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

10.1371/journal.pone.0091418
Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses
Cited by: 19
Author(s): Woncheoul Park, Jaemin Kim, Yang Soo Kim, Jae-Young Choi, Jeong-Woong Park, Hyun-Woo Cho, Byeong-Woo Kim, Myung Hum Park, Teak-Soon Shin, Seong-Keun Cho, Jun-Kyu Park, Heebal Kim, Jin-Hee Hwang, Chang Kyu Lee, Hak-Kyo Lee, Seoae Cho, Byung-Wook Cho
Software Mentions: 2
Published: over 10 years ago
10.1093/database/bax074
Echinobase: an expanding resource for echinoderm genomic information
Cited by: 60
Author(s): Parul Kudtarkar, R. Andrew Cameron
Software Mentions: 2
Published: almost 8 years ago
10.1016/j.ydbio.2012.03.024
The transcriptional programme controlled by Runx1 during early embryonic blood development
Cited by: 41
Author(s): Yosuke Tanaka, Anagha Joshi, Nicola K. Wilson, Sarah Kinston, Shin‐Ichi Nishikawa, Berthold Göttgens
Software Mentions: 2
Published: over 12 years ago
10.1242/dev.136051
microRNA deep sequencing in two adult stem cell populations identifies miR-501 as novel regulator of myosin heavy chain during muscle regeneration
Cited by: 15
Author(s): Amir Mizbani, Edlira Luca, Elisabeth J. Rushing, Jan Krützfeldt
Software Mentions: 2
Published: almost 9 years ago
10.3390/diagnostics10090701
Sepsis Diagnostics: Intensive Care Scoring Systems Superior to MicroRNA Biomarker Testing
Cited by: 1
Author(s): Fabian Link, Knut Krohn, Anna-Maria Burgdorff, Annett Christel, Julia Schümann
Software Mentions: 2
Published: about 4 years ago
10.1038/emboj.2013.177
Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor
Cited by: 192
Author(s): Graziano Martello, Paul Bertone, Austin Smith
Software Mentions: 2
Published: over 11 years ago
10.15252/embj.201695323
<scp>GT</scp> ‐rich promoters can drive <scp>RNA</scp> pol <scp>II</scp> transcription and deposition of H2A.Z in African trypanosomes
Cited by: 65
Author(s): Carolin Wedel, Konrad U. Förstner, Ramona Derr, T. Nicolai Siegel
Software Mentions: 2
Published: over 7 years ago
10.15252/embj.201592532
Sororin actively maintains sister chromatid cohesion
Cited by: 84
Author(s): René Ladurner, Emanuel Kreidl, Miroslav P Ivanov, Heinz Ekker, Maria Helena Idarraga-Amado, Georg A. Busslinger, Gordana Wutz, David A. Cisneros, Jan‐Michael Peters
Software Mentions: 2
Published: over 8 years ago
10.15252/embj.2020107455
<i>HASTY</i> , the <i>Arabidopsis EXPORTIN5</i> ortholog, regulates cell‐to‐cell and vascular microRNA movement
Cited by: 27
Author(s): Florian Brioudes, Florence Jay, Alexis Sarazin, Thomas Grentzinger, Emanuel A. Devers, Olivier Voinnet
Software Mentions: 2
Published: over 3 years ago
10.15252/embr.201947789
Dynamic expression of tRNA‐derived small RNAs define cellular states
Cited by: 89
Author(s): Srikar Krishna, Daniel Yim, Vairavan Lakshmanan, Varsha Tirumalai, Judice L.Y. Koh, Jung Eun Park, Jit Kong Cheong, Joo-Leng Low, Michelle Gek Liang Lim, Siu Kwan Sze, P. V. Shivaprasad, Akash Gulyani, Srikala Raghavan, Dasaradhi Palakodeti, Ramanuj DasGupta
Software Mentions: 2
Published: over 5 years ago
10.1080/22221751.2019.1637702
Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles
Cited by: 59
Author(s): Yuki Matsumoto, Takeshi Kinjo, Daisuke Motooka, Daijiro Nabeya, Nicolas Jung, Kohei Uechi, Toshihiro Horii, Tetsuya Iida, Jiro Fujita, Shota Nakamura
Software Mentions: 2
Published: almost 6 years ago
10.1186/1756-8935-8-8
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements
Cited by: 57
Author(s): Matthew S. Wilken, Joseph A. Brzezinski, Anna La Torre, Kyle Siebenthall, Robert E. Thurman, Peter J. Sabo, Richard Sandstrom, Jeff Vierstra, Theresa K. Canfield, R. Scott Hansen, Michael A. Bender, J Stamatoyannopoulos, Thomas A. Reh
Software Mentions: 2
Published: over 9 years ago
10.1186/s13072-019-0290-9
Hyperinsulinemia promotes aberrant histone acetylation in triple-negative breast cancer
