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: bowtie

https://packages.ecosyste.ms/registries/pypi.org/packages/bowtie

Interactive Dashboard Toolkit.
43 versions
Latest release: about 6 years ago
1 dependent package
221 downloads last month

Papers Mentioning bowtie 1,566

10.1002/1878-0261.12853
Genome‐scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib‐resistant lung cancer
Cited by: 10
Author(s): Jieun Lee, Ahyoung Choi, Sung Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, Charles Lee
Software Mentions: 5
Published: almost 4 years ago
10.1186/s12864-015-2246-1
High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: almost 9 years ago
10.7554/eLife.32537
The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture
Cited by: 57
Author(s): Athma A. Pai, Telmo Henriques, Kayla McCue, Adam Burkholder, Karen Adelman, Christopher B. Burge
Software Mentions: 5
Published: almost 7 years ago
10.1111/mec.13550
Bs<scp>RAD</scp>seq: screening <scp>DNA</scp> methylation in natural populations of non‐model species
Cited by: 95
Author(s): Emiliano Trucchi, Anna B. Mazzarella, Gregor D. Gilfillan, María Teresa Cáceres Lorenzo, Peter Schönswetter, Ovidiu Paun
Software Mentions: 5
Published: over 8 years ago
10.1016/j.molcel.2018.09.033
Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: about 6 years ago
10.7554/eLife.02024
MOF-associated complexes ensure stem cell identity and Xist repression
Cited by: 73
Author(s): Tomasz Chelmicki, Friederike Dündar, Matthew James Turley, Tasneem Khanam, Tuğçe Aktaş, Fidel Ramírez, Anne-Valérie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke, Asifa Akhtar
Software Mentions: 5
Published: over 10 years ago
10.1242/dev.146811
Epigenetic resetting of human pluripotency
Cited by: 210
Author(s): Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel A. Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith
Software Mentions: 5
Published: over 7 years ago
10.15252/embj.2020105776
Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency
Cited by: 22
Author(s): Andreas Lackner, Robert Sehlke, Marius Garmhausen, Giuliano Giuseppe Stirparo, Michelle Huth, Fabian Titz-Teixeira, Petra van der Lelij, Julia Ramesmayer, Henry F. Thomas, Markus Ralser, Laura Santini, Elena Galimberti, Mihail Sarov, A. Francis Stewart, Austin Smith, Andreas Beyer, Martin Leeb
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.23645
Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation
Cited by: 27
Author(s): Sarah Elizabeth Albritton, Anna Lena Kranz, Lara Winterkorn, Lena Annika Street, Sevinç Ercan
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pcbi.1002887
Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: almost 12 years ago
10.7554/eLife.02200
Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms
Cited by: 206
Author(s): Mary A. Allen, Zdeněk Andrysík, Veronica L. Dengler, Hestia Mellert, Anna L. Guarnieri, John H. Freeman, Kelly D. Sullivan, Matthew D. Galbraith, Xin Luo, W. Lee Kraus, Robin D. Dowell, Joaquín M. Espinosa
Software Mentions: 5
Published: over 10 years ago
10.1371/journal.pcbi.1006982
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Cited by: 83
Author(s): Ivan Jurić, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Maowen Hu
Software Mentions: 5
Published: over 5 years ago
10.1186/s12862-019-1572-3
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish
Cited by: 4
Author(s): Mauricio Losilla, David Luecke, Jason R. Gallant
Software Mentions: 5
Published: almost 5 years ago
10.1016/j.celrep.2021.109101
Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.04530
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation
Cited by: 142
Author(s): Vladislava Chalei, Stephen N. Sansom, Lesheng Kong, Sheena Lee, Juan Montiel, Keith W. Vance, Chris P. Ponting
Software Mentions: 5
Published: about 10 years ago
10.1155/2021/8880585
Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: over 3 years ago
10.1084/jem.20171738
A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: almost 7 years ago
10.7554/eLife.58305
Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila
Cited by: 38
Author(s): Robin E. Harris, Michael J. Stinchfield, Spencer L. Nystrom, Daniel J. McKay, Iswar K. Hariharan
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-021-92448-w
Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemia
Cited by: 8
Author(s): Amit Jaiswal, Hellen Truong, Tiffany Tran, Tasha Lin, David Casero, Michael O. Alberti, Dinesh S. Rao
Software Mentions: 5
Published: over 3 years ago
10.1016/j.cell.2021.03.062
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-021-93297-3
Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0105097
Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance
Cited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: over 10 years ago
10.1371/journal.pone.0151917
Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns
Cited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: over 8 years ago
10.1371/journal.pone.0159093
Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: over 8 years ago
10.1038/s41598-021-86919-3
Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0184471
Genome-wide miRNA response to anacardic acid in breast cancer cells
Cited by: 14
Author(s): David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine Waigel, Carolyn M. Klinge
Software Mentions: 5
Published: about 7 years ago
10.1371/journal.pone.0119027
Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: over 9 years ago
10.1038/s41598-021-81297-2
CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
Cited by: 3
Author(s): Victor Aprilyanto, Redi Aditama, Zulfikar Achmad Tanjung, Condro Utomo, Tony Liwang
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pbio.3000396
Inverted translational control of eukaryotic gene expression by ribosome collisions
Cited by: 39
Author(s): Heungwon Park, Arvind R. Subramaniam
Software Mentions: 5
Published: about 5 years ago
10.1038/s41598-021-82136-0
A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Cited by: 13
Author(s): Nivedita, Abdul Rawoof, Nirala Ramchiary, M. Z. Abdin
Software Mentions: 5
Published: almost 4 years ago
10.7554/eLife.63093
MITF reprograms the extracellular matrix and focal adhesion in melanoma
Cited by: 42
Author(s): Ramile Dilshat, Valerie Fock, Colin Kenny, Ilse Gerritsen, Romain Lasseur, Jana Trávníčková, Ossia M. Eichhoff, Philipp Cerny, Katrín Möller, Sara Sigurbjörnsdóttir, Kritika Kirty, Berglind O. Einarsdottir, Phil F. Cheng, Mitchell P. Levesque, Robert A. Cornell, E. Elizabeth Patton, Lionel Larue, Marie de Tayrac, Erna Magnúsdóttir, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 5
Published: almost 4 years ago
10.1093/gigascience/giz145
Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples
Cited by: 31
Author(s): Hong Zheng, Kevin Brennan, Mikel Hernáez, Olivier Gevaert
Software Mentions: 5
Published: almost 5 years ago
10.18632/oncotarget.16493
ERK signalling modulates epigenome to drive epithelial to mesenchymal transition
Cited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: over 7 years ago
10.1186/s13059-017-1310-3
Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation
Cited by: 26
Author(s): Kevin Van Bortle, Douglas H. Phanstiel, M Snyder
Software Mentions: 5
Published: about 7 years ago
10.18632/oncotarget.14091
The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma
Cited by: 13
Author(s): Raphaela Schwentner, David Herrero-Martín, Maximilian Kauer, Cornelia Mutz, Anna M. Katschnig, Grzegorz Sienski, Javier Alonso, Dave N.T. Aryee, Heinrich Kovar
Software Mentions: 5
Published: almost 8 years ago
10.1186/s13059-015-0856-1
Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
Cited by: 85
