Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: deepTools
https://packages.ecosyste.ms/registries/pypi.org/packages/deepTools
Useful tools for exploring deep sequencing data.
59 versions
Latest release: about 1 year ago
4 dependent packages
1,952 downloads last month
Papers Mentioning deepTools 435
10.15252/msb.20209438
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomicsCited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago
10.1371/journal.pone.0256196
Finding differentially expressed sRNA-Seq regions with srnadiffCited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: about 3 years ago
10.1186/s13148-021-01173-8
Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolismCited by: 5
Author(s): Kristyna Kupkova, Savera J. Shetty, Rashidul Haque, William A. Petri, David T. Auble
Software Mentions: 14
Published: about 3 years ago
10.12688/f1000research.15140.2
Recommendations for the packaging and containerizing of bioinformatics softwareCited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: over 5 years ago
10.1186/s13072-020-00343-x
BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracksCited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
Software Mentions: 13
Published: over 4 years ago
10.7554/eLife.50087
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycleCited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: almost 5 years ago
10.7554/eLife.37551
Species and cell-type properties of classically defined human and rodent neurons and gliaCited by: 55
Author(s): Xiao Xu, Elitsa I Stoyanova, Agata E. Lemiesz, Jie Xing, Deborah C. Mash, Nathaniel Heintz
Software Mentions: 12
Published: about 6 years ago
10.3389/fimmu.2020.00444
JunB Controls Intestinal Effector Programs in Regulatory T CellsCited by: 8
Author(s): Joshua D. Wheaton, Maria Ciofani
Software Mentions: 12
Published: over 4 years ago
10.1186/s13059-021-02493-x
Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafishCited by: 7
Author(s): Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles Kaufman, Stephen L. Johnson, Ting Wang
Software Mentions: 12
Published: about 3 years ago
10.1371/journal.pgen.1009240
Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behaviorCited by: 5
Author(s): Colleen M Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G Brovero, Michelle N. Arbeitman
Software Mentions: 11
Published: over 3 years ago
10.1038/s41598-017-02464-y
UROPA: a tool for Universal RObust Peak AnnotationCited by: 38
Author(s): Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Software Mentions: 11
Published: over 7 years ago
10.15252/emmm.201911900
Epigenetic gene expression links heart failure to memory impairmentCited by: 13
Author(s): Rezaul Islam, Dawid Lbik, M. Sadman Sakib, Raoul Maximilian Hofmann, Tea Berulava, Martí Jiménez Mausbach, Julia Cha, Maria Amélia Azevêdo Goldberg, Elerdashvili Vakhtang, Christian Schiffmann, Anke Zieseniß, Dörthe M. Katschinski, Farahnaz Sananbenesi, Karl Toischer, André Fischer
Software Mentions: 11
Published: almost 4 years ago
10.1016/j.molcel.2019.12.001
PRC1 Catalytic Activity Is Central to Polycomb System FunctionCited by: 163
Author(s): Neil P. Blackledge, Nadezda A. Fursova, Jessica R. Kelley, Miles K. Huseyin, Angelika Feldmann, Robert J. Klose
Software Mentions: 11
Published: almost 5 years ago
10.7554/eLife.51276
A genome-wide view of the de-differentiation of central nervous system endothelial cells in cultureCited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: almost 5 years ago
10.1016/j.molcel.2019.03.024
Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene RepressionCited by: 187
Author(s): Nadezda A. Fursova, Neil P. Blackledge, Manabu Nakayama, Shinsuke Ito, Haruhiko Koseki, Anca M. Farcas, Hamish W King, Haruhiko Koseki, Robert J. Klose
Software Mentions: 11
Published: over 5 years ago
10.1016/j.devcel.2018.11.009
From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In VivoCited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: almost 6 years ago