Cited by: 21
Author(s): Parijat Senapati, Hiroyuki Kato, Michael Lee, Amy Leung, Christine Thai, Angelica Sanchez, Emily J. Gallagher, Derek LeRoith, Victoria L. Seewaldt, David K. Ann, Dustin E. Schones
Software Mentions: 2
Published: over 5 years ago
10.1186/s13072-019-0313-6
Chromatin accessibility and transcription dynamics during in vitro astrocyte differentiation of Huntington’s Disease Monkey pluripotent stem cells
Cited by: 7
Author(s): Alexandra V. Goodnight, Isaac Kremsky, Sujittra Khampang, Younghun Jung, James M. Billingsley, Steven E. Bosinger, Victor G. Corcés, Anthony W.S. Chan
Software Mentions: 2
Published: about 5 years ago
10.1038/ejhg.2014.281
Huntington’s disease biomarker progression profile identified by transcriptome sequencing in peripheral blood
Cited by: 69
Author(s): Anastasios Mastrokolias, Yavuz Ariyürek, Jelle J. Goeman, Erik van Duijn, Raymund A.C. Roos, Roos C. van der Mast, Gert‐Jan B. van Ommen, Johan T. den Dunnen, Peter A C ‘t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 2
Published: almost 10 years ago
10.1002/evl3.71
Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments
Cited by: 33
Author(s): Andreas Härer, Axel Meyer, Julián Torres‐Dowdall
Software Mentions: 2
Published: over 6 years ago
10.1038/s12276-019-0267-6
IRF1 is critical for the TNF-driven interferon response in rheumatoid fibroblast-like synoviocytes
Cited by: 39
Author(s): Michael Bonelli, K Dalwigk, Alexander Platzer, Isabel Olmos Calvo, Silvia Hayer, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Thomas Pap, Günter Steiner, Giulio Superti‐Furga, Josef S Smolen, Hans P. Kiener, Thomas Karonitsch
Software Mentions: 2
Published: over 5 years ago
10.1096/fj.201801638R
NF‐κB p65 dimerization and DNA‐binding is important for inflammatory gene expression
Cited by: 26
Author(s): Tabea Riedlinger, Robert Liefke, Johanna Meier-Soelch, Liane Jurida, Andrea Nist, Thorsten Stiewe, Michael Kracht, M. Lienhard Schmitz
Software Mentions: 2
Published: almost 6 years ago
10.1002/2211-5463.12377
Micro RNA profiling during directed differentiation of cortical interneurons from human‐induced pluripotent stem cells
Cited by: 9
Author(s): Jiajie Tu, Dandan Cao, Li Lü, Hoi‐Hung Cheung, Wai‐Yee Chan
Software Mentions: 2
Published: almost 7 years ago
10.3389/fnbeh.2015.00255
Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps
Cited by: 7
Author(s): Joke J.F.A. van Vugt, Katja M. Hoedjes, H.C. van de Geest, Elio W. G. M. Schijlen, Louise E. M. Vet, Hans M. Smid
Software Mentions: 2
Published: about 9 years ago
10.3389/fcell.2020.568116
Systematic Analysis of tRNA-Derived Small RNAs Discloses New Therapeutic Targets of Caloric Restriction in Myocardial Ischemic Rats
Cited by: 17
Author(s): Wenjing Liu, Yang Liu, Zhaohai Pan, Xin Zhang, Yao Jun Qin, Xiaojie Chen, Minjing Li, Xiaoyu Chen, Qiusheng Zheng, Xiaona Liu, Defang Li
Software Mentions: 2
Published: about 4 years ago
10.3389/fcimb.2020.625576
Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium
Cited by: 12
Author(s): Sara Tomaiuolo, Samira Boarbi, Tiziano Fancello, Patrick P. Michel, Damien Desqueper, Fabien Grégoire, Jozefien Callens, David Frétin, Bert Devriendt, Eric Cox, Marcella Mori
Software Mentions: 2
Published: over 3 years ago
10.3389/fcimb.2021.673966
In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum
Cited by: 4
Author(s): Yanwei Qi, Yuhong Zhang, Guixing Zheng, Bingxia Chen, Mengxin Zhang, Jian Li, Tao Peng, Jun Huang, Xinhua Wang
Software Mentions: 2
Published: over 3 years ago
10.3389/fcimb.2021.555072
Microbiota Detection Patterns Correlate With Presence and Severity of Barrett’s Esophagus
Cited by: 4
Author(s): Ikenna Okereke, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Clark R. Andersen, Richard B. Pyles
Software Mentions: 2
Published: over 3 years ago