Author(s): Stephan Busche, Xiaojian Shao, Maxime Caron, Tony Kwan, Fiona Allum, Warren A. Cheung, Bing Ge, Susan Westfall, Simon Maguire, Amy Barrett, Jordana T. Bell, Mark I. McCarthy, Panos Deloukas, Mathieu Blanchette, Guillaume Bourque, Timothy D. Spector, Mark Lathrop, Tomi Pastinen, Elin Grundberg
Software Mentions: 5
Published: almost 9 years ago
10.1186/gm377
Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
Cited by: 47
Author(s): Pär G. Engström, Diva Tommei, Stefan H. Stricker, Christine Ender, Steven M. Pollard, Paul Bertone
Software Mentions: 5
Published: almost 13 years ago
10.1371/journal.ppat.1009217
EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape
Cited by: 14
Author(s): Nathan Ungerleider, Whitney Bullard, Mehmet Kara, Xia Wang, Claire Roberts, Rolf Renne, Scott A. Tibbetts, Erik K. Flemington
Software Mentions: 5
Published: over 3 years ago
10.18632/oncotarget.8192
Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: over 8 years ago
10.3390/ijms22020678
JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions
Cited by: 15
Author(s): Tara Procida, Tobias Friedrich, Antonia Jack, Martina Peritore, Clemens Bönisch, H. Christian Eberl, Nadine Daus, Konstantin Kletenkov, Andrea Nist, Thorsten Stiewe, Tilman Borggrefe, Matthias Mann, Marek Bartkuhn, Sandra B. Hake
Software Mentions: 5
Published: almost 4 years ago
10.1186/s13059-019-1857-2
eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5′UTR
Cited by: 34
Author(s): Ania Wilczynska, Sarah L. Gillen, Tobias Schmidt, Hedda A. Meijer, Rebekah Jukes-Jones, Claudia Langlais, Kari Kopra, Wei-Ting Lu, Jack D. Godfrey, Ben R Hawley, Kelly Hodge, Sara Zanivan, Kelvin Cain, John Le Quesne, Martin Bushell
Software Mentions: 5
Published: almost 5 years ago
10.3390/ijms21031067
Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress
Cited by: 32
Author(s): Zhaoyang Hu, Yufei Zhang, Yue Ping He, Qingqing Cao, Ting Zhang, Laiqing Lou, Qingqing Cai
Software Mentions: 5
Published: almost 5 years ago
10.1186/s13059-019-1721-4
Chromatin accessibility plays a key role in selective targeting of Hox proteins
Cited by: 35
Author(s): Damiano Porcelli, Bettina Fischer, Steven Russell, Robert A. White
Software Mentions: 5
Published: over 5 years ago
10.3390/ijms17060956
Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes
Cited by: 58
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 5
Published: over 8 years ago
10.1186/s13059-021-02263-9
Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs
Cited by: 62
Author(s): Yang Zhang, Tuan M. Nguyen, Xiao‐Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy, Pier Paolo Pandolfi
Software Mentions: 5
Published: almost 4 years ago
10.1186/s13059-021-02464-2
Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: about 3 years ago
10.1186/s13059-021-02494-w
Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization
Cited by: 12
Author(s): Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell, Ania Wilczynska
Software Mentions: 5
Published: about 3 years ago
10.1186/s13059-015-0840-9
A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
Cited by: 126
Author(s): Xiaomin Bao, Adam J. Rubin, Kun Qu, Jiajing Zhang, Paul G. Giresi, Howard Y. Chang, Paul A. Khavari
Software Mentions: 5
Published: almost 9 years ago
10.1186/s13059-017-1302-3
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Cited by: 127
Author(s): Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey, James Whelan
Software Mentions: 5
Published: about 7 years ago
10.1093/gbe/evz150
Evolution of Phototransduction Genes in Lepidoptera
Cited by: 26
Author(s): Aide Macias-Muñoz, Aline G. Rangel Olguin, Adriana D. Briscoe
Software Mentions: 5
Published: over 5 years ago
10.1186/s13059-016-0882-7
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
Cited by: 50
Author(s): Brandon C. Sos, Ho-Lim Fung, Derek Gao, Trina Osothprarop, Amirali Kia, M.M. He, Kun Zhang
Software Mentions: 4
Published: almost 9 years ago
