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: cran: STAR

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/STAR

Spike Train Analysis with R
6 versions
Latest release: over 11 years ago
3 dependent packages
0 downloads

Papers Mentioning STAR 5,759

10.7717/peerj.8690
Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid <i>Lonicera japonica</i>
Cited by: 7
Author(s): Hongli Wang, Yanqun Li, Sibo Wang, Dexin Kong, Sunil Kumar Sahu, Mei Bai, Haoyuan Li, Linzhou Li, Yan Xu, Hongping Liang, Sunil Kumar Sahu
Software Mentions: 1
Published: about 4 years ago
10.3389/fonc.2019.01120
Epstein-Barr Virus BART Long Non-coding RNAs Function as Epigenetic Modulators in Nasopharyngeal Carcinoma
Cited by: 43
Author(s): Rob J. A. Verhoeven, S. Y. Tong, Bobo Wing-Yee Mok, Jiayan Liu, Songtao He, Jingfeng Zong, Yixin Chen, Sai‐Wah Tsao, Maria Li Lung, Honglin Chen
Software Mentions: 1
Published: over 4 years ago
10.3389/fonc.2021.622244
Patient-Derived Nasopharyngeal Cancer Organoids for Disease Modeling and Radiation Dose Optimization
Cited by: 11
Author(s): Sasidharan Swarnalatha Lucky, Martin Law, Man Tin Lui, Jamie Mong, Jin Shi, Sidney Yu, Do Kun Yoon, Shih Kien Djeng, Ji‐Guang Wang, Chwee Ming Lim, Min Tan
Software Mentions: 1
Published: over 3 years ago
10.3389/fonc.2021.612354
Inhibition of HSP90 as a Strategy to Radiosensitize Glioblastoma: Targeting the DNA Damage Response and Beyond
Cited by: 10
Author(s): Michael Orth, Valérie Albrecht, Karin Seidl, Linda Kinzel, Kristian Unger, Julia Heß, Lisa Kreutzer, Na Sun, Benjamin Stegen, Alexander Nieto, Jessica Maas, Nicolas Winssinger, Anna A. Friedl, Axel Walch, Claus Belka, Horst Zitzelsberger, Maximilian Niyazi, Kirsten Lauber
Software Mentions: 1
Published: about 3 years ago
10.3389/fonc.2020.632187
A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects
Cited by: 14
Author(s): Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Software Mentions: 1
Published: over 3 years ago
10.7717/peerj.8009
Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs
Cited by: 3
Author(s): Yu Lin, Qianzi Tang, Yan Li, Mengnan He, Long Jin, Jideng Ma, Xun Wang, Keren Long, Zhiqing Huang, Xuewei Li, Yiren Gu, Mingzhou Li
Software Mentions: 1
Published: over 4 years ago
10.3389/fonc.2020.00982
RNA-Seq Profiling of Serum Exosomal Circular RNAs Reveals Circ-PNN as a Potential Biomarker for Human Colorectal Cancer
Cited by: 67
Author(s): Yan Xie, Juan Li, Peilong Li, Ning Li, Ying Zhang, Helen Binang, Yinghui Zhao, Weili Duan, Yingjie Chen, Yunshan Wang, Du Li, Chuanxin Wang
Software Mentions: 1
Published: almost 4 years ago
10.7717/peerj.8461
Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue
Cited by: 5
Author(s): Emilie E. Vomhof-DeKrey, Josey Umthun, Marc D. Basson
Software Mentions: 1
Published: over 4 years ago
10.7717/peerj.3548
Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences
Cited by: 9
Author(s): Matthew A. Campbell, Michael E. Alfaro, Max Belasco, J. Andrés López
Software Mentions: 1
Published: over 6 years ago
10.1186/s13059-020-02094-0
Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
Cited by: 52
Author(s): Qingxin Song, Atsumi Ando, Ning Jiang, Yoko Ikeda, Z Jeffrey Chen
Software Mentions: 1
Published: almost 4 years ago
10.3390/cells8050461
The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae
Cited by: 16
Author(s): L. V. Trilisenko, Anton Zvonarev, Airat Valiakhmetov, Aleksey A. Penin, Irina A. Eliseeva, V. G. Ostroumov, Ivan V. Kulakovskiy, T. V. Kulakovskaya
Software Mentions: 1
Published: about 5 years ago
10.7717/peerj.5759
Sequence variant analysis of RNA sequences in severe equine asthma
Cited by: 8
Author(s): Laurence Tessier, Olivier Côté, Dorothee Bienzle
Software Mentions: 1
Published: over 5 years ago
10.3390/cells9081806
In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences
Cited by: 16
Author(s): Annie Robic, Julie Demars, Christa Kühn
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.66808