10.3389/fcimb.2019.00123
Genomic and Epidemiological Evidence of a Dominant Panton-Valentine Leucocidin-Positive Methicillin Resistant Staphylococcus aureus Lineage in Sri Lanka and Presence Among Isolates From the United Kingdom and Australia
Cited by: 8
Author(s): Sharla M. McTavish, Sarah J Snow, Ellie C Cook, Bruno Pichon, Sarah Coleman, Geoffrey W. Coombs, Stanley Pang, César A. Arias, Lorena Díaz, Emma Boldock, Sue Davies, M. Udukala, Angela Kearns, Sisira Siribaddana, Thushan I. de Silva
Software Mentions: 2
Published: over 5 years ago
10.3389/fncel.2017.00003
Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors
Cited by: 17
Author(s): Nikolina Jovancevic, Kirsten A. Wunderlich, Claudia Haering, Caroline Flegel, Désirée Maßberg, Markus Weinrich, Lea Weber, Lars Tebbe, Anselm Kampik, Günter Gisselmann, Uwe Wolfrum, Hanns Hatt, Lian Gelis
Software Mentions: 2
Published: almost 8 years ago
10.3389/fncel.2017.00348
Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
Cited by: 7
Author(s): Nikolay Aseyev, Aliya Vinarskaya, Matvey Roshchin, Tatiana Korshunova, Aleksey Malyshev, Alena B. Zuzina, Victor N. Ierusalimsky, M. S. Lemak, И. С. Захаров, Novikov Ia, P. M. Kolosov, Е. А. Чеснокова, С. А. Волкова, Artem S. Kasianov, Л. А. Урошлев, Yekaterina Popova, Richard D. Boyle, P. M. Balaban
Software Mentions: 2
Published: about 7 years ago
10.3389/fendo.2018.00611
Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome
Cited by: 5
Author(s): Candice M. Lavelle, L. Cody Smith, Joseph H. Bisesi, Fahong Yu, Cecilia Silva-Sanchez, David Moraga-Amador, A. Buerger, Natàlia García-Reyero, Tara Sabo‐Attwood, Nancy D. Denslow
Software Mentions: 2
Published: about 6 years ago
10.3389/fendo.2019.00739
Circulating miRNA Expression Profiling in Primary Aldosteronism
Cited by: 20
Author(s): Ábel Decmann, G Nyírő, Ottó Darvasi, Péter István Turai, Irina Bancos, Ravinder Kaur, Raffaele Pezzani, Maurizio Iacobone, Ivana Kraljević, Darko Kaštelan, Mirko Parasiliti-Caprino, Mauro Maccario, Nina Nirschl, Daniel A. Heinrich, Martín Reincke, Attila Patócs, Péter Igaz
Software Mentions: 2
Published: about 5 years ago
10.3389/fgene.2019.00531
RNA-Seq Revealed Novel Non-proliferative Retinopathy Specific Circulating MiRNAs in T2DM Patients
Cited by: 24
Author(s): Zimeng Li, Ying Dong, Chang He, Xingchen Pan, Dianyuan Liu, Jianli Yang, Liankun Sun, Peng Chen, Qing Wang
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2019.00296
Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice
Cited by: 7
Author(s): Hao Zhang, Sifei Liu, Haowu Chang, Mengping Zhan, Qing‐Ming Qin, Borui Zhang, Zhi Li, Yuanning Liu
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2021.634635
Research on the Mechanism of Soybean Resistance to Phytophthora Infection Using Machine Learning Methods
Cited by: 5
Author(s): Junxia Chi, Shizeng Song, Hao Zhang, Yuanning Liu, Hengyi Zhao, Liyan Dong
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2021.660366
UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction
Cited by: 4
Author(s): Maria Tsagiopoulou, Μαρία Μανιού, Nikolaos Pechlivanis, Anastasis Togkousidis, Michaela Kotrová, Tobias Hutzenlaub, Ilias Kappas, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.00375
Identifying Candida albicans Gene Networks Involved in Pathogenicity
Cited by: 4
Author(s): Graham H. Thomas, Judith M. Bain, Susan Budge, Alistair J. P. Brown, Ryan M. Ames
Software Mentions: 2
Published: over 4 years ago
10.3389/fgene.2021.602528
Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication
Cited by: 10
Author(s): Xiaolei Yu, Wenxiu Wang, Hongxia Yang, Xiaoying Zhang, Dan Wang, Xiaoxuan Tian
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2019.01183
Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep
Cited by: 25
Author(s): Deyin Zhang, Xiaoxue Zhang, Fadi Li, Chong Li, Yongfu La, Futao Mo, Guoze Li, Yukun Zhang, Xiaolong Li, Qizhi Song, Yuan Zhao, Weimin Wang
