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: over 5 years ago
1 dependent package
221 downloads last month
Papers Mentioning bowtie 1,566
10.1111/1751-7915.12757
Relative abundance of ‘ <i>Candidatus</i> Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode communityCited by: 25
Author(s): Anthony P. Malanoski, Baochuan Lin, Brian J. Eddie, Zheng Wang, W. Judson Hervey, Sarah M. Glaven
Software Mentions: 5
Published: almost 7 years ago
10.1016/j.stem.2019.03.017
Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive PluripotencyCited by: 78
Author(s): Tüzer Kalkan, Susanne Bornelöv, Carla Mulas, Evangelia Diamanti, Tim Lohoff, Markus Ralser, Sjors Middelkamp, Patrick Lombard, Jennifer Nichols, Austin Smith
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pcbi.1002887
Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced SignalingCited 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: over 11 years ago
10.1371/journal.pcbi.1006982
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experimentsCited 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: about 5 years ago
10.1186/s12862-019-1572-3
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fishCited by: 4
Author(s): Mauricio Losilla, David Luecke, Jason R. Gallant
Software Mentions: 5
Published: over 4 years ago
10.3389/fmicb.2020.587306
An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration SitesCited by: 4
Author(s): Nicolas Rosewick, Vincent Hahaut, Keith Durkin, Maria Artesi, Snehal D. Karpe, Jérôme Wayet, Philip Griebel, Natasa Arsic, Ambroise Marçais, Olivier Hermine, Arsène Burny, Michel Georges, Anne Van den Broeke
Software Mentions: 5
Published: over 3 years ago
10.1016/j.celrep.2021.109101
Chromatin accessibility governs the differential response of cancer and T cells to arginine starvationCited 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: about 3 years ago
10.1111/mec.13550
Bs<scp>RAD</scp>seq: screening <scp>DNA</scp> methylation in natural populations of non‐model speciesCited by: 95
Author(s): Emiliano Trucchi, Anna B. Mazzarella, Gregor D. Gilfillan, María Teresa Cáceres Lorenzo, Peter Schönswetter, Ovidiu Paun
Software Mentions: 5
Published: about 8 years ago
10.7554/eLife.32537
The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architectureCited by: 57
Author(s): Athma A. Pai, Telmo Henriques, Kayla McCue, Adam Burkholder, Karen Adelman, Christopher B. Burge
Software Mentions: 5
Published: over 6 years ago
10.1371/journal.pgen.1006639
The highly buffered Arabidopsis immune signaling network conceals the functions of its componentsCited by: 102
Author(s): Rachel Hillmer, Kazuhiko Tsuda, Ghanasyam Rallapalli, Shuji Asai, William Truman, Matthew D Papke, Hitoshi Sakakibara, Jonathan D. G. Jones, Chad L. Myers, Fumiaki Katagiri
Software Mentions: 5
Published: about 7 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 variantsCited 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: over 8 years ago
10.1093/bib/bbab055
RNA2HLA: HLA-based quality control of RNA-seq datasetsCited by: 9
Author(s): Irina Chelysheva, Andrew J. Pollard, Daniel O’Connor
Software Mentions: 5
Published: about 3 years ago
10.1016/j.cell.2021.03.062
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicingCited 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: almost 3 years ago
10.7554/eLife.02024
MOF-associated complexes ensure stem cell identity and Xist repressionCited 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: about 10 years ago
10.1534/g3.119.400770
Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree SeedlingsCited by: 10
Author(s): Luke Browne, Alayna Mead, Courtney Horn, Kevin W. Chang, Zeynep A Celikkol, Claudia L. Henriquez, Feiyang Ma, Eric Beraut, Rachel S. Meyer, Victoria L. Sork
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0105097
Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease ResistanceCited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: almost 10 years ago
10.1371/journal.pone.0151917
Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification PatternsCited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: about 8 years ago
10.3390/genes12010048
Probably Correct: Rescuing Repeats with Short and Long ReadsCited by: 3
Author(s): Monika Čechová
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0159093
Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal CortexCited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: almost 8 years ago
10.7554/eLife.63093
MITF reprograms the extracellular matrix and focal adhesion in melanomaCited 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: over 3 years ago
10.7554/eLife.23645
Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensationCited by: 27
Author(s): Sarah Elizabeth Albritton, Anna Lena Kranz, Lara Winterkorn, Lena Annika Street, Sevinç Ercan
Software Mentions: 5
Published: almost 7 years ago
10.1371/journal.pone.0184471
Genome-wide miRNA response to anacardic acid in breast cancer cellsCited 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: over 6 years ago
10.1371/journal.pone.0119027
Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss MutantCited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: about 9 years ago
10.7554/eLife.02200
Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanismsCited 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: almost 10 years ago
10.1371/journal.pbio.3000396
Inverted translational control of eukaryotic gene expression by ribosome collisionsCited by: 39
Author(s): Heungwon Park, Arvind R. Subramaniam
Software Mentions: 5
Published: over 4 years ago
10.1186/1756-0500-4-171
CloudAligner: A fast and full-featured MapReduce based tool for sequence mappingCited by: 101
Author(s): Tung Nguyen, Wei Shi, Douglas M. Ruden
Software Mentions: 5
Published: almost 13 years ago
10.3390/ijms22020678
JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory RegionsCited 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: over 3 years ago
10.18632/oncotarget.16493
ERK signalling modulates epigenome to drive epithelial to mesenchymal transitionCited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: about 7 years ago
10.18632/oncotarget.14091
The role of miR-17-92 in the miRegulatory landscape of Ewing sarcomaCited 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: over 7 years ago
10.18632/oncotarget.8192
Integrated analysis of long non-coding RNAs in human colorectal cancerCited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: about 8 years ago
10.1038/s41598-021-86919-3
Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesisCited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: about 3 years ago
10.12688/f1000research.6536.1
A reanalysis of mouse ENCODE comparative gene expression dataCited by: 90
Author(s): Yoav Gilad, Orna Mizrahi-Man
Software Mentions: 5
Published: about 9 years ago
10.1038/s41598-021-92448-w
Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemiaCited by: 8
Author(s): Amit Jaiswal, Hellen Truong, Tiffany Tran, Tasha Lin, David Casero, Michael O. Alberti, Dinesh S. Rao
Software Mentions: 5
Published: almost 3 years ago
10.1242/dev.146811
Epigenetic resetting of human pluripotencyCited 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: almost 7 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 ESCsCited 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: almost 3 years ago
10.12688/f1000research.21779.2
A role for MIR828 in pineapple fruit developmentCited by: 6
Author(s): Christopher D. Rock
Software Mentions: 5
Published: about 4 years ago
10.1038/s41598-018-19984-w
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stageCited by: 51
Author(s): Jun Wang, Zhu Jun, Yadong Zhang, Fangjun Fan, Wenqi Li, Fangquan Wang, Zhong WeiGong, Cailin Wang, Jie Yang
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-017-17408-9
Model-based genome-wide determination of RNA chain elongation rates in Escherichia coliCited by: 7
Author(s): Peter Großmann, Anja Lück, Christoph Kaleta
Software Mentions: 5
Published: over 6 years ago
10.3390/ijms17060956
Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological ProcessesCited by: 58