10.3390/ijms22083975
Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive CompoundsCited by: 11
Author(s): Debosmita Sardar, Brittney Lozzi, Junsung Woo, Teng-Wei Huang, Caroline Cvetkovic, Chad J. Creighton, Robert Krencik, Benjamin Deneen
Software Mentions: 10
Published: over 3 years ago
10.7554/eLife.62250
Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cellsCited by: 11
Author(s): Helen M Tauc, Imilce A. Rodriguez‐Fernandez, Jason A. Hackney, Michał Pawlak, Tal Oron, Jerome Korzelius, Hagar F. Moussa, Subhra Chaudhuri, Zora Modrušan, Bruce A Edgar, Heinrich Jasper
Software Mentions: 10
Published: over 3 years ago
10.1242/dev.193060
Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafishCited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: almost 5 years ago
10.1007/s10456-020-09743-9
Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cellsCited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: about 4 years ago
10.1186/s13059-020-02245-3
High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative startsCited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 10
Published: almost 4 years ago
10.7554/eLife.43257
Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculaturesCited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 5 years ago
10.7554/eLife.36187
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cellsCited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: about 6 years ago
10.1371/journal.pgen.1009376
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzaeCited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: almost 4 years ago
10.3389/fcell.2021.643603
Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish BrainCited by: 8
Author(s): Samuel E. Ross, Daniel Hesselson, Ozren Bogdanović
Software Mentions: 9
Published: over 3 years ago
10.3389/fnmol.2021.664912
Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for CognitionCited by: 9
Author(s): Sergio Espeso‐Gil, Aliaksei Z. Holik, Sarah Bonnin, Shalu Jhanwar, Sandhya Chandrasekaran, Roger Piqué-Regi, Júlia Albaigès-Ràfols, Michael P. Maher, Jon Permanyer, Manuel Irimia, Marc R. Friedländer, Meritxell Pons-Espinal, Schahram Akbarian, Mara Dierssen, Philipp G. Maass, Charlotte N. Hor, Stephan Ossowski
Software Mentions: 9
Published: over 3 years ago
10.3389/fcell.2021.708066
Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer CellsCited by: 15
Author(s): Xuelong Wang, Jizhou Yan, Baiyong Shen, Gang Wei
Software Mentions: 9
Published: over 3 years ago
10.1126/sciadv.abc8492
Persistent epigenetic reprogramming of sweet taste by dietCited by: 29
Author(s): Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, Monica Dus
Software Mentions: 9
Published: almost 4 years ago
10.1038/s42003-021-01945-1
Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expressionCited by: 5
Author(s): Andrea Cerase, Alexander N. Young, Nerea Ruiz, Andreas Buneß, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, Giuseppe Trigiante, Sarah Marzi, Philip Avner
Software Mentions: 9
Published: over 3 years ago
10.1186/s13059-021-02374-3
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycleCited by: 18
Author(s): Mayra Furlan-Magaril, Masami Ando-Kuri, Rodrigo G. Arzate-Mejía, Jörg Morf, Jonathan Cairns, Abraham Román-Figueroa, Luis Tenorio-Hernández, Augusto César Poot-Hernández, Simon Andrews, Csilla Várnai, Boo Virk, Steven Wingett, Peter Fraser
Software Mentions: 9
Published: over 3 years ago
10.7554/eLife.65537
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPACited by: 32
Author(s): Matthew T Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel F. A. Tomé, Xuhong Yu, Pascal G.P. Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 9
Published: over 3 years ago
10.1186/s13059-020-02008-0
scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing dataCited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 4 years ago
10.1016/j.molcel.2018.11.006
Interactome Rewiring Following Pharmacological Targeting of BET BromodomainsCited by: 117