Software Mentions: 2
Published: about 5 years ago
10.3389/fgene.2019.00957
Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes
Cited by: 7
Author(s): Jiarong Guo, John F. Quensen, Yanni Sun, Qiong Wang, C. Titus Brown, James R. Cole, James M. Tiedje
Software Mentions: 2
Published: about 5 years ago
10.3389/fgene.2021.695178
Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation
Cited by: 0
Author(s): Basharat Ahmad Bhat, Nazir Ahmad Ganai, Ashutosh Singh, Rakeeb Ahmad Mir, Syed Mudasir Ahmad, Sajad Majeed Zargar, Firdose Ahmad Malik
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2019.00105
Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5′ and 3′ End Small RNAs
Cited by: 14
Author(s): Xiao Xu, Haishuo Ji, Xiufeng Jin, Zhi Cheng, Xuemei Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Shan Gao
Software Mentions: 2
Published: almost 6 years ago
10.3389/fimmu.2020.00027
Computational Prediction and Validation of Tumor-Associated Neoantigens
Cited by: 72
Author(s): Vladimir Roudko, Benjamin Greenbaum, Nina Bhardwaj
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2017.00126
Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs
Cited by: 5
Author(s): Ling‐Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jianhua Yang, Zhao‐Rong Lun, Liang‐Hu Qu
Software Mentions: 2
Published: almost 8 years ago
10.3389/fmicb.2021.683481
Bacteriomic Analyses of Asian Citrus Psyllid and Citrus Samples Infected With “Candidatus Liberibacter asiaticus” in Southern California and Huanglongbing Management Implications
Cited by: 4
Author(s): Jiaquan Huang, Zhigang Dai, Zheng Zhang, Priscila A da Silvia, Lucita Kumagai, Qijun Xiang, Jianchi Chen, Xiaoling Deng
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-016-0915-2
CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
Cited by: 64
Author(s): Florian Heigwer, Tianzuo Zhan, Marco Breinig, J. Winter, Dirk Brügemann, Svenja Leible, Michael Boutros
Software Mentions: 2
Published: over 8 years ago
10.1186/s13059-016-1032-y
Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation
Cited by: 108
Author(s): Kaushik Panda, Lexiang Ji, Drexel A. Neumann, Josquin Daron, Robert J. Schmitz, R. Keith Slotkin
Software Mentions: 2
Published: over 8 years ago
10.1186/s13059-017-1291-2
Conservation and divergence of small RNA pathways and microRNAs in land plants
Cited by: 76
Author(s): Chenjiang You, Jie Cui, Hui Wang, Xun Qi, Li Chung Kuo, Hong Mā, Lei Gao, Beixin Mo, Xuemei Chen
Software Mentions: 2
Published: about 7 years ago
10.1186/s13059-017-1345-5
Functional assessment of human enhancer activities using whole-genome STARR-sequencing
Cited by: 85
Author(s): Yuwen Liu, Shan Yu, Vineet K. Dhiman, Tonya M. Brunetti, Heather Eckart, Kevin P. White
Software Mentions: 2
Published: about 7 years ago
10.1186/s13059-018-1499-9
Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture
Cited by: 59
Author(s): Xavier Grau‐Bové, Iñaki Ruiz‐Trillo, Manuel Irimia
Software Mentions: 2
Published: about 6 years ago
10.1186/s13059-019-1621-7
Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens
Cited by: 34
Author(s): Jean‐Philippe Fortin, Jenille Tan, Karen E. Gascoigne, Peter M. Haverty, William F. Forrest, Michael R. Costa, Scott E. Martin
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13059-019-1724-1
Genomics and data science: an application within an umbrella
Cited by: 42
Author(s): Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson, Mark Gerstein
Software Mentions: 2
Published: over 5 years ago
10.1186/s13059-019-1722-3
Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana
Cited by: 25
Author(s): Stefan Grob, Ueli Grossniklaus
Software Mentions: 2
Published: over 5 years ago
10.1186/s13059-020-02043-x
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data