Expansion of CD10neg neutrophils and CD14+HLA-DRneg/low monocytes driving proinflammatory responses in patients with acute myocardial infarction
Cited by: 18
Author(s): Daniela Fraccarollo, Jonas Neuser, Julian Möller, Christian Riehle, Paolo Galuppo, Johann Bauersachs
Software Mentions: 1
Published: almost 3 years ago
10.1186/s13059-020-02180-3
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
Cited by: 89
Author(s): Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jèssica Gómez‐Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo‐Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, André Corvelo, Leonor Frías, Marta Gut, Toni Gabaldón, Alberto Pallavicini, Carlos Canchaya, Beatriz Novoa, Tyler Alioto, David Posada, António Figueras
Software Mentions: 1
Published: over 3 years ago
10.3390/cells9071683
Inter-Tumor Heterogeneity—Melanomas Respond Differently to GM-CSF-Mediated Activation
Cited by: 10
Author(s): Adi Moshe, Sivan Izraely, Orit Sagi‐Assif, Sapir Malka, Shlomit Ben‐Menachem, Tsipi Meshel, Metsada Pasmanik‐Chor, Dave S. B. Hoon
Software Mentions: 1
Published: almost 4 years ago
10.3390/cells9030783
A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma
Cited by: 8
Author(s): Marianna Szemes, Zsombor Melegh, Jacob Bellamy, Alexander Greenhough, Madhu Kollareddy, Daniel Catchpoole, Karim Malik
Software Mentions: 1
Published: about 4 years ago
10.3390/cells9010162
Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN)
Cited by: 6
Author(s): Tian-Li Duan, Han Yi Jiao, Guang‐Jun He, Yong-Bin Yan
Software Mentions: 1
Published: over 4 years ago
10.3390/cells9102333
Tafazzin Mutation Affecting Cardiolipin Leads to Increased Mitochondrial Superoxide Anions and Mitophagy Inhibition in Barth Syndrome
Cited by: 12
Author(s): Patrice X. Petit, Hector Ardilla-Osorio, Lucile Penalvia, Nathan Earl Rainey
Software Mentions: 1
Published: over 3 years ago
10.3390/cells9020516
Transcriptional and Ultrastructural Analyses Suggest Novel Insights into Epithelial Barrier Impairment in Celiac Disease
Cited by: 7
Author(s): Agnieszka Sowińska, Yasser Morsy, E. Czarnowska, Beata Oralewska, Ewa Konopka, Marek Woynarowski, Sylwia Szymańska, Maria Ejmont, Michael Scharl, Joanna B. Bierła, Marcin Wawrzyniak, Božena Cukrowská
Software Mentions: 1
Published: over 4 years ago
10.1016/j.cels.2021.04.006
Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity
Cited by: 16
Author(s): Joanna M. Chustecki, Daniel J. Gibbs, George W. Bassel, Iain G. Johnston
Software Mentions: 1
Published: about 3 years ago
10.1186/s13059-021-02350-x
Intergenic RNA mainly derives from nascent transcripts of known genes
Cited by: 13
Author(s): Antonella Federico, Julian A. Zagalak, Jan Attig, Jernej Ule, Nicholas M. Luscombe
Software Mentions: 1
Published: about 3 years ago
10.1016/j.cels.2018.02.004
Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction
Cited by: 61
Author(s): Manuel Razo-Mejia, Stephanie L. Barnes, Nathan M. Belliveau, Griffin Chure, Tal Einav, Mitchell Lewis, Rob Phillips
Software Mentions: 1
Published: about 6 years ago
10.1186/s13059-021-02399-8
LIQA: long-read isoform quantification and analysis
Cited by: 37
Author(s): Yu Hu, Fang Li, Xuelian Chen, Jiang Zhong, Mingyao Li, Kai Wang
Software Mentions: 1
Published: almost 3 years ago
10.1186/s13059-021-02434-8
Specific splice junction detection in single cells with SICILIAN
Cited by: 12
Author(s): Roozbeh Dehghannasiri, Julia Eve Olivieri, Ana Damljanovic, Julia Salzman
Software Mentions: 1
Published: almost 3 years ago
10.3390/nu11040709
High Levels of Prebiotic Resistant Starch in Diet Modulate Gene Expression and Metabolomic Profile in Pancreatic Cancer Xenograft Mice
Cited by: 9
Author(s): Concetta Panebianco, Antonio Villani, Valerio Pazienza
Software Mentions: 1
Published: about 5 years ago
10.1016/j.xcrm.2020.100036
Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-Term Population-Scale Immunity
Cited by: 59
Author(s): Mark Yarmarkovich, John M. Warrington, Alvin Farrel, John M. Maris