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 5
Published: almost 8 years ago
10.1038/s41598-021-81297-2
CROP: a CRISPR/Cas9 guide selection program based on mapping guide variantsCited by: 3
Author(s): Victor Aprilyanto, Redi Aditama, Zulfikar Achmad Tanjung, Condro Utomo, Tony Liwang
Software Mentions: 5
Published: over 3 years ago
10.1038/srep43793
Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genomeCited by: 24
Author(s): Guogui Ning, Cheng Xu, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Software Mentions: 5
Published: about 7 years ago
10.15252/embr.201846960
Nucleosome dynamics of human iPSC during neural differentiationCited by: 5
Author(s): Janet Harwood, Nicholas A. Kent, Nicholas Denby Allen, Adrian J. Harwood
Software Mentions: 5
Published: about 5 years ago
10.3389/fmicb.2017.00773
The 25–26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous GenesCited by: 28
Author(s): Jinbu Jia, Wenqin Lu, Chengcheng Zhong, Ran Zhou, Junjie Xu, Wei Liu, Xiuhong Gou, Qinhu Wang, Junliang Yin, Changwu Xu, Weixing Shan
Software Mentions: 5
Published: about 7 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 stressCited by: 13
Author(s): Nivedita, Abdul Rawoof, Nirala Ramchiary, M. Z. Abdin
Software Mentions: 5
Published: about 3 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 StressCited by: 32
Author(s): Zhaoyang Hu, Yufei Zhang, Yue Ping He, Qingqing Cao, Ting Zhang, Laiqing Lou, Qingqing Cai
Software Mentions: 5
Published: over 4 years ago
10.3389/fimmu.2018.02406
Molecular Signature of Aluminum Hydroxide Adjuvant in Ovine PBMCs by Integrated mRNA and microRNA Transcriptome SequencingCited by: 15
Author(s): Endika Varela-Martínez, Naiara Abendaño, Javier Asín, Maialen Sistiaga-Poveda, Marta Pérez, Ramsés Reina, D. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 5
Published: over 5 years ago
10.3389/fimmu.2020.02129
Transcriptome Profiling of Human Monocyte-Derived Macrophages Upon CCL2 Neutralization Reveals an Association Between Activation of Innate Immune Pathways and Restriction of HIV-1 Gene ExpressionCited by: 7
Author(s): Daniela Angela Covino, Karolina Elżbieta Kaczor‐Urbanowicz, Jing Lü, Maria Vincenza Chiantore, Gianna Fiorucci, Maria Fenicia Vescio, Laura Catapano, Cristina Purificato, Clementina Maria Galluzzo, Roberta Amici, Mauro Andreotti, Maria Cristina Gauzzi, Matteo Pellegrini, Laura Fantuzzi
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2017.00168
A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for ToxicogenomicsCited by: 44
Author(s): John S. House, Fabian A. Grimm, Dereje D. Jima, Yifeng Zhou, Ivan Rusyn, Fred A. Wright
Software Mentions: 5
Published: over 6 years ago
10.15252/embj.2020105776
Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotencyCited 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: about 3 years ago
10.3389/fgene.2021.695124
Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2Cited by: 1
Author(s): Lorenza Garribba, Ivan Vogel, Mads Lerdrup, Marisa M Gonçalves Dinis, Liqun Ren, Ying Liu
Software Mentions: 5
Published: almost 3 years ago
10.3390/ijms19092500
Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood MetabolitesCited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-021-88709-3
Regulatory role of non-coding RNA in ginseng rusty root symptom tissueCited by: 5
Author(s): Xingbo Bian, Pengcheng Yu, Ling Dong, Yan Zhao, Yang He, Yongzhong Han, Lianxue Zhang
Software Mentions: 4
Published: about 3 years ago
10.1038/s41598-021-92932-3
Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hensCited by: 6
Author(s): Muhammad Arsalan Iqbal, Asghar Ali, Frieder Hadlich, Michael Oster, Henry Reyer, Nares Trakooljul, Vera Sommerfeld, M. Rodehutscord, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: almost 3 years ago
10.3389/fcimb.2016.00193
Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureusCited by: 41
Author(s): Lingzhao Fang, Yali Hou, Jinpeng An, Bingjie Li, Mengyuan Song, Xiao Wang, Peter Sørensen, Yichun Dong, Chao Liu, Yachun Wang, Huabin Zhu, Shengli Zhang, Ying Yu