Cited by: 68
Author(s): Liqing Tian, Yongjin Li, Michael N. Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael Rusch, John Easton, Jing Ma, Eric M. Davis, Austyn Trull, J. Robert Michael, Karol Szlachta, Charles G. Mullighan, Suzanne J. Baker, James R. Downing, David W. Ellison, Jinghui Zhang
Software Mentions: 2
Published: over 4 years ago
10.1186/s13059-020-02173-2
Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens
Cited by: 54
Author(s): Merve Dede, Megan McLaughlin, Eiru Kim, Traver Hart
Software Mentions: 2
Published: about 4 years ago
10.1186/s13059-020-02246-2
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development
Cited by: 14
Author(s): Guillermo E. Parada, Roberto Munita, Ilias Georgakopoulos-Soares, Hugo J. R. Fernandes, Veronika R. Kedlian, Emmanouil Metzakopian, Marı́a Estela Andrés, Eric A. Miska, Martin Hemberg
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13059-021-02319-w
Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
Cited by: 3
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: over 3 years ago
10.1093/gbe/evu142
Sequence-Level Mechanisms of Human Epigenome Evolution
Cited by: 17
Author(s): James Prendergast, Emily Chambers, Colin A. Semple
Software Mentions: 2
Published: over 10 years ago
10.1093/gbe/evz092
Ancient Polyploidy and Genome Evolution in Palms
Cited by: 24
Author(s): Craig F. Barrett, Michael R. McKain, Brandon T. Sinn, Xue Jun Ge, Yu‐Qu Zhang, Alexandre Antonelli, Christine D. Bacon
Software Mentions: 2
Published: over 5 years ago
10.1186/2047-217X-3-1
CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy
Cited by: 67
Author(s): Saskia Hiltemann, Hailiang Mei, Mattias de Hollander, Ivo Palli, Peter van der Spek, Guido Jenster, Andrew Stubbs
Software Mentions: 2
Published: almost 11 years ago
10.1093/gigascience/gix135
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation
Cited by: 40
Author(s): Jason R. Miller, Sergey Koren, Kari A. Dilley, Vinita Puri, David Brown, Derek M. Harkins, Françoise Thibaud‐Nissen, Benjamin D. Rosen, Xiaoguang Chen, Zhijian Tu, Igor V. Sharakhov, Maria V. Sharakhova, Robert Sebra, Timothy B. Stockwell, Nicholas H. Bergman, Granger Sutton, Adam M. Phillippy, Peter M. Piermarini, Reed S. Shabman
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41438-021-00542-x
Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome
Cited by: 65
Author(s): Pengjie Wang, Jiaxin Yu, Shan Jin, Shuai Chen, Chuan Yue, Wenling Wang, Shuilian Gao, Hongli Cao, Yuanrun Zheng, Mengya Gu, Xuejin Chen, Yun Sun, Yuqiong Guo, Jing Yang, Xingtan Zhang, Naixing Ye
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-017-0012-z
Histological, hormonal and transcriptomic reveal the changes upon gibberellin-induced parthenocarpy in pear fruit
Cited by: 72
Author(s): Lulu Liu, Zhigang Wang, Jianlong Liu, Fengxia Liu, Rui Zhai, Chunqin Zhu, Huibin Wang, Fengwang Ma, Lingfei Xu
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41438-021-00474-6
Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass
Cited by: 23
Author(s): Pei-Rong Li, Tongbing Su, Deshuang Zhang, Weihong Wang, Xiaoyun Xin, Yangjun Yu, Xiuyun Zhao
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-020-0336-y
Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds
Cited by: 38
Author(s): Hong Zhu, Pao‐Yang Chen, Silin Zhong, Chris Dardick, Ann M. Callahan, Yong-Qiang An, Steve van Knocker, Yingzhen Yang, Gan-Yuan Zhong, Albert G. Abbott, Zongrang Liu
Software Mentions: 2
Published: over 4 years ago
10.1186/s40104-018-0269-6
The dynamics of the piglet gut microbiome during the weaning transition in association with health and nutrition
Cited by: 139
Author(s): Robin B. Guevarra, Sang Hyun Hong, Jin Ho Cho, Bo Ra Kim, Jiwon Shin, Jun Hyung Lee, Bong Jin Kang, Young Hwa Kim, Suphot Wattanaphansak, Richard E. Isaacson, Min Ho Song, Hyeun Bum Kim
Software Mentions: 2