Software Mentions: 1
Published: about 4 years ago
10.1016/j.celrep.2020.108368
Intramacrophage ROS Primes the Innate Immune System via JAK/STAT and Toll Activation
Cited by: 57
Author(s): Sveta Chakrabarti, Sandhya S. Visweswariah
Software Mentions: 1
Published: over 3 years ago
10.1093/gbe/evz141
The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus
Cited by: 25
Author(s): Nikola Palevich, Paul Maclean, Abdul Baten, Richard W. Scott, David M Leathwick
Software Mentions: 1
Published: almost 5 years ago
10.1093/gbe/evz176
Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly
Cited by: 4
Author(s): Lars Höök, Luis Leal, Venkat Talla, Niclas Backström
Software Mentions: 1
Published: almost 5 years ago
10.1016/j.celrep.2019.08.057
GEF-H1 Signaling upon Microtubule Destabilization Is Required for Dendritic Cell Activation and Specific Anti-tumor Responses
Cited by: 37
Author(s): Abhishek S. Kashyap, Laura Fernandez-Rodriguez, Yun Zhao, Gianni Monaco, Marcel P. Trefny, Naohiro Yoshida, Kea Martin, Ashwani Sharma, Natacha Olieric, Pankaj Shah, Michal A. Stanczak, Nicole Kirchhammer, Sung-Moo Park, Sébastien Wieckowski, Heinz Läubli, Rachid Zagani, Benjamin Kasenda, Michel O. Steinmetz, Hans Christian Reinecker, Alfred Zippelius
Software Mentions: 1
Published: almost 5 years ago
10.3390/pathogens9080620
Bovine Polyomavirus 2 is a Probable Cause of Non-Suppurative Encephalitis in Cattle
Cited by: 7
Author(s): Melanie M. Hierweger, Michel C. Koch, Torsten Seuberlich
Software Mentions: 1
Published: almost 4 years ago
10.1093/gbe/evaa195
Comprehensive Transcriptome of the Maize Stalk Borer,<i>Busseola fusca</i>, from Multiple Tissue Types, Developmental Stages, and Parasitoid Wasp Exposures
Cited by: 1
Author(s):
Software Mentions: 1
Published: over 3 years ago
10.1093/gbe/evaa235
A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis
Cited by: 27
Author(s): Eiichi Shoguchi, Girish Beedessee, Kanako Hisata, Isao Tada, Haruhi Narisoko, Noriyuki Satoh, Masanobu Kawachi, Chuya Shinzato
Software Mentions: 1
Published: over 3 years ago
10.1016/j.celrep.2021.108756
Itaconate confers tolerance to late NLRP3 inflammasome activation
Cited by: 85
Author(s): Monika Bambousková, Lucie Potůčková, Tomáš Paulenda, Martina Kerndl, Denis A. Mogilenko, Kate Lizotte, Amanda Swain, Sebastian Hayes, Ryan D. Sheldon, Hyeryun Kim, Unnati Kapadnis, Abigail E. Ellis, Christine Isaguirre, Samantha Burdess, Anwesha Laha, Gaya K. Amarasinghe, Victor Chubukov, Thomas P. Roddy, Michael S. Diamond, Russell G. Jones, Donald M. Simons, Maxim N. Artyomov
Software Mentions: 1
Published: over 3 years ago
10.1093/gbe/evab178
The Genome of the Haptophyte <i>Diacronema lutheri</i> (<i>Pavlova lutheri</i>, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae
Cited by: 5
Author(s): Chris J. Hulatt, René H. Wijffels, Matthew C. Posewitz
Software Mentions: 1
Published: almost 3 years ago
10.1186/s13073-015-0152-4
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
Cited by: 71
Author(s): Patrick Deelen, Daria V. Zhernakova, Mark de Haan, Marijke van der Sijde, Marc Jan Bonder, Juha Karjalainen, K. Joeri van der Velde, Kristin M. Abbott, Jingyuan Fu, Cisca Wijmenga, Richard J. Sinke, Morris A. Swertz, Lude Franke
Software Mentions: 1
Published: about 9 years ago
10.3390/pathogens10040405
Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota
Cited by: 18
Author(s): Anna Matysiak, Michał Kabza, Justyna A. Karolak, Marcelina M. Jaworska, Małgorzata Rydzanicz, Rafał Płoski, Jacek P. Szaflik, Marzena Gajęcka
Software Mentions: 1
Published: about 3 years ago
10.1016/j.celrep.2020.01.099
Type I Interferons Suppress Anti-parasitic Immunity and Can Be Targeted to Improve Treatment of Visceral Leishmaniasis
Cited by: 29