Author(s): Jean-Philippe Lambert, S. Picaud, Takao Fujisawa, Huayun Hou, P. Savitsky, Liis Uusküla-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen‐Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St‐Denis, Joseph A. Newman, Manuel Stucki, Laurence Pelletier, Nuno Bandeira, Michael D. Wilson, P. Filippakopoulos, Anne‐Claude Gingras
Software Mentions: 9
Published: almost 6 years ago
10.7554/eLife.44036
Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific lociCited by: 38
Author(s): Sonia Sen, Sachin Chanchani, Tony D. Southall, Chris Q. Doe
Software Mentions: 8
Published: almost 6 years ago
10.1016/j.molcel.2020.06.002
Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation RatesCited by: 41
Author(s): Tomasz W. Turowski, Elisabeth Petfalski, Benjamin D. Goddard, Sarah L. French, Aleksandra Helwak, David Tollervey
Software Mentions: 8
Published: over 4 years ago
10.15252/embj.2020106423
Activation of endogenous retroviruses during brain development causes an inflammatory responseCited by: 27
Author(s): Marie E. Jönsson, Raquel Garza, Yogita Sharma, Rebecca Petri, Erik Södersten, Jenny Johansson, Peter Johansson, Diahann A. M. Atacho, Karolina Pircs, Sofia Madsen, David Yudovich, Ramprasad Ramakrishnan, Johan Holmberg, Jonas Larsson, Patric Jern, Johan Jakobsson
Software Mentions: 8
Published: over 3 years ago
10.15252/msb.20199002
Endogenous fluctuations of <scp>OCT</scp> 4 and <scp>SOX</scp> 2 bias pluripotent cell fate decisionsCited by: 35
Author(s): Daniel Strebinger, Cédric Deluz, Elias T Friman, Subashika Govindan, Andrea Brigitta Alber, David M. Suter
Software Mentions: 8
Published: about 5 years ago
10.1186/s13059-021-02260-y
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regionsCited by: 31
Author(s): Maša Roller, Ericca L. Stamper, Diego Villar, Osagie Izuogu, Fergal J. Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0249691
Profiling DNA break sites and transcriptional changes in response to contextual fear learningCited by: 25
Author(s): Ryan Stott, Oleg Kritsky, Li‐Huei Tsai
Software Mentions: 8
Published: over 3 years ago
10.1038/srep40655
Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiaeCited by: 66
Author(s): Elena Gómez-Díaz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Anna Cohuet, M. Jordan Rowley, Jean-Bosco Ouédraogo, Victor G. Corcés
Software Mentions: 8
Published: almost 8 years ago
10.1186/s13072-019-0305-6
CGGBP1 regulates CTCF occupancy at repeatsCited by: 12
Author(s): Divyesh Patel, Manthan Patel, Subhamoy Datta, Uma Singh
Software Mentions: 8
Published: about 5 years ago
10.1038/tp.2015.169
Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brainCited by: 56
Author(s): Aslihan Dincer, David P. Gavin, Ke Xu, B Zhang, Joel T. Dudley, Eric E. Schadt, Schahram Akbarian
Software Mentions: 8
Published: almost 9 years ago
10.1016/j.isci.2021.102762
NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cellsCited by: 9
Author(s): Azzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber, Robin Allshire, Kamil R. Kranc, David Tollervey, Dónal O’Carroll
Software Mentions: 8
Published: over 3 years ago
10.1186/s13059-019-1855-4
Common DNA sequence variation influences 3-dimensional conformation of the human genomeCited by: 66
Author(s): David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen, Bing Ren
Software Mentions: 8
Published: almost 5 years ago
10.1186/s12859-019-3090-0
CSA: a web service for the complete process of ChIP-Seq analysisCited by: 2
Author(s): Min Li, Li Tang, Fang‐Xiang Wu, Yi Pan, Jianxin Wang
Software Mentions: 8
Published: almost 5 years ago
10.1038/s41598-021-98889-7
Productive visualization of high-throughput sequencing data using the SeqCode open portable platformCited by: 7
Author(s): Enrique Blanco, Mar González-Ramírez, Luciano Di Croce
Software Mentions: 8
Published: about 3 years ago
10.7554/eLife.62161
Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zonesCited by: 18
