
Software Mentions: 3
Published: over 5 years ago

10.1242/dev.199628

LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells
Cited by: 8
Author(s): Juli Liu, Sheng Liu, Lei Han, Sheng Yi, Yucheng Zhang, Il-man Kim, Jun Wan, Lei Yang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006793

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain
Cited by: 110
Author(s): Sabine Lagger, John C. Connelly, Gabriele Schweikert, Shaun Webb, Jim Selfridge, Bernard Ramsahoye, Miao Yu, Chuan He, Guido Sanguinetti, Lawrence C. Sowers, Malcolm D. Walkinshaw, Adrian Bird
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.33920

MCM2–7-dependent cohesin loading during S phase promotes sister-chromatid cohesion
Cited by: 56
Author(s): Zheng Ge, Mohammed Kanchwala, Chao Xing, Hongtao Yu
Software Mentions: 3
Published: over 6 years ago

10.1093/database/bav050

A general concept for consistent documentation of computational analyses
Cited by: 9
Author(s): Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz
Software Mentions: 3
Published: almost 10 years ago

10.7554/eLife.46976

HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis
Cited by: 44
Author(s): Shuping Zhang, Alejandra Macias-Garcia, Jacob C. Ulirsch, Jason Velazquez, Vincent Butty, Stuart S. Levine, Vijay G. Sankaran, Jane-Jane Chen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0233191

Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene
Cited by: 3
Author(s): Jaafar Alomairi, Anne Molitor, Nori Sadouni, Saadat Hussain, Magali Torres, Wiam Saadi, Lan T M Dao, Guillaume Charbonnier, David Santiago-Algarra, Jean-Christophe Andrau, Denis Puthier, Tom Sexton, Salvatore Spicuglia
Software Mentions: 3
Published: over 4 years ago

10.1186/s13072-020-00348-6

HiCoP, a simple and robust method for detecting interactions of regulatory regions
Cited by: 8
Author(s): Yan Zhang, Zhaoqiang Li, Shasha Bian, Hao Zhao, Delong Feng, Yanhong Chen, Yuhe Hou, Qifa Liu, Bingtao Hao
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009318

Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis
Cited by: 10
Author(s): Jonathan Lenz, Robert Liefke, Julianne Funk, Samuel Shoup, Andrea Nist, Thorsten Stiewe, Robert A. Schulz, Yumiko Tokusumi, Lea Albert, Hartmann Raifer, Klaus Förstemann, Olalla Vázquez, Tsuyoshi Tokusumi, Nancy Fossett, Alexander Brehm
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-021-07795-9

A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis
Cited by: 5
Author(s): Joshua Disatham, Lisa A. Brennan, Daniel Chauss, Jason Kantorow, Behdad Afzali, Marc Kantorow
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-2285-7

cChIP-seq: a robust small-scale method for investigation of histone modifications
Cited by: 13
Author(s): Cristina Valensisi, Jo Ling Liao, Colin Andrus, Stephanie L. Battle, R. David Hawkins
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.63368

Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila
Cited by: 24
Author(s): Bhavatharini Kasinathan, Serafin U. Colmenares, Hannah McConnell, Janet M. Young, Gary H. Karpen, Harmit S. Malik
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms21041248

NCAPG Dynamically Coordinates the Myogenesis of Fetal Bovine Tissue by Adjusting Chromatin Accessibility
Cited by: 5
Author(s): Xin Hu, Yishen Xing, Xing Fu, Qiyuan Yang, Ling Ren, Yahui Wang, Qian Li, Junya Li, Lupei Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-018-4542-z

Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling
Cited by: 31
Author(s): Tanvi Shashikant, Jian Ming Khor, Charles A. Ettensohn
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.62548

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees
Cited by: 11
Author(s): Briana E Mittleman, Sebastian Pott, Shane Warland, Kenneth Barr, Claudia Cuevas, Yoav Gilad
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13072-021-00386-8

Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
Cited by: 20
Author(s): Bradley P. Balaton, Oriol Fornés, Wyeth W. Wasserman, Carolyn J. Brown
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1009252

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program
Cited by: 4
Author(s): Rajalakshmi Srinivasan, Adhish Walvekar, Zeenat Rashida, Aswin Sai Narain Seshasayee, Sunil Laxman
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008964

The evolution and functional divergence of the histone H2B family in plants
Cited by: 42
Author(s): Dazong Jiang, Michael Borg, Zdravko J. Lorković, Sean A. Montgomery, Akihisa Osakabe, Ramesh Yelagandula, Elin Axelsson, Frédéric Berger
Software Mentions: 3
Published: over 4 years ago

10.1016/j.celrep.2021.108759

Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
Cited by: 22
Author(s): Jianming Wang, Patricia Rojas, Jingwen Mao, Martina Mustè Sadurnì, Olivia Garnier, Songshu Xiao, Martin R. Higgs, Paloma García, Marco Saponaro
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1007088

Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB's innate function as the repressor of DREAM target genes
Cited by: 27
Author(s): Paul D. Goetsch, Jacob M. Garrigues, Susan Strome
Software Mentions: 3
Published: about 7 years ago

10.1186/s13059-021-02476-y

H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha
Cited by: 6
Author(s): S. Liu, Minerva S. Trejo-Arellano, Yue Qiu, D. Magnus Eklund, Claudia Köhler, Lars Hennig
Software Mentions: 3
Published: about 3 years ago

Projects: pypi: deepTools

Papers Mentioning deepTools 435