Author(s): Rajiv Kumar, Patrick T. Bunn, Siddharth Singh, Susanna S. Ng, Marcela Montes de, Fabian de Labastida Rivera, S. V. S. Chauhan, Neetu Singh, Rebecca J. Faleiro, Chelsea L. Edwards, Teija C.M. Frame, Meru Sheel, Rebecca Austin, Steven Lane, Tobias Bald, Mark J. Smyth, Geoffrey R. Hill, Shannon E. Best, Ashraful Haque, Dillon Corvino, Nic Waddell, Lambross Koufariotis, Pamela Mukhopadhay, Madhukar Rai, Jaya Chakravarty, O. P. Singh, David L. Sacks, Susanne Nylén, Jude Uzonna, Christian Engwerda
Software Mentions: 1
Published: over 4 years ago
10.1016/j.celrep.2019.05.095
Small Extracellular Vesicles Are Key Regulators of Non-cell Autonomous Intercellular Communication in Senescence via the Interferon Protein IFITM3
Cited by: 169
Author(s): Michela Borghesan, Juan Fafián-Labora, Olga Eleftheriadou, Paula Carpintero-Fernández, Marta Pàez-Ribes, Gema Vizcay‐Barrena, Avital Swisa, Dror Kolodkin-Gal, Pilar Ximénez-Embún, Robert Lowe, Belén Martı́n-Martı́n, Héctor Peinado, Javier Muñoz, Roland A. Fleck, Yuval Dor, Ittai Ben-Porath, Anna Vossenkämper, Daniel Muñoz‐Espín, Ana O’Loghlen
Software Mentions: 1
Published: about 5 years ago
10.1186/s13071-020-04085-3
Species and sex-specific chemosensory gene expression in Anopheles coluzzii and An. quadriannulatus antennae
Cited by: 6
Author(s): Giridhar Athrey, Zachary R. Popkin-Hall, Luciano V. Cosme, Willem Takken, Michel A. Slotman
Software Mentions: 1
Published: about 4 years ago
10.1186/s13073-018-0567-9
Single-cell transcriptome analysis of lineage diversity in high-grade glioma
Cited by: 157
Author(s): Jinzhou Yuan, Hanna Mendes Levitin, Véronique Frattini, Erin C. Bush, Deborah Boyett, Jorge Samanamud, Michele Ceccarelli, Athanassios Dovas, George Zanazzi, Peter Canoll, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter A. Sims
Software Mentions: 1
Published: almost 6 years ago
10.1186/s13073-019-0635-9
TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Cited by: 41
Author(s): Quanyi Zhao, Robert Wirka, Trieu Nguyen, Manabu Nagao, Paul Cheng, Clint L. Miller, Juyong Brian Kim, Milos Pjanic, Thomas Quertermous
Software Mentions: 1
Published: about 5 years ago
10.1016/j.celrep.2016.12.002
A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior
Cited by: 20
Author(s): Ingrid Ehrmann, Matthew R. Gazzara, Vittoria Pagliarini, Caroline Dalgliesh, Mahsa Kheirollahi-Chadegani, Yaobo Xu, E. Cesari, Marina Danilenko, Marie Maclennan, Kate Lowdon, Tanja Vogel, Piia Keskivali-Bond, Sara Wells, Heather Cater, Philippe Fort, Mauro Santibanez‐Koref, Silvia Middei, Claudio Sette, Gavin J. Clowry, Yoseph Barash, Mark O. Cunningham, David J. Elliott
Software Mentions: 1
Published: over 7 years ago
10.1186/s13073-020-00746-1
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
Cited by: 21
Author(s): Francesc Muyas, Luís Zapata, Roderic Guigó, Stephan Ossowski
Software Mentions: 1
Published: about 4 years ago
10.3390/cancers12030620
RNA Immune Signatures from Pan-Cancer Analysis Are Prognostic for High-Grade Serous Ovarian Cancer and Other Female Cancers
Cited by: 12
Author(s): Wendell Jones, Chad M. Michener, Charles V. Biscotti, Elena Ioana Braicu, Jalid Sehouli, Mahrukh K. Ganapathi, Ram Ganapathi
Software Mentions: 1
Published: about 4 years ago
10.3390/cancers13092250
IGF2 Mediates Resistance to Isoform-Selective-Inhibitors of the PI3K in HPV Positive Head and Neck Cancer
Cited by: 6
Author(s): Mai Badarni, Manu Prasad, Artemiy Golden, Baisali Bhattacharya, Liron Levin, Ksenia M. Yegodayev, Orr Dimitstein, Ben‐Zion Joshua, Limor Cohen, Ekaterina Khrameeva, Dexin Kong, Angel Porgador, Alex Braiman, Jennifer R. Grandis, Barak Rotblat, Moshe Elkabets
Software Mentions: 1
Published: about 3 years ago
10.3390/cancers12071719
Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes
Cited by: 5
Author(s): Timothy J. Lavelle, Tine Norman Alver, Karen‐Marie Heintz, Patrik Wernhoff, Vegard Nygaard, Sigve Nakken, Geir Frode Øy, Sigurd Leinæs Bøe, Alfonso Urbanucci, Eivind Hovig
Software Mentions: 1
Published: almost 4 years ago
10.3390/cancers13071546
Pulsed-Focused Ultrasound Slows B16 Melanoma and 4T1 Breast Tumor Growth through Differential Tumor Microenvironmental Changes