Author(s): Nina Kirstein, Alexander Buschle, Xia Wu, Stefan Krebs, Helmut Blum, Elisabeth Kremmer, Ina Vorberg, Wolfgang Hammerschmidt, Laurent Lacroix, Olivier Hyrien, Benjamin Audit, Aloys Schepers
Software Mentions: 7
Published: over 3 years ago
10.7554/eLife.22631
The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cellsCited by: 184
Author(s): Hamish W King, Robert J. Klose
Software Mentions: 7
Published: over 7 years ago
10.1016/j.celrep.2019.12.057
Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem CellsCited by: 118
Author(s): James Rhodes, Angelika Feldmann, Benjamín Hernández-Rodríguez, Noèlia Díaz, Jill M. Brown, Nadezda A. Fursova, Neil P. Blackledge, Praveen Prathapan, Paula Dobrinić, Miles K. Huseyin, Aleksander Szczurek, Kai Kruse, K Nasmyth, Veronica J. Buckle, Juan M. Vaquerizas, Robert J. Klose
Software Mentions: 7
Published: almost 5 years ago
10.7554/eLife.59610
Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryosCited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: over 4 years ago
10.26508/lsa.202101080
Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changesCited by: 9
Author(s): Melissa Bothe, René Buschow, Sebastiaan H. Meijsing
Software Mentions: 7
Published: about 3 years ago
10.26508/lsa.201800085
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cellsCited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: over 6 years ago
10.7554/eLife.53360
Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male miceCited by: 25
Author(s): Mohamed Mahgoub, Jacob Paiano, Melania Bruno, Wei Wu, Sarath Pathuri, Xing Zhang, Sherry Ralls, Xiaodong Cheng, André Nussenzweig, Todd S. Macfarlan
Software Mentions: 7
Published: over 4 years ago
10.1038/s41598-017-14366-0
Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor CellsCited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: about 7 years ago
10.1186/s12915-020-0752-3
Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cellsCited by: 33
Author(s): Donnchadh S. Dunican, Heidi K. Mjoseng, Leanne Duthie, Ilya M. Flyamer, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 7
Published: over 4 years ago
10.1016/j.ccell.2019.08.008
An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in CancerCited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: about 5 years ago
10.1371/journal.pgen.1009763
Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesionCited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: about 3 years ago
10.1126/sciimmunol.abg0833
SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivationCited by: 127
Author(s): Bingyu Yan, Tilo Freiwald, Daniel Chauss, Luopin Wang, Erin E. West, Carmen Mirabelli, Zhang Cj, Eva-Maria Nichols, Nazish T. Malik, Richard I. Gregory, Marcus Bantscheff, Sonja Ghidelli-Disse, Martin Kolev, Tristan Frum, Jason R. Spence, Jonathan Z. Sexton, Konstantinos D. Alysandratos, Darrell N. Kotton, Stefania Pittaluga, Jack Bibby, Nathalie Niyonzima, Matthew R. Olson, Shahram Kordasti, Didier Portilla, Christiane E. Wobus, Arian Laurence, Michail S Lionakis, Claudia Kemper, Behdad Afzali, Majid Kazemian
Software Mentions: 7
Published: over 3 years ago
10.3389/fgene.2021.641788
Successful ATAC-Seq From Snap-Frozen Equine TissuesCited by: 8
Author(s): Sichong Peng, Rebecca R. Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno
Software Mentions: 7
Published: over 3 years ago
10.1186/s12920-020-0695-0
Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brainCited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.pgen.1007784
Maternal and zygotic gene regulatory effects of endogenous RNAi pathwaysCited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: over 5 years ago
10.1186/s13059-017-1197-z
H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activityCited by: 66
Author(s): Yue Zhou, Francisco J. Romero–Campero, Ángeles Gómez-Zambrano, Franziska Turck, Myriam Calonje
Software Mentions: 7
Published: over 7 years ago
10.1186/1471-2105-16-S9-S2
Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysisCited by: 17