Published: over 6 years ago
10.1093/jxb/erx111
Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars
Cited by: 106
Author(s): Satendra K. Mangrauthia, Sailaja Bhogireddy, Shubhi Agarwal, V. Vishnu Prasanth, S. R. Voleti, Sarla Neelamraju, D. Subrahmanyam
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.ppat.1004609
Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1
Cited by: 77
Author(s): Luis Apolonia, Reiner Schulz, Tomaž Curk, Paula Rocha, Chad M. Swanson, Torsten Schaller, Jernej Ule, Michael H. Malim
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.ppat.1004744
Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk
Cited by: 122
Author(s): Sebastian Schulz, Denitsa Eckweiler, Agata Bielecka, Tanja Nicolai, Raimo Franke, Andreas Dötsch, Klaus Hornischer, Sebastian Bruchmann, Juliane Düvel, Susanne Häußler
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.ppat.1005473
High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling
Cited by: 179
Author(s): Nerea Irigoyen, Andrew E. Firth, Joshua D. Jones, Betty Y.-W. Chung, Stuart G. Siddell, Ian Brierley
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.ppat.1005640
Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum
Cited by: 71
Author(s): Sonia Campo, Kerrigan B. Gilbert, James C. Carrington
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.ppat.1006080
Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning
Cited by: 17
Author(s): Elisabeth Silberhorn, Uwe Schwartz, Patrick Löffler, Samuel Schmitz, Anne Symelka, Tania F. de Koning-Ward, Rainer Merkl, Gernot Längst
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.ppat.1006708
Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas
Cited by: 15
Author(s): Sanandan Malhotra, Shelby Winans, Grace Kee See Lam, James Justice, Robin Morgan, Karen Beemon
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.ppat.1007644
Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector
Cited by: 24
Author(s): James Phelan, Arthur B. Kern, Meghan E. Ramsey, Maureen E. Lundt, Bijaya Sharma, Tao Lin, Lihui Gao, Steven J. Norris, Jenny A. Hyde, Jon T. Skare, Linden T. Hu
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.ppat.1008566
Tn-Seq reveals hidden complexity in the utilization of host-derived glutathione in Francisella tularensis
Cited by: 14
Author(s): Kathryn M. Ramsey, Hannah E. Ledvina, Tenayaann M. Tresko, Jamie M. Wandzilak, Catherine A. Tower, Thomas Tallo, Caroline E. Schramm, S. Brook Peterson, Shawn J. Skerrett, Joseph D. Mougous, Simon L. Dove
Software Mentions: 2
Published: over 4 years ago
10.1016/j.pneurobio.2020.101903
Uncovering memory-related gene expression in contextual fear conditioning using ribosome profiling
Cited by: 5
Author(s): Konstanze Simbriger, Inês S. Amorim, Gilliard Lach, Kleanthi Chalkiadaki, Stella Kouloulia, Seyed Mehdi Jafarnejad, Arkady Khoutorsky, Christos G. Gkogkas
Software Mentions: 2
Published: almost 4 years ago
10.1007/s13238-017-0475-6
Correction of β-thalassemia mutant by base editor in human embryos
Cited by: 164
Author(s): Puping Liang, Chenhui Ding, Hongwei Sun, Xiaowei Xie, Yanwen Xu, Xiya Zhang, Yu Sun, Yuanyan Xiong, Wenbin Ma, Yongxiang Liu, Yali Wang, Jian-Pei Fang, Dan Liú, Zhou Songyang, Canquan Zhou, Junjiu Huang
Software Mentions: 2
Published: about 7 years ago
10.1007/s13238-020-00754-2
Tumor-derived neomorphic mutations in ASXL1 impairs the BAP1-ASXL1-FOXK1/K2 transcription network
Cited by: 14
Author(s): Yukun Xia, Yirong Zeng, Mengli Zhang, Peng Liu, Fang Liu, Hao Zhang, Chenxi He, Yiping Sun, Jinye Zhang, Cheng Zhang, Lei Song, Ding Chen, Yujie Tang, Zhen Yang, Chen Yang, Pu Wang, Kun‐Liang Guan, Yue Xiong, Dan Ye
Software Mentions: 2
Published: over 4 years ago
10.1080/15476286.2018.1514236
Evaluation of methodologies for microRNA biomarker detection by next generation sequencing.