Software Mentions: 4
Published: over 7 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 DisorderCited 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: over 4 years ago
10.3390/ijms22010135
Circulating tRNA Fragments as a Novel Biomarker Class to Distinguish Acute Stroke SubtypesCited 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: over 3 years ago
10.1186/s13048-021-00802-3
Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growthCited by: 7
Author(s): Derek Toms, Bo Pan, Yinshan Bai, Julang Li
Software Mentions: 4
Published: about 3 years ago
10.18632/oncotarget.13169
Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA and lncRNA expression by ChIP sequencing and RNA sequencingCited by: 6
Author(s): Yuan Li, Mei Luo, Xuejiao Shi, Zhiliang Lu, Shengrong Sun, Jianbing Huang, Zhaoli Chen, Jié He
Software Mentions: 4
Published: over 7 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 sequencingCited by: 25
Author(s): Jun Zhou, Hongtao Chen, Yu Fan
Software Mentions: 4
Published: over 6 years ago
10.1128/JVI.00589-18
Transcriptional and Translational Landscape of Equine TorovirusCited by: 22
Author(s): Hazel Stewart, Katherine A. Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Software Mentions: 4
Published: over 5 years ago
10.3389/fgene.2021.662468
Hypoxia-Induced miR-148a Downregulation Contributes to Poor Survival in Colorectal CancerCited by: 15
Author(s): Stepan Nersisyan, A. V. Galatenko, Milena Chekova, Alexander G. Tonevitsky
Software Mentions: 4
Published: almost 3 years ago
10.15252/embj.201798133
Interplay of cell–cell contacts and RhoA/ <scp>MRTF</scp> ‐A signaling regulates cardiomyocyte identityCited by: 65
Author(s): Tatjana Dorn, Jessica Kornherr, Elvira Immacolata Parrotta, Dorota Zawada, Harold Ayetey, Gianluca Santamaria, Laura Iop, Elisa Mastantuono, Daniel Sinnecker, Alexander Goedel, Ralf J. Dirschinger, Ilaria My, Svenja Laue, Tarik Bozoglu, Christian Baarlink, Tilman Ziegler, Elisabeth Graf, Rabea Hinkel, Giovanni Cuda, Stefan Kääb, Andrew A. Grace, Robert Grosse, Christian Kupatt, Thomas Meitinger, Austin Smith, Karl‐Ludwig Laugwitz, Alessandra Moretti
Software Mentions: 4
Published: about 6 years ago
10.3389/fgene.2021.635794
Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic SystemCited by: 3
Author(s): Kevin Gley, Frieder Hadlich, Nares Trakooljul, Fiete Haack, Eduard Muráni, Ulrike Gimsa, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: almost 3 years ago
10.3389/fgene.2020.566948
Thermotolerance of tax-2 Is Uncoupled From Life Span Extension and Influenced by Temperature During Development in C. elegansCited by: 1
Author(s): Jiou Wang, Laura Dankovich, Jiou Wang
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2021.663736
MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis PatientsCited by: 8
Author(s): Fatima Heinicke, Xiao Zhong, Siri Tennebø Flåm, Johannes Breidenbach, Magnus Leithaug, Marthe Thoresen Mæhlen, Siri Lillegraven, Anna‐Birgitte Aga, Ellen Sauar Norli, Maria D Mjaavatten, Espen A. Haavardsholm, Manuela Zucknick, Simon Rayner, Benedicte A. Lie
Software Mentions: 4
Published: about 3 years ago
10.1002/embj.201386225
The long non-coding RNA Paupar regulates the expression of both local and distal genesCited by: 183
Author(s): Keith W. Vance, Stephen N. Sansom, Sheena Lee, Vladislava Chalei, Lesheng Kong, Sarah Cooper, Peter L. Oliver, Chris P. Ponting
Software Mentions: 4
Published: over 10 years ago
10.15252/embj.2020105564
Integrator is recruited to promoter‐proximally paused RNA Pol II to generate <i>Caenorhabditis elegans</i> piRNA precursorsCited by: 21
Author(s): Toni Beltran, Eleni Pahita, Subhanita Ghosh, Boris Lenhard, Peter Sarkies
Software Mentions: 4
Published: over 3 years ago
10.1093/database/bau076
APADB: a database for alternative polyadenylation and microRNA regulation eventsCited by: 88
Author(s): Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter
Software Mentions: 4
Published: almost 10 years ago
10.1038/srep17901
Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome AnalysisCited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: over 8 years ago
10.1038/srep25866
Hot spots of DNA double-strand breaks in human rDNA units are produced in vivoCited 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: about 8 years ago
10.1038/srep38439
RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machineryCited by: 40
Author(s): Siim Sõber, Kristiina Rull, Mario Reiman, Piret Ilisson, Pirkko Mattila, Maris Laan
Software Mentions: 4
Published: over 7 years ago
10.1038/srep38820
Acfs: accurate circRNA identification and quantification from RNA-Seq dataCited by: 67
Author(s): Xintian You, Tim Conrad
Software Mentions: 4
Published: over 7 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 mammalCited by: 37
Author(s): Jane Khudyakov, Cory D. Champagne, Lorenzo Meneghetti, Daniel E. Crocker
Software Mentions: 4
Published: over 7 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 MG1655Cited 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: about 7 years ago
10.1038/s41598-017-07100-3
Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcriptionCited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: almost 7 years ago
10.1186/s13072-017-0153-1
Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin stateCited by: 25
Author(s): Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
Software Mentions: 4
Published: over 6 years ago
10.1186/s13072-015-0040-6
RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationshipsCited by: 127
Author(s): Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, N. Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey A. Jeddeloh, Cristina Montagna, Aaron Golden, Cathal Seoighe, John M. Greally
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-018-36912-0
DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patientsCited 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: over 5 years ago
10.12688/f1000research.15604.1
Androgen-dependent alternative mRNA isoform expression in prostate cancer cellsCited by: 14
Author(s): Jennifer Munkley, Teresa Maia, Jesús Ibarluzea, Karen E. Livermore, Daniel Vodák, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa‐Morais, David Elliott
Software Mentions: 4
Published: almost 6 years ago
10.1038/s41598-019-39395-9
Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophagesCited by: 24
Author(s): Cheng Wang, Luca Nanni, Boris Novakovic, Wout Megchelenbrink, Т. Н. Кузнецова, Hendrik G. Stunnenberg, Stefano Ceri, Colin Logie
Software Mentions: 4
Published: about 5 years ago
10.1038/s41598-019-40127-2
Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesisCited by: 7
Author(s): Elisavet Kaitetzidou, Ioanna Katsiadaki, Jacques Lagnel, Efthimia Antonopoulou, Elena Sarropoulou
Software Mentions: 4
Published: about 5 years ago
10.1242/dev.139857
Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fateCited by: 41
Author(s): Nadine Obier, Pierre Cauchy, Salam A. Assi, Jane Gilmour, Michael Lie-A-Ling, Monika Lichtinger, Maarten Hoogenkamp, Laura Noailles, Peter N. Cockerill, Georges Lacaud, Valérie Kouskoff, Constanze Bonifer
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 chickenCited 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: over 4 years ago
10.1038/s41598-019-48283-1
De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genesCited by: 9
Author(s): Tessa M. Page, Carmel McDougall, Guillermo Díaz-Pulido
Software Mentions: 4
Published: over 4 years ago
10.1038/s41598-020-79436-2
Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrimaCited by: 12
Author(s): David J. Quispe-Parra, Joshua G. Medina-Feliciano, Sebastián Cruz-González, Humberto Ortíz-Zuazaga, José E. García‐Arrarás
Software Mentions: 4
Published: over 3 years ago
10.7554/eLife.15477
Increasing Notch signaling antagonizes PRC2-mediated silencing to promote reprograming of germ cells into neuronsCited by: 31
Author(s): Stefanie Seelk, Irene Adrian‐Kalchhauser, Balázs Hargitai, Martina Hajdůšková, Silvia Gutnik, Baris Tursun, Rafal Ciosk
Software Mentions: 4
Published: over 7 years ago
10.7554/eLife.35551
Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespanCited by: 54
Author(s): Zheng Hu, Bo Xia, Spike D. L. Postnikoff, Zih Jie Shen, Alin Tomoiaga, Troy A. A. Harkness, Ja Hwan Seol, Wei Li, Kaifu Chen, Jessica K. Tyler
Software Mentions: 4
Published: almost 6 years ago
10.7554/eLife.19893
The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation statusCited by: 16
Author(s): Dongming Li, Ana Marie S. Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A. Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon H. Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A. Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen, Julie A. Law
Software Mentions: 4
Published: about 7 years ago
10.7554/eLife.47891
Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylationCited by: 54
Author(s): Jered M. Wendte, Yinwen Zhang, Lexiang Ji, Xiulin Shi, Rashmi R. Hazarika, Yadollah Shahryary, Frank Johannes, Robert J. Schmitz
Software Mentions: 4
Published: almost 5 years ago
10.7554/eLife.25607
lncRNA requirements for mouse acute myeloid leukemia and normal differentiationCited by: 47
Author(s): M. Joaquina Delás, Leah R. Sabin, Egor Dolzhenko, Simon Knott, Ester Munera Maravilla, Benjamin T. Jackson, Sophia A Wild, Tatjana Kovačević, Eva Maria Stork, Meng Zhou, Nicolas Erard, Emily Lee, David R. Kelley, Mareike Roth, Inês Barbosa, Johannes Zuber, John L. Rinn, Andrew D. Smith, Gregory J. Hannon
Software Mentions: 4
Published: over 6 years ago
10.1128/mSystems.00284-18
Systems-Level Analysis of Oxygen Exposure in <i>Zymomonas mobilis</i> : Implications for Isoprenoid ProductionCited by: 22
Author(s): Julia Martien, Alexander S. Hebert, David Stevenson, Matthew Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador‐Noguez
Software Mentions: 4
Published: about 5 years ago
10.7717/peerj.5089
Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced lociCited by: 31
Author(s): Bruno A. S. de Medeiros, Brian D. Farrell
Software Mentions: 4
Published: almost 6 years ago
10.1128/mSystems.00980-20
Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel RelationshipsCited by: 22
Author(s): Kumari Sonal Choudhary, Julia A. Kleinmanns, Katherine Decker, Anand V. Sastry, Ye Gao, Richard Szubin, Yara Seif, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 3 years ago
10.1002/pld3.241
Control of translation during the unfolded protein response in maize seedlings: Life without PERKsCited by: 9
Author(s): Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell
Software Mentions: 4
Published: almost 4 years ago
10.1128/mBio.02262-18
Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 RoleCited by: 13
Author(s): Jolene R. Bowers, Michael Valentine, Veronica Harrison, Viacheslav Y. Fofanov, John D. Gillece, Josie Delisle, Bethany K. Patton, James M. Schupp, Krystal Sheridan, Darrin Lemmer, Scott Ostdiek, Harlori K. Bains, Jennifer Heim, Tammy Sylvester, Siru Prasai, Melissa Kretschmer, Nicole Fowle, Kenneth Komatsu, Shane Brady, Susan Robinson, Kathryn Fitzpatrick, Gholamabbas Amin Ostovar, Eric Alsop, Elizabeth Hutchins, Kendall Jensen, Paul Keim, David M. Engelthaler
Software Mentions: 4
Published: about 5 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 domesticationCited 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: about 8 years ago
10.1371/journal.ppat.1009644
Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infectionCited 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: almost 3 years ago
10.1007/s13238-017-0480-9
TDP-43 regulates cancer-associated microRNAsCited 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: over 6 years ago
10.1186/s12870-019-2193-0
Variation in plastid genomes in the gynodioecious species Silene vulgarisCited by: 7
Author(s): Manuela Krüger, Oushadee A. J. Abeyawardana, Miloslav Juříček, Claudia Krüger, Helena Štorchová
Software Mentions: 4
Published: over 4 years ago
10.1186/1471-2105-14-326
snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencingCited by: 6
Author(s): Ali Al‐Shahib, Anthony Underwood
Software Mentions: 4
Published: over 10 years ago