Author(s): Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
Software Mentions: 7
Published: over 9 years ago
10.1186/s13059-020-1948-0
Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibilityCited by: 42
Author(s): Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L. Johnson
Software Mentions: 7
Published: over 4 years ago
10.1186/s12864-017-3580-2
NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing dataCited by: 37
Author(s): Yevhen Vainshtein, Karsten Rippe, Vladimir B. Teif
Software Mentions: 7
Published: over 7 years ago
10.12688/f1000research.14880.4
SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysisCited by: 0
Author(s): Syed Hussain Ather, Olaitan I. Awe, Thomas J. Butler, Tamiru Denka, Stephen A. Semick, Wanhu Tang, Ben Busby
Software Mentions: 7
Published: about 4 years ago
10.1186/s12864-016-2963-0
iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip dataCited by: 2
Author(s): Chi Yang, Erik H. Andrews, Min-Hsuan Chen, Wanyu Wang, Jeremy J.W. Chen, Mark Gerstein, Chun-Chi Liu, Chao Cheng
Software Mentions: 6
Published: about 8 years ago
10.1016/j.molcel.2021.02.034
POINT technology illuminates the processing of polymerase-associated intact nascent transcriptsCited by: 44
Author(s): Rui Sousa-Luís, Geneviève Dujardin, Inna Zukher, Hiroshi Kimurâ, Carika Weldon, Maria Carmo‐Fonseca, Nick J. Proudfoot, Takayuki Nojima
Software Mentions: 6
Published: over 3 years ago
10.1186/s13072-021-00391-x
Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogasterCited by: 15
Author(s): Marat Sabirov, Olga Kyrchanova, Galina V. Pokholkova, Artem Bonchuk, Natalia Klimenko, Elena Belova, И. Ф. Жимулев, Oksana Maksimenko, Pavel Georgiev
Software Mentions: 6
Published: over 3 years ago
10.7554/eLife.65557
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in DrosophilaCited by: 24
Author(s): Evelyn L Eastwood, Kayla A Jara, Susanne Bornelöv, Marzia Munafò, Vasileios Frantzis, Emma Kneuss, Elisar Barbar, Benjamin Czech, Gregory J. Hannon
Software Mentions: 6
Published: almost 4 years ago
10.7554/eLife.57189
Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinomaCited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: about 4 years ago
10.1534/g3.120.401050
The <i>Gossypium longicalyx</i> Genome as a Resource for Cotton Breeding and EvolutionCited by: 29
Author(s): Corrinne E. Grover, Mengqiao Pan, Daojun Yuan, Mark A. Arick, Guanjing Hu, Logan Brase, David M. Stelly, Zefu Lu, Robert J. Schmitz, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall
Software Mentions: 6
Published: over 4 years ago
10.7554/eLife.20235
Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosisCited by: 4
Author(s): Christina Ernst, Jeremy Pike, Sarah J. Aitken, Hannah K. Long, Nils Eling, Lovorka Stojic, Michelle C. Ward, Frances Connor, Timothy F. Rayner, Margus Lukk, Robert J. Klose, Claudia Kutter, Duncan T. Odom
Software Mentions: 6
Published: almost 8 years ago
10.3390/genes10030231
H3K27me3 Depletion during Differentiation Promotes Myogenic Transcription in Porcine Satellite CellsCited by: 12
Author(s): Sheng Wang, Yan Sun, Ruimin Ren, Junhui Xie, Xiaohuan Tian, Shuhong Zhao, Xinyun Li, Jianhua Cao
Software Mentions: 6
Published: over 5 years ago
10.3389/fimmu.2021.651254
High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial CellsCited by: 5
Author(s): Kensei Kishimoto, Catera L. Wilder, Justin Buchanan, Minh Anh Nguyen, Chidera Okeke, Alexander Hoffmann, Quen J. Cheng
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pgen.1008250
Molecular dissection of the oncogenic role of ETS1 in the mesenchymal subtypes of head and neck squamous cell carcinomaCited by: 22
Author(s): Christian Gluck, Alexandra Ruth Glathar, Maria Tsompana, Norma J. Nowak, Lee Ann Garrett‐Sinha, Michael Buck, Satrajit Sinha
Software Mentions: 6
Published: over 5 years ago
10.1016/j.csbj.2021.07.010
Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genomeCited by: 3