Cited by: 5
Author(s): Gadi Cohen, Parwathy Chandran, Rebecca M. Lorsung, Ömer Aydın, Lauren E. Tomlinson, Robert Rosenblatt, Scott R. Burks, Joseph A. Frank
Software Mentions: 1
Published: about 3 years ago
10.7554/eLife.28652
Host proteostasis modulates influenza evolution
Cited by: 30
Author(s): Angela M Phillips, Luna O Gonzalez, Emmanuel E Nekongo, Anna I. Ponomarenko, Sean M. McHugh, Vincent Butty, Stuart S. Levine, Yu‐Shan Lin, Leonid A. Mirny, Matthew D. Shoulders
Software Mentions: 1
Published: over 6 years ago
10.5808/GI.2019.17.1.e3
Identification of ERBB Pathway-Activated Cells in Triple-Negative Breast Cancer
Cited by: 8
Author(s): Soo Young Cho
Software Mentions: 1
Published: about 5 years ago
10.5808/GI.2019.17.3.e32
Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing
Cited by: 29
Author(s): Sol A Jeon, Jong‐Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong‐Sung Kim, Jin Cheon Kim, Seon‐Young Kim
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0200477
SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus
Cited by: 14
Author(s): Preetika Gupta, Ogul E. Uner, Soumyashant Nayak, Gregory R. Grant, Robert G. Kalb
Software Mentions: 1
Published: almost 6 years ago
10.5808/GI.2020.18.1.e10
Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms
Cited by: 29
Author(s): Karl R. Franke, Erin L. Crowgey
Software Mentions: 1
Published: about 4 years ago
10.1016/j.gpb.2016.02.003
Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts
Cited by: 74
Author(s): Tobias Jakobi, Lisa F. Czaja-Hasse, Richard Reinhardt, Christoph Dieterich
Software Mentions: 1
Published: almost 8 years ago
10.1016/j.gpb.2020.10.005
Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients
Cited by: 384
Author(s): Zheng Zhao, Kenan Zhang, Qiangwei Wang, Guanzhang Li, Fan Zeng, Ying Zhang, Fan Wu, Rui‐Chao Chai, Zheng Wang, Chuanbao Zhang, Wei Zhang, Zhaoshi Bao, Tao Jiang
Software Mentions: 1
Published: over 3 years ago
10.1186/s13742-015-0105-2
Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
Cited by: 2
Author(s): Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves‐Carvalho, Alexan Andrieux, Raluca Uricaru, Pierre Peterlongo
Software Mentions: 1
Published: over 8 years ago
10.7554/eLife.59303
One-shot analysis of translated mammalian lncRNAs with AHARIBO
Cited by: 13
Author(s): L. Minati, Claudia Firrito, Alessia Del Piano, Alberto Peretti, Simone Sidoli, Daniele Peroni, Romina Belli, Francesco Gandolfi, Alessandro Romanel, Paola Bernabò, Jacopo Zasso, Alessandro Quattrone, Graziano Guella, Fabio Lauria, Gabriella Viero, Massimiliano Clamer
Software Mentions: 1
Published: over 3 years ago
10.1093/gigascience/gix012
RED-ML: a novel, effective RNA editing detection method based on machine learning
Cited by: 27
Author(s): Heng Xiong, Dongbing Liu, Qiye Li, Mengyue Lei, Liqin Xu, Liang Wu, Zongji Wang, Shancheng Ren, Wangsheng Li, Min Xia, Lihua Lü, Haorong Lu, Yong Hou, Shida Zhu, Xin Liu, Ying Sun, Jian Wang, Huanming Yang, Kui Wu, Xun Xu, Leo J. Lee
Software Mentions: 1
Published: over 7 years ago
10.1093/gigascience/gix035
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana
Cited by: 45
Author(s): Reuben W. Nowell, Benjamin Elsworth, Vicencio Oostra, Bas J. Zwaan, Christopher W. Wheat, Marjo Saastamoinen, Ilik J. Saccheri, Arjen E Van’t Hof, Bethany R. Wasik, Heidi Connahs, Muhammad Aslam, Sujai Kumar, Richard Challis, Antónia Monteiro, Paul M. Brakefield, Mark Blaxter
Software Mentions: 1
Published: about 7 years ago
10.1093/gigascience/gix122
VaDiR: an integrated approach to Variant Detection in RNA
Cited by: 14
Author(s): Lisa Neums, Seiji Suenaga, Peter Beyerlein, Sara Anders, Devin C. Koestler, Andrea Mariani, Jeremy Chien
Software Mentions: 1
Published: over 6 years ago
10.1093/gigascience/giy008
Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning
Cited by: 12
Author(s): Bradley M. Colquitt, David G. Mets, Michael S. Brainard
Software Mentions: 1
Published: over 6 years ago