10.1186/s13059-015-0746-6
Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.ppat.1008984
Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
Cited by: 13
Author(s): Nicola F. Müller, Daniel Wüthrich, Nina Goldman, Nadine Sailer, Claudia Saalfrank, Myrta Brunner, Noémi Augustin, Helena M. B. Seth-Smith, Yvonne Hollenstein, Mohammedyaseen Syedbasha, Daniela Lang, Richard A. Neher, Olivier Dubuis, Michael Naegele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Brian M. Lang, James Hadfield, Trevor Bedford, Manuel Battegay, Rita Schneider-Sliwa, Adrian Egli, Tanja Stadler
Software Mentions: 4
Published: about 4 years ago
10.3390/ijms20236040
Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 5 years ago
10.1093/gbe/evaa094
piRNA and Transposon Dynamics in Drosophila: A Female Story
Cited by: 17
Author(s): Bastien Saint-Leandre, Pierre Capy, Aurélie Hua-Van, Jonathan Filée
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-015-0742-x
Extensive identification and analysis of conserved small ORFs in animals
Cited by: 162
Author(s): Sebastian D. Mackowiak, Henrik Zauber, Chris Bielow, Denise Thiel, Kamila Kutz, Lorenzo Calviello, Guido Mastrobuoni, Nikolaus Rajewsky, Stefan Kempa, Matthias Selbach, Benedikt Obermayer
Software Mentions: 4
Published: about 9 years ago
10.18632/oncotarget.13169
Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA and lncRNA expression by ChIP sequencing and RNA sequencing
Cited by: 6
Author(s): Yuan Li, Mei Luo, Xuejiao Shi, Zhiliang Lu, Shengrong Sun, Jianbing Huang, Zhaoli Chen, Jié He
Software Mentions: 4
Published: about 8 years ago
10.18632/oncotarget.22130
Systematic analysis of the expression profile of non-coding RNAs involved in ischemia/reperfusion-induced acute kidney injury in mice using RNA sequencing
Cited by: 25
Author(s): Jun Zhou, Hongtao Chen, Yu Fan
Software Mentions: 4
Published: about 7 years ago
10.3390/ijms19092500
Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: about 6 years ago
10.1186/s13059-021-02390-3
Transcription shapes DNA replication initiation to preserve genome integrity
Cited by: 17
Author(s): Yang Liu, Chen Ai, Tingting Gan, Jinchun Wu, Yongpeng Jiang, Xuhao Liu, Ru-Sen Lu, Ning Gao, Qing Li, Ji Xiong, Jiazhi Hu
Software Mentions: 4
Published: over 3 years ago
10.3390/ijms22010135
Circulating tRNA Fragments as a Novel Biomarker Class to Distinguish Acute Stroke Subtypes
Cited by: 13
Author(s): Thủy Nguyễn, M. Leontien van der Bent, Marieke J.H. Wermer, Ido R. van den Wijngaard, Erik W. van Zwet, Bas de Groot, Paul H.A. Quax, Nyika D. Kruyt, A. Yaël Nossent
Software Mentions: 4
Published: almost 4 years ago
10.1074/jbc.RA120.015896
YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: almost 4 years ago
10.1007/s13238-017-0480-9
TDP-43 regulates cancer-associated microRNAs
Cited by: 28
Author(s): Xiaowei Chen, Zhen Fan, W Ambrose McGee, Mengmeng Chen, Ruirui Kong, Pushuai Wen, Tengfei Xiao, Xiaomin Chen, Jianghong Liu, Li Zhu, Runsheng Chen, Jane Y. Wu
Software Mentions: 4
Published: about 7 years ago
10.1371/journal.ppat.1009644
Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection
Cited by: 46
Author(s): Liliana Echavarría-Consuegra, G. M. W. Cook, Idoia Busnadiego, Charlotte Lefèvre, Sarah Keep, Katherine A. Brown, Nicole Doyle, Giulia Dowgier, Krzysztof Franaszek, Nathan Moore, Stuart G. Siddell, Erica Bickerton, Benjamin G. Hale, Andrew E. Firth, Ian Brierley, Nerea Irigoyen
Software Mentions: 4
Published: over 3 years ago
10.1186/s12284-018-0211-8
Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses
Cited by: 27
Author(s): Lei Tian, Shaohua Shi, Fahad Nasir, Chunguang Chang, Weiqiang Li, Lam‐Son Phan Tran, Chunjie Tian
Software Mentions: 4
Published: over 6 years ago
10.1186/s13048-021-00802-3
Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth
Cited by: 7
Author(s): Derek Toms, Bo Pan, Yinshan Bai, Julang Li