Author(s): Márton Miskei, Adrienn Horváth, Lívia Viola, L. Varga, Éva Nagy, Orsolya Feró, Zsolt Karányi, Jason Roszik, Csaba Miskey, Zoltán Ivics, Lóránt Székvölgyi
Software Mentions: 6
Published: almost 4 years ago
10.3389/fmicb.2019.01408
Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6ACited by: 19
Author(s): Anthony J. Saviola, Cosima Zimmermann, Michael Mariani, Sylvia Signorelli, Diana L. Gerrard, Joseph R. Boyd, Darren J. Wight, Guillaume Morissette, Annie Gravel, Isabelle Dubuc, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 6
Published: over 5 years ago
10.7554/eLife.45672
Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determinationCited by: 27
Author(s): Lee Langer, James M. Ward, Trevor Archer
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pgen.1009338
Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinizationCited by: 15
Author(s): Margarita V. Brovkina, Rachel Duffié, Abbigayl E. C. Burtis, E. Josephine Clowney
Software Mentions: 6
Published: over 3 years ago
10.1038/s42003-018-0219-z
RELACS nuclei barcoding enables high-throughput ChIP-seqCited by: 27
Author(s): Laura Arrigoni, Hoor Al-Hasani, Fidel Ramírez, Ilaria Panzeri, Devon P. Ryan, Diana Santacruz, Nadia Kress, J. Andrew Pospisilik, Ulrike Bönisch, Thomas Manke
Software Mentions: 6
Published: almost 6 years ago
10.1128/mBio.01714-20
Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus <i>Verticillium</i>Cited by: 20
Author(s): Michael Seidl, Holger Kramer, David E. Cook, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Luigi Faino, B.P.H.J. Thomma
Software Mentions: 6
Published: about 4 years ago
10.1016/j.ajhg.2019.05.010
Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human LiverCited by: 33
Author(s): Minal Çalışkan, Elisabetta Manduchi, Harish Rao, Julian A. Segert, Márcia Holsbach Beltrame, Marco Trizzino, YoSon Park, Samuel White Baker, Alessandra Chesi, Matthew E. Johnson, Kenyaita M. Hodge, Michelle E. Leonard, Bao‐Li Loza, Xin Dong, Andrea M. Berrido, Nicholas J. Hand, Robert C. Bauer, Andrew D. Wells, Kim M. Olthoff, Abraham Shaked, Daniel J. Rader, Struan F.A. Grant, Christopher D. Brown
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-020-68879-2
Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteinsCited by: 2
Author(s): S. Yu. Funikov, Alexander P. Rezvykh, Д. А. Куликова, E. S. Zelentsova, Lyudmila A. Protsenko, Lyubov N. Chuvakova, Venera Tyukmaeva, Irina R. Arkhipova, Michael B. Evgen’ev
Software Mentions: 6
Published: over 4 years ago
10.1084/jem.20200829
The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell functionCited by: 80
Author(s): Christopher Mapperley, Louie Van De Lagemaat, Hannah Lawson, Andrea Tavosanis, J Paris, Joana Campos, David Wotherspoon, Jozef Durko, Annika Sarapuu, Joong-Seon Choe, Ivayla Ivanova, Daniela Krause, Alex von Kriegsheim, Christian Much, Marcos Morgan, Richard I. Gregory, Adam J. Mead, Dónal O’Carroll, Kamil R. Kranc
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pbio.3000378
Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cellsCited by: 33
Author(s): Yiqin Ma, Daniel J. McKay, Laura Buttitta
Software Mentions: 6
Published: about 5 years ago
10.3389/fcell.2021.583555
DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch TelencephalonCited by: 8
Author(s): Jolien Diddens, Louis Coussement, Carolina Frankl-Vilches, Gaurav Majumdar, Sandra Steyaert, Sita M. ter Haar, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Wim Van Criekinge, Charlotte Cornil, Jacques Balthazart, Annemie Van der Linden, Tim De Meyer, Wim Vanden Berghe
Software Mentions: 6
Published: over 3 years ago
10.3389/fcell.2021.723676
Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer PredispositionCited by: 5
Author(s): Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li, Jing Li, Jinjian Yang
Software Mentions: 6
Published: about 3 years ago
10.1371/journal.pone.0218458
p73 regulates epidermal wound healing and induced keratinocyte programmingCited by: 18