10.1093/gigascience/giy010
The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)
Cited by: 37
Author(s): Matteo Buti, Marco Moretto, Elena Barghini, Flavia Mascagni, Lucia Natali, Matteo Brilli, Alexandre Lomsadze, Paolo Sonego, L. Giongo, Michael Alonge, Riccardo Velasco, Claudio Varotto, Nada Šurbanovski, Mark Borodovsky, J. A. Ward, Kristof Engelen, Andrea Cavallini, Alessandro Cestaro, Daniel J. Sargent
Software Mentions: 1
Published: over 7 years ago
10.1093/gigascience/gix081
Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
Cited by: 8
Author(s): Koen Kole, Yutaro Komuro, Jan Provazník, Jelena Pistolic, Vladimı́r Beneš, Paul Tiesinga, Tansu Celikel
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pone.0125414
The Expansion of Thymopoiesis in Neonatal Mice Is Dependent on Expression of High Mobility Group A 2 Protein (Hmga2)
Cited by: 5
Author(s): Beata Berent-Maoz, Encarnación Montecino-Rodriguez, Michael P. Fice, David Casero, Christopher S. Seet, William E. Lowry, Kenneth Dorshkind
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pone.0187773
Lung epithelial response to cigarette smoke and modulation by the nicotinic alpha 7 receptor
Cited by: 18
Author(s): Lorise C. Gahring, Elizabeth J. Myers, Diane M. Dunn, Robert B. Weiss, Scott W. Rogers
Software Mentions: 1
Published: over 6 years ago
10.1523/ENEURO.0276-17.2018
Translatome Regulation in Neuronal Injury and Axon Regrowth
Cited by: 25
Author(s): Meir Rozenbaum, Marek Rajman, Ida Rishal, Indrek Koppel, Sandip Koley, Katalin F. Medzihradszky, Juan Oses-Prieto, Riki Kawaguchi, Paul S. Amieux, Alma L. Burlingame, Giovanni Coppola, Mike Fainzilber
Software Mentions: 1
Published: over 6 years ago
10.1038/srep22177
Evolution of the assassin’s arms: insights from a phylogeny of combined transcriptomic and ribosomal DNA data (Heteroptera: Reduvioidea)
Cited by: 33
Author(s): Junxia Zhang, Eric R. L. Gordon, Michael Forthman, Wei Song Hwang, Kimberly K. O. Walden, Daniel R. Swanson, Kevin P. Johnson, Rudolf Meier, Christiane Weirauch
Software Mentions: 1
Published: over 8 years ago
10.1038/srep26200
Possible mechanisms of host resistance to Haemonchus contortus infection in sheep breeds native to the Canary Islands
Cited by: 57
Author(s): Zhengyu Guo, J. González, Julia N. Hernández, Tom N. McNeilly, Yolanda Corripio-Miyar, David Frew, Tyler Morrison, Peng Yu, Robert W. Li
Software Mentions: 1
Published: about 8 years ago
10.1038/srep30311
Transcriptome sequencing wide functional analysis of human mesenchymal stem cells in response to TLR4 ligand
Cited by: 26
Author(s): Sun Hwa Kim, Amitabh Das, Jin Choul Chai, Bert Binas, Mi Ran Choi, Kyoung Sun Park, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 1
Published: almost 8 years ago
10.1038/srep33209
STAR: a simple TAL effector assembly reaction using isothermal assembly
Cited by: 13
Author(s): Sabine Gogolok, Claudia Garcia-Diaz, Steven M. Pollard
Software Mentions: 1
Published: over 7 years ago
10.1038/srep34863
Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin
Cited by: 35
Author(s): Pablo Sandoval, J’Neka S. Claxton, Jae Woo Lee, Fahad Saeed, Jason D. Hoffert, Mark A. Knepper
Software Mentions: 1
Published: over 7 years ago
10.1038/srep35228
Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes
Cited by: 17
Author(s): Jing‐Woei Li, Heung‐Man Lee, Ying Wang, Amy Hin-Yan Tong, Kevin Y. Yip, Stephen Kwok‐Wing Tsui, Si Lok, Risa Ozaki, Andrea O. Y. Luk, Alice Pik‐Shan Kong, Wing–Yee So, C. Ronald, Juliana C.N. Chan, Ting-Fung Chan
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0232081
Engineering a 3D in vitro model of human skeletal muscle at the single fiber scale
Cited by: 15
Author(s): Anna Urciuolo, Elena Serena, Rusha Ghua, Susi Zatti, Monica Giomo, Nicolò Mattei, Massimo Vetralla, Giulia Selmin, Camilla Luni, Nicola Vitulo, Giorgio Valle, Libero Vitiello, Nicola Elvassore
Software Mentions: 1
Published: about 4 years ago
10.1038/srep37235