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.ppat.1006302
Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Cited by: 87
Author(s): Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M. Barros, J. G. Baldwin, A Mortazavi, Adler R. Dillman
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.ppat.1009208
A multi-omics approach to Epstein-Barr virus immortalization of B-cells reveals EBNA1 chromatin pioneering activities targeting nucleotide metabolism
Cited by: 20
Author(s): Jason Lamontagne, Samantha S. Soldan, Chenhe Su, Andreas Wiedmer, Kyoung Jae Won, Fang Lü, Aaron R. Goldman, Jayamanna Wickramasinghe, Hsin‐Yao Tang, David W. Speicher, Louise C. Showe, Andrew V. Kossenkov, Paul M. Lieberman
Software Mentions: 4
Published: almost 4 years ago
10.1128/JVI.00589-18
Transcriptional and Translational Landscape of Equine Torovirus
Cited by: 22
Author(s): Hazel Stewart, Katherine A. Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Software Mentions: 4
Published: about 6 years ago
10.1038/s41598-017-02110-7
Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 7 years ago
10.1038/s41598-017-07100-3
Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription
Cited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: over 7 years ago
10.1038/srep38439
RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery
Cited by: 40
Author(s): Siim Sõber, Kristiina Rull, Mario Reiman, Piret Ilisson, Pirkko Mattila, Maris Laan
Software Mentions: 4
Published: almost 8 years ago
10.1038/srep25866
Hot spots of DNA double-strand breaks in human rDNA units are produced in vivo
Cited by: 16
Author(s): Nickolai A. Tchurikov, Dmitry V. Yudkin, М. А. Горбачева, Anastasia I. Kulemzina, I. V. Grischenko, Д. М. Федосеева, D. V. Sosin, Yuri V. Kravatsky, О. В. Кретова
Software Mentions: 4
Published: over 8 years ago
10.1038/srep38820
Acfs: accurate circRNA identification and quantification from RNA-Seq data
Cited by: 67
Author(s): Xintian You, Tim Conrad
Software Mentions: 4
Published: almost 8 years ago
10.1002/pld3.241
Control of translation during the unfolded protein response in maize seedlings: Life without PERKs
Cited by: 9
Author(s): Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell
Software Mentions: 4
Published: over 4 years ago
10.1038/srep17901
Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis
Cited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: almost 9 years ago
10.1038/srep42110
Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal
Cited by: 37
Author(s): Jane Khudyakov, Cory D. Champagne, Lorenzo Meneghetti, Daniel E. Crocker
Software Mentions: 4
Published: almost 8 years ago
10.1186/gb-2014-15-4-r57
Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: almost 11 years ago
10.1186/gb-2013-14-11-r131
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: almost 12 years ago
10.1186/s13059-014-0410-6
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 10 years ago
10.1186/s12870-019-2193-0
Variation in plastid genomes in the gynodioecious species Silene vulgaris
Cited by: 7
Author(s): Manuela Krüger, Oushadee A. J. Abeyawardana, Miloslav Juříček, Claudia Krüger, Helena Štorchová
Software Mentions: 4
Published: almost 5 years ago
10.1186/1471-2105-14-326
snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing
Cited by: 6
Author(s): Ali Al‐Shahib, Anthony Underwood
Software Mentions: 4
Published: about 11 years ago
10.1186/gb-2011-12-8-r76
The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Cited by: 110
Author(s): Thomas Sandmann, Matthias Christian Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer
Software Mentions: 4
Published: almost 14 years ago
10.1371/journal.pone.0242516
The small RNA locus map for Chlamydomonas reinhardtii
Cited by: 4
Author(s): Sebastian Müller, Nicholas E. Matthews, Adrián Vallí, David C. Baulcombe
Software Mentions: 4
Published: about 4 years ago