Author(s): J. Scott Beeler, Clayton B. Marshall, Paula I. González-Ericsson, Timothy M. Shaver, Gabriela L. Santos Guasch, Spencer Lea, Kimberly N. Johnson, Hailing Jin, Bryan J. Venters, Melinda E. Sanders, Jennifer A. Pietenpol
Software Mentions: 6
Published: over 5 years ago
10.1038/s41597-020-0458-y
Epigenomic profiling of neuroblastoma cell linesCited by: 23
Author(s): Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M. Kendsersky, Karina L. Conkrite, Robyn T. Sussman, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Paolo Fortina, Sharon J. Diskin, John M. Maris, Jo Lynne Rokita
Software Mentions: 6
Published: over 4 years ago
10.1186/s13045-021-01131-0
High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasisCited by: 16
Author(s): Bo Ren, Jinshou Yang, Yuming Wang, Gang Ye, Huanyu Wang, Chen Yuan, Ruiyuan Xu, Xu-Ning Fan, Lei You, Taiping Zhang, Yupei Zhao
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0157033
Pattern Recognition on Read Positioning in Next Generation SequencingCited by: 0
Author(s): Boseon Byeon, Igor Kovalchuk
Software Mentions: 6
Published: over 8 years ago
10.1002/1878-0261.12968
Phosphorylation of the androgen receptor at Ser81 is co‐sustained by CDK1 and CDK9 and leads to AR‐mediated transactivation in prostate cancerCited by: 14
Author(s): Xintao Gao, Jintai Liang, LiYang Wang, Zhaoyang Zhang, Peipei Yuan, Jiaxin Wang, Youhe Gao, Fen Ma, Carla Calagua, Huihui Ye, Olga Voznesensky, Shaogang Wang, Tao Wang, Jihong Liu, Shaoyong Chen, Xiaohui Liu
Software Mentions: 6
Published: over 3 years ago
10.1002/1878-0261.12954
The evolutionarily conserved long non‐coding RNA <i>LINC00261</i> drives neuroendocrine prostate cancer proliferation and metastasis <i>via</i> distinct nuclear and cytoplasmic mechanismsCited by: 21
Author(s): Rebecca Mather, Abhijit Parolia, Sandra E. Carson, Erik Venalainen, David Roig-Carles, Mustapha Jaber, Shih‐Chun Chu, Ilaria Alborelli, Rebecca Wu, Dong Lin, Noushin Nabavi, Elena Jachetti, Mario P. Colombo, Hui Xue, Perla Pucci, Xinpei Ci, Cheryl A. Hawkes, Yinglei Li, Hardev Pandha, Igor Ulitsky, Crystal N. Marconett, Luca Quagliata, Wei Jiang, Ignacio A. Romero, Yuzhuo Wang, Francesco Crea
Software Mentions: 6
Published: over 3 years ago
10.1186/s13072-017-0144-2
Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential functionCited by: 19
Author(s): Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein‐Hitpass, Anupam Sinha, Karl‐Heinz Jöckel, Markus M. Nöthen, Per Hoffmann, Markus M. Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
Software Mentions: 6
Published: over 7 years ago
10.1186/s13059-021-02339-6
Functional mapping of androgen receptor enhancer activityCited by: 15
Author(s): Chia Chi Flora Huang, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altıntaş, Mohammadali Saffarzadeh, Stéphane Le Bihan, Brian McConeghy, Bengul Gokbayrak, Felix Y. Feng, Martin Gleave, Andries M. Bergman, Colin C. Collins, Faraz Hach, Wilbert Zwart, Eldon Emberly, Nathan A. Lack
Software Mentions: 6
Published: over 3 years ago
10.1111/cgf.13727
Tasks, Techniques, and Tools for Genomic Data VisualizationCited by: 48
Author(s): Sabrina Nusrat, Theresa Harbig, Nils Gehlenborg
Software Mentions: 6
Published: over 5 years ago
10.1186/s13059-020-02190-1
DNA polymerase epsilon is required for heterochromatin maintenance in ArabidopsisCited by: 12
Author(s): Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed, Olivier Mathieu
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13059-020-02216-8
Histone modifications during the life cycle of the brown alga EctocarpusCited by: 21
Author(s): Simon Bourdareau, Leïla Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho, J. Mark Cock
Software Mentions: 6
Published: almost 4 years ago
10.3389/fgene.2021.664379
Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine TissuesCited by: 19
Author(s): Claire P. Prowse-Wilkins, Jianghui Wang, Ruidong Xiang, Josie B. Garner, Michael E. Goddard, Amanda J. Chamberlain
Software Mentions: 6
Published: over 3 years ago