Nitrogen-induced metabolic changes and molecular determinants of carbon allocation in Dunaliella tertiolecta
Cited by: 49
Author(s): Kenneth Wei Min Tan, Huixin Lin, Hui Shen, Yuan Kun Lee
Software Mentions: 1
Published: over 7 years ago
10.1038/srep37412
Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1
Cited by: 20
Author(s): Savita Sankar, Dhananjay Yellajoshyula, Bo Zhang, Bryan W. Teets, Nicole B. Rockweiler, Kristen L. Kroll
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0122602
Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism
Cited by: 23
Author(s): Shai Abehsera, Lilah Glazer, Jenny Tynyakov, Inbar Plaschkes, Vered Chalifa‐Caspi, Isam Khalaila, Eliahu D. Aflalo, Amir Sagi
Software Mentions: 1
Published: about 9 years ago
10.1038/srep38624
Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome
Cited by: 25
Author(s): Assaf Malik, Vered Domankevich, Lijuan Han, Xiaodong Fang, Abraham B. Korol, Aaron Avivi, Imad Shams
Software Mentions: 1
Published: over 7 years ago
10.1038/srep39094
Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle
Cited by: 21
Author(s): Anne-Laure Bougé, Eva M. Murauer, Emmanuelle Beyne, Julie Miro, Jessica Varilh, Magali Taulan, M. Kœnig, Mireille Claustres, Sylvie Tuffery‐Giraud
Software Mentions: 1
Published: over 7 years ago
10.1038/srep40214
Aminophylline suppresses stress-induced visceral hypersensitivity and defecation in irritable bowel syndrome
Cited by: 16
Author(s): Teita Asano, Ken Ichiro Tanaka, Arisa Tada, Hikaru Shimamura, Rikako Tanaka, Hiroki Maruoka, Mitsuko Takenaga, Tohru Mizushima
Software Mentions: 1
Published: over 7 years ago
10.7554/eLife.13374
Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation
Cited by: 404
Author(s): Xinde Zheng, Leah Boyer, Mingji Jin, Jérôme Mertens, Yongsung Kim, Li Ma, Michael W. Hamm, Fred H. Gage, Tony Hunter
Software Mentions: 1
Published: almost 8 years ago
10.1051/parasite/2020022
Development of a workflow for identification of nuclear genotyping markers for <i>Cyclospora cayetanensis</i>
Cited by: 13
Author(s): Katelyn Houghton, Alexandre Lomsadze, Subin Park, Fernanda S. Nascimento, Joel Barratt, Michael J. Arrowood, Erik VanRoey, Eldin Talundzic, Mark Borodovsky, Yvonne Qvarnström
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0192170
Induction of epigenetic variation in Arabidopsis by over-expression of DNA METHYLTRANSFERASE1 (MET1)
Cited by: 14
Author(s): Samuel George Philip Brocklehurst, Michael R. Watson, Ian Carr, Suzan Out, Iris Heidmann, Peter Meyer
Software Mentions: 1
Published: over 6 years ago
10.1038/srep43745
Dietary restriction protects against diethylnitrosamine-induced hepatocellular tumorigenesis by restoring the disturbed gene expression profile
Cited by: 16
Author(s): Ting Duan, Wenjie Sun, Mohan Zhang, Juan Ge, Yansu He, Jun Zhang, Yifan Zheng, Wei Yang, Han‐Ming Shen, Jun Yang, Xinqiang Zhu, Peilin Yu
Software Mentions: 1
Published: about 7 years ago
10.12688/wellcomeopenres.15711.1
The role of the Xist 5’ m6A region and RBM15 in X chromosome inactivation
Cited by: 36
Author(s): Heather Coker, Guifeng Wei, Benoît Moindrot, Shabaz Mohammed, Tatyana B. Nesterova, Neil Brockdorff
Software Mentions: 1
Published: over 4 years ago
10.1038/srep46440
LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes
Cited by: 8
Author(s): Hyung Chan Suh, Touati Benoukraf, S. Pavithra, Tong Yin, Qi Cao, Jonathan Said, Stephen Lee, Raymond Boon Tar Lim, Henry Yang, Jacqueline Salotti, Peter F. Johnson, Vikas Madan, H. Phillip Koeffler
Software Mentions: 1
Published: about 7 years ago
10.1038/s41598-017-00575-0
Eμ and 3′RR IgH enhancers show hierarchic unilateral dependence in mature B-cells
Cited by: 17
Author(s): Alexis Saintamand, Christelle Vincent-Fabert, Marie Marquet, Nour Ghazzaui, Virginie Magnone, Eric Pinaud, Michel Cogné, Yves Denizot
Software Mentions: 1
Published: about 7 years ago
10.1038/s41598-017-00801-9
Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum
Cited by: 13