Cited by: 44
Author(s): Anna M.L. Coenen-Stass, Iddo Magen, Tony Brooks, Iddo Z. Ben‐Dov, Linda Greensmith, Eran Hornstein, Pietro Fratta
Software Mentions: 2
Published: about 6 years ago
10.1080/15476286.2019.1667741
Systematic assessment of commercially available low-input miRNA library preparation kits
Cited by: 26
Author(s): Fatima Heinicke, Xiao Zhong, Manuela Zucknick, Johannes Breidenbach, Arvind Sundaram, Siri Tennebø Flåm, Magnus Leithaug, Marianne Dalland, Andrew Farmer, Jordana M. Henderson, Melanie Hussong, Pamela Renate Moll, Lan Nguyễn, Amanda McNulty, James Shaffer, Sabrina Shore, Hoichong Karen Yip, Jana Vitkovska, Simon Rayner, Benedicte A. Lie, Gregor D. Gilfillan
Software Mentions: 2
Published: about 5 years ago
10.1016/j.redox.2019.101397
Effects of diets high in animal or plant protein on oxidative stress in individuals with type 2 diabetes: A randomized clinical trial
Cited by: 20
Author(s): Olga Pivovarova-Ramich, Mariya Markova, Daniela Weber, Stephanie Sucher, Silke Hornemann, Natalia Rudovich, Jens Raila, Daniele Yumi Sunaga-Franze, Sascha Sauer, Sascha Rohn, Andreas F. H. Pfeiffer, Tilman Grune
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12931-017-0576-z
Genome-wide DNA methylation analysis in lung fibroblasts co-cultured with silica-exposed alveolar macrophages
Cited by: 17
Author(s): Juan Li, Wu Yao, Lin Zhang, Lei Bao, Huiting Chen, Di Wang, Zhongzheng Yue, Yiping Li, Miao Zhang, Changfu Hao
Software Mentions: 2
Published: over 7 years ago
10.1186/s12931-017-0708-5
GM-CSF overexpression after influenza a virus infection prevents mortality and moderates M1-like airway monocyte/macrophage polarization
Cited by: 56
Author(s): E. Scott Halstead, Todd M. Umstead, Michael L. Davies, Yuka Imamura Kawasawa, Patricia Silveyra, Judie Howyrlak, Linlin Yang, Weichao Guo, Sanmei Hu, Eranda Kurundu Hewage, Zissis C. Chroneos
Software Mentions: 2
Published: almost 7 years ago
10.1186/s12977-014-0132-6
Endogenous CCL2 neutralization restricts HIV-1 replication in primary human macrophages by inhibiting viral DNA accumulation
Cited by: 29
Author(s): Michela Sabbatucci, Daniela Angela Covino, Cristina Purificato, Alessandra Mallano, Maurizio Federico, Jing Lü, Arturo Rinaldi, Matteo Pellegrini, Roberta Bona, Zuleika Michelini, Andrea Cara, Stefano Vella, Sandra Gessani, Mauro Andreotti, Laura Fantuzzi
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12977-018-0394-5
Ribosome profiling of the retrovirus murine leukemia virus
Cited by: 15
Author(s): Nerea Irigoyen, Adam M. Dinan, Ian Brierley, Andrew E. Firth
Software Mentions: 2
Published: almost 7 years ago
10.1186/s12284-014-0020-7
Differentially-expressed genes in rice infected by Xanthomonas oryzae pv. oryzae relative to a flagellin-deficient mutant reveal potential functions of flagellin in host–pathogen interactions
Cited by: 17
Author(s): Chao Yu, Huamin Chen, Tian Fang, Jan E. Leach, Chenyang He
Software Mentions: 2
Published: about 10 years ago
10.1038/srep05559
Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process
Cited by: 55
Author(s): Oliver Smith, A. R. Clapham, Pam Rose, Yuan Liu, Jun Wang, Robin G. Allaby
Software Mentions: 2
Published: over 10 years ago
10.1038/srep11953
Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs
Cited by: 91
Author(s): Jing Lü, Ye Hou, Hui Wu, Yuanxin Miao, Xinyun Li, Jianhua Cao, John M. Brameld, Tim Parr, Zhao Song
Software Mentions: 2
Published: over 9 years ago
10.1038/srep19943
GRHL2-miR-200-ZEB1 maintains the epithelial status of ovarian cancer through transcriptional regulation and histone modification
Cited by: 115
Author(s): Vin Yee Chung, Tuan Zea Tan, Ming Tan, Ming Keong Wong, Kuee Theng Kuay, Zhe Yang, Jieru Ye, Julius Müller, Cheryl M. Koh, Ernesto Guccione, Jean Paul Thiery, Ruby Yun‐Ju Huang
Software Mentions: 2
Published: almost 9 years ago
10.1038/srep21635
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling
Cited by: 20
Author(s): Hadas Zur, Ranen Aviner, Tamir Tuller