10.1186/gb-2014-15-2-r32
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: almost 11 years ago
10.1111/tpj.15250
The chemical compound ‘Heatin’ stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1‐subfamily of nitrilases
Cited by: 7
Author(s): Lennard van der Woude, Markus Piotrowski, Gruson Klaasse, Judith K Paulus, Daniel Krahn, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Ondřej Novák, Karin Ljung, Suzanne Bulder, Marcel van Verk, L. Basten Snoek, Martijn Fiers, Nathaniel I. Martin, R.A.L. van der Hoorn, Stéphanie Robert, Sjef Smeekens, Martijn van Zanten
Software Mentions: 4
Published: over 3 years ago
10.7717/peerj.2056
SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals
Cited by: 9
Author(s): Yevgeny Nikolaichik, Aliaksandr U. Damienikan
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pone.0187542
Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome
Cited by: 10
Author(s): Anette McLeod, Ellen Færgestad Mosleth, Ida Rud, Filipe Branco dos Santos, Lars-Gustav Snipen, Kristian Hovde Liland, Lars Axelsson
Software Mentions: 4
Published: about 7 years ago
10.1038/s41598-018-36912-0
DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients
Cited by: 10
Author(s): Alessandro Corti, Raina Sota, Matteo Dugo, Raffaele Calogero, Benedetta Terragni, Massimo Mantegazza, Silvana Franceschetti, Michela Restelli, Patrizia Gasparini, Daniele Lecis, Krystyna Chrzanowska, Domenico Delia
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-018-4783-x
The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum
Cited by: 27
Author(s): Chuanlin Yin, Meizhen Li, Jian Hu, Kun Lang, Qiming Chen, Jinding Liu, Dan Guo, Kang He, Yipei Dong, Jiapeng Luo, Zhenkun Song, James R. Walters, Wenqing Zhang, Fĕi Li, Xue-Xin Chen
Software Mentions: 4
Published: over 6 years ago
10.1534/g3.118.200789
Dynamic Interactions Between the Genome and an Endogenous Retrovirus: <i>Tirant</i> in <i>Drosophila simulans</i> Wild-Type Strains
Cited by: 4
Author(s): Marie Fablet, Angelo Jacquet, Rita Rebollo, Annabelle Haudry, Colette Rey, Judit Salces-Ortiz, Prajakta Bajad, Nelly Burlet, Michael F. Jantsch, Maria Pilar García Guerreiro, Cristina Vieira
Software Mentions: 4
Published: over 5 years ago
10.1186/s12870-015-0632-0
Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet
Cited by: 10
Author(s): Fei Yi, Jian Chen, Jingjuan Yu
Software Mentions: 4
Published: about 9 years ago
10.1186/s12870-016-0788-2
Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication
Cited by: 33
Author(s): Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jingzhong Xie, Shan Gao
Software Mentions: 4
Published: over 8 years ago
10.1186/1471-2164-14-S1-S9
Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 12 years ago
10.3390/genes8020068
Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
Cited by: 34
Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
Software Mentions: 4
Published: almost 8 years ago
10.1534/g3.114.013508
<i>De Novo</i> Assembly and Annotation of the Transcriptome of the Agricultural Weed <i>Ipomoea purpurea</i> Uncovers Gene Expression Changes Associated with Herbicide Resistance
Cited by: 41
Author(s): Trent A Leslie, Regina S. Baucom
Software Mentions: 4
Published: about 10 years ago
10.3390/pathogens8040183
Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0238546
MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: about 4 years ago
10.3389/fpls.2020.01003
The MADS-Box Gene MdDAM1 Controls Growth Cessation and Bud Dormancy in Apple
Cited by: 33
Author(s): Mirko Moser, Elisa Asquini, Giulia Valentina Miolli, Kathleen Weigl, Magda‐Viola Hanke, Henryk Flachowsky, Azeddine Si‐Ammour
Software Mentions: 4
Published: over 4 years ago
10.7717/peerj.5089
Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci
Cited by: 31
Author(s): Bruno A. S. de Medeiros, Brian D. Farrell
Software Mentions: 4
Published: over 6 years ago