Author(s): Sherwin Chan, Jun-Hong Ch’ng, Mats Wahlgren, Jessada Thutkawkorapin
Software Mentions: 1
Published: about 7 years ago
10.1038/s41598-017-01165-w
Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
Cited by: 7
Author(s): Zhibiao Mai, Chuan-Le Xiao, Jingjie Jin, Gong Zhang
Software Mentions: 1
Published: about 7 years ago
10.1038/s41598-017-01377-0
Transcriptomic response of durum wheat to nitrogen starvation
Cited by: 103
Author(s): Pasquale Luca Curci, Riccardo Aiese Cigliano, Diana L. Zuluaga, Michela Janni, Walter Sanseverino, Gabriella Sonnante
Software Mentions: 1
Published: about 7 years ago
10.1038/s41598-017-02520-7
Tropospheric Warming Over The Past Two Decades
Cited by: 20
Author(s): Benjamin D. Santer, Susan Solomon, F. J. Wentz, Qiang Fu, Stephen Po‐Chedley, C. A. Mears, Jeffrey F. Painter, C. Bonfils
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.pone.0207503
Distinct vascular genomic response of proton and gamma radiation—A pilot investigation
Cited by: 3
Author(s): Emanuela Ricciotti, Dimitra Sarantopoulou, Gregory R. Grant, Jenine K. Sanzari, Gabriel Krigsfeld, Amber J. Kiliti, Ann R. Kennedy, Tilo Großer
Software Mentions: 1
Published: over 5 years ago
10.7554/eLife.65482
Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
Cited by: 27
Author(s): Brian R. Lee, Agata Budzillo, Kristen Hadley, Jeremy A. Miller, Tim Jarsky, Katherine Baker, DiJon Hill, Lisa Kim, Rusty Mann, Lindsay Ng, Aaron Oldre, Ram Rajanbabu, Jessica Trinh, Sara Vargas, Thomas Braun, Rachel Dalley, Nathan W. Gouwens, Brian Kalmbach, Tae Kyung Kim, Kimberly A. Smith, Gilberto Soler-Llavina, Staci A. Sorensen, Bosiljka Tasic, Jonathan T. Ting, Ed Lein, Hongkui Zeng, Gabe J. Murphy, Jim Berg
Software Mentions: 1
Published: almost 3 years ago
10.12688/wellcomeopenres.14360.1
Transcriptomic profiling of human skin biopsies in the clinical trial setting: A protocol for high quality RNA extraction from skin tumours
Cited by: 6
Author(s): Marina Danilenko, Robert Stones, Neil Rajan
Software Mentions: 1
Published: about 6 years ago
10.1038/s41598-017-04333-0
Hypoxia is a Key Driver of Alternative Splicing in Human Breast Cancer Cells
Cited by: 52
Author(s): Jian Han, Jia Li, Jeongwon Ho, Grace Sushin Chia, Hiroyuki Kato, Sudhakar Jha, Henry Yang, Lorenz Poellinger, Kian Leong Lee
Software Mentions: 1
Published: almost 7 years ago
10.1038/s41598-017-04356-7
Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains
Cited by: 28
Author(s): Qianhui Yu, Zhisong He
Software Mentions: 1
Published: almost 7 years ago
10.1038/s41598-017-04654-0
Synergistic cellular effects including mitochondrial destabilization, autophagy and apoptosis following low-level exposure to a mixture of lipophilic persistent organic pollutants
Cited by: 18
Author(s): Nathan Earl Rainey, Ana Šarić, Alexandre Leberre, Etienne Dewailly, Christian Slomianny, Guillaume Vial, Harold I. Zeliger, Patrice X. Petit
Software Mentions: 1
Published: almost 7 years ago
10.1038/s41598-017-05720-3
Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder
Cited by: 36
Author(s): Efrain Ribeiro, Joseph R. Scarpa, Susanna P. Garamszegi, Andrew Kasarskis, Deborah C. Mash, Eric J. Nestler
Software Mentions: 1
Published: almost 7 years ago
10.7554/eLife.09207
SPOP mutation leads to genomic instability in prostate cancer
Cited by: 142
Author(s): Gunther Boysen, Christopher E. Barbieri, Davide Prandi, Mirjam Blattner, Sung-Suk Chae, Arun Dahija, Srilakshmi Nataraj, Dennis Huang, Clarisse Marotz, Limei Xu, Julie Huang, Paola Lecca, Sagar Chhangawala, Liu D, Pengbo Zhou, Andrea Sboner, Johann S. de Bono, Francesca Demichelis, Yariv Houvras, Mark A. Rubin
Software Mentions: 1
Published: over 8 years ago
10.3390/v13081536
Detection of Human Papillomavirus Integration in Brain Metastases from Oropharyngeal Tumors by Targeted Sequencing
Cited by: 5
Author(s): Brian McEllin, Brian C. Searle, Lisa DePledge, George Sun, Charles S. Cobbs, Mohsen Karimi
Software Mentions: 1
Published: almost 3 years ago