Software Mentions: 2
Published: over 8 years ago
10.1038/srep25039
Characterization of piRNAs across postnatal development in mouse brain
Cited by: 34
Author(s): Yanal Ghosheh, Loqmane Seridi, Tae Woo Ryu, Hazuki Takahashi, Valerio Orlando, Piero Carninci, Timothy Ravasi
Software Mentions: 2
Published: over 8 years ago
10.1038/srep38531
FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines
Cited by: 105
Author(s): Joshua I. Warrick, Vonn Walter, Haruo Yamashita, Eunah Chung, Lauren Shuman, Vasty Osei Amponsa, Zongyu Zheng, Wilson Chan, Tiffany Whitcomb, Feng Yue, Tejaswi Iyyanki, Yuka Imamura Kawasawa, Matthew Kaag, Wansong Guo, Jay D. Raman, Joo Seop Park, David J. DeGraff
Software Mentions: 2
Published: almost 8 years ago
10.1038/srep41114
Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes
Cited by: 55
Author(s): Olga Petrova, Fernando García-Alcalde, Claudia Zampaloni, Karin Sauer
Software Mentions: 2
Published: almost 8 years ago
10.1038/srep46107
Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana)
Cited by: 6
Author(s): Hansheng Zhao, Huayu Sun, Lichao Li, Yonggen Lou, Rongsheng Li, Lin Qi, Zhimin Gao
Software Mentions: 2
Published: over 7 years ago
10.1038/srep08248
Whole-genome sequencing reveals that mutations in myosin-5 confer resistance to the fungicide phenamacril in Fusarium graminearum
Cited by: 58
Author(s): Zong‐Ping Zheng, Yiping Hou, Yiqiang Cai, Yu Zhang, Yanjun Li, Mingguo Zhou
Software Mentions: 2
Published: almost 10 years ago
10.1038/srep08753
Transcriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production
Cited by: 25
Author(s): Yoshihiko Onda, Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Roger S. Seymour, Yui Umekawa, Stergios Pirintsos, Kazuo Shinozaki, Kikukatsu Ito
Software Mentions: 2
Published: over 9 years ago
10.1038/s41598-017-00150-7
Reciprocal regulation of γ-globin expression by exo-miRNAs: Relevance to γ-globin silencing in β-thalassemia major
Cited by: 14
Author(s): Kuo‐Ting Sun, Yu-Nan Huang, Kalaiselvi Palanisamy, Shih‐Sheng Chang, I‐Kuan Wang, Kang‐Hsi Wu, Ping Chen, Ching‐Tien Peng, Chi Yuan Li
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-03083-3
Comparative morphology and transcriptome analysis reveals distinct functions of the primary and secondary laticifer cells in the rubber tree
Cited by: 16
Author(s): Tan D, Xiaowen Hu, Lili Fu, Anuwat Kumpeangkeaw, Zehong Ding, Xiaoyan Sun, Jiaming Zhang
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-03487-1
Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome
Cited by: 30
Author(s): Eugeni Belda, Boubacar Coulibaly, Abdrahamane Fofana, Abdoul Habib Béavogui, Sékou F. Traorè, Daryl M. Gohl, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-06939-w
Circulating microRNA profiles of Hendra virus infection in horses
Cited by: 15
Author(s): Christopher Cowled, Chwan Hong Foo, Céline Deffrasnes, Christina L. Rootes, David T. Williams, Deborah Middleton, Lin‐Fa Wang, Andrew G. D. Bean, Cameron R. Stewart
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-08370-7
Regulation of tumour related genes by dynamic epigenetic alteration at enhancer regions in gastric epithelial cells infected by Epstein-Barr virus
Cited by: 26
Author(s): Atsushi Okabe, Sayaka Funata, Keisuke Matsusaka, Hiroe Namba, Masaki Fukuyo, Bahityar Rahmutulla, Motohiko Oshima, Atsushi Iwama, Masashi Fukayama, Atsushi Kaneda
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-018-24477-x
Analysis of microRNA reveals cleistogamous and chasmogamous floret divergence in dimorphic plant
Cited by: 10
Author(s): Fan Wu, Daiyu Zhang, Blaise Pascal Muvunyi, Yan Qi, Yufei Zhang, Yan Zhang, Mingshu Cao, Yanrong Wang, Jiyu Zhang
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-25963-y
Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells
Cited by: 18
Author(s): Junko Hasegawa, Takuya Sakamoto, Shinsaku Fujimoto, Tomoe Yamashita, Takamasa Suzuki, Sachihiro Matsunaga
Software Mentions: 2
Published: over 6 years ago