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
10.1002/bit.27209
Comparative genome‐scale analysis of <i>Pichia pastoris</i> variants informs selection of an optimal base strainCited by: 31
Author(s): Joseph Brady, Charles A. Whittaker, Melody C. Tan, D. Lee Kristensen, Duanduan Ma, Neil C. Dalvie, Kerry R. Love, J. Christopher Love
Software Mentions: 7
Published: over 4 years ago
10.1186/s12859-018-2445-2
Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performanceCited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: over 5 years ago
10.15252/embr.201642378
Linear ubiquitination by <scp>LUBEL</scp> has a role in <i>Drosophila</i> heat stress responseCited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: over 7 years ago
10.1111/1751-7915.13634
Soil microbiota influences clubroot disease by modulating <i>Plasmodiophora brassicae</i> and <i>Brassica napus</i> transcriptomesCited by: 19
Author(s): Stéphanie Daval, Kévin Gazengel, Arnaud Belcour, Juliette Linglin, Anne‐Yvonne Guillerm‐Erckelboudt, Alain Sarniguet, Maria Manzanares-Dauleux, Lionel Lebreton, Christophe Mougel
Software Mentions: 7
Published: almost 4 years ago
10.1038/s41598-019-52584-w
Identifying inaccuracies in gene expression estimates from unstranded RNA-seq dataCited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: over 4 years ago
10.1186/s13007-019-0440-x
Comparing time series transcriptome data between plants using a network module finding algorithmCited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: about 5 years ago
10.3390/plants9121700
Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) RootsCited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: over 3 years ago
10.15252/emmm.202012525
<scp>LSD</scp> 1 inhibition induces differentiation and cell death in Merkel cell carcinomaCited by: 36
Author(s): Lukas Leiendecker, Pauline S. Jung, Izabela Krecioch, Tobias Neumann, Alexander Schleiffer, Karl Mechtler, Thomas Wiesner, Anna C. Obenauf
Software Mentions: 7
Published: over 3 years ago
10.1186/s13062-016-0169-7
Sensitivity, specificity, and reproducibility of RNA-Seq differential expression callsCited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: over 7 years ago
10.1038/s41598-017-05377-y
Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genesCited by: 33
Author(s): Zupeng Wang, Yifei Liu, Li Li, Dawei Li, Qiong Zhang, Yangtao Guo, Shuaibin Wang, Caihong Zhong, Hongwen Huang
Software Mentions: 7
Published: almost 7 years ago
10.1038/s41598-017-05927-4
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identityCited by: 35
Author(s): Handan Melike Dönertaş, Hamit İzgi, Altuğ Kamacıoğlu, Zhisong He, Philipp Khaitovich, Mehmet Somel
Software Mentions: 7
Published: almost 7 years ago
10.1186/1471-2105-16-S9-S2
Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysisCited by: 17
Author(s): Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
Software Mentions: 7
Published: about 9 years ago
10.1038/s41598-017-13397-x
The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pestCited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: over 6 years ago
10.15252/embj.2020105565
The RNA polymerase II subunit RPB‐9 recruits the integrator complex to terminate <i>Caenorhabditis elegans</i> piRNA transcriptionCited by: 13
Author(s): Ahmet C. Berkyurek, Giulia Furlan, Lisa Lampersberger, Toni Beltran, Eva-Maria Weick, Emily Nischwitz, Isabela Cunha Navarro, Fabian Braukmann, Alper Akay, Jonathan Price, Falk Butter, Peter Sarkies, Eric A. Miska
Software Mentions: 7
Published: over 3 years ago
10.1093/g3journal/jkab255
Improved draft reference genome for the Glassy-winged Sharpshooter (<i>Homalodisca vitripennis</i>), a vector for Pierce’s diseaseCited by: 8
Author(s): Cassandra L. Ettinger, Frank J. Byrne, Matthew A. Collin, Derreck Carter-House, Linda L. Walling, Peter W. Atkinson, Rick A Redak, Jason E. Stajich
Software Mentions: 7
Published: almost 3 years ago
10.3390/genes11091107
Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticinaCited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: over 3 years ago
10.1186/s12859-018-2353-5
XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence dataCited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: over 5 years ago
10.1002/jcsm.12665
Myogenesis modelled by human pluripotent stem cells: a multi‐omic study of Duchenne myopathy early onsetCited by: 28
Author(s): Virginie Mournetas, Emmanuelle Massouridès, Jean-Baptiste Dupont, Étienne Kornobis, Hélène Polveche, Margot Jarrige, Alan R L Dorval, Maxime R. F. Gosselin, Antigoni Manousopoulou, Spiros D. Garbis, Dariusz C. Górecki, Christian Pinset
Software Mentions: 7
Published: over 3 years ago
10.1186/s13195-020-00654-x
Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through RNA sequencing analysisCited by: 44
Author(s): Daichi Shigemizu, Tomohisa Mori, Shintaro Akiyama, Sayuri Higaki, Hiroshi Watanabe, Takashi Sakurai, Shumpei Niida, Kouichi Ozaki
Software Mentions: 7
Published: almost 4 years ago
10.1097/j.pain.0000000000001416
Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injuryCited by: 41
Author(s): Georgios Baskozos, J. D. K. Dawes, Jean-Sébastien Austin, Ana Antunes-Martins, Lucy A. McDermott, Alex Clark, Teodora Trendafilova, Jon Lees, Stephen B. McMahon, Jeffrey S. Mogil, Christine Orengo, David L.H. Bennett
Software Mentions: 7
Published: over 5 years ago
10.1186/s12864-021-07744-6
The effect of methanol fixation on single-cell RNA sequencing dataCited by: 19
Author(s): Xinlei Wang, Yu Liu, Angela Ruohao Wu
Software Mentions: 7
Published: almost 3 years ago
10.1186/s12870-020-02808-3
Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel OrangeCited by: 18
Author(s): Haipeng Zhang, Jiajing Chen, Zhaoxin Peng, Meiyan Shi, Xiao Liu, Wen Huang, Youwu Jiang, Yunjiang Cheng, Juan Xu, Hongyan Zhang
Software Mentions: 7
Published: over 3 years ago
10.1186/1472-6807-13-2
Designing and benchmarking the MULTICOM protein structure prediction systemCited by: 25
Author(s): Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng
Software Mentions: 7
Published: over 11 years ago
10.1186/s12864-016-3300-3
Assessing characteristics of RNA amplification methods for single cell RNA sequencingCited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: over 7 years ago
10.3390/cells10071576
Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine ModelCited by: 7
Author(s): Leszek Gromadziński, Łukasz Paukszto, Agnieszka Skowrońska, Piotr Holak, Michał Smoliński, Elżbieta Łopieńska–Biernat, Ewa Lepiarczyk, Aleksandra Lipka, J Jastrzebski, Marta Majewska
Software Mentions: 7
Published: almost 3 years ago
10.3390/cells10050973
Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA SequencingCited by: 5
Author(s): Shaojian Gao, Zhijie Wu, Jeerthi Kannan, Liza Mathews, Xingmin Feng, Sachiko Kajigaya, Neal S. Young
Software Mentions: 7
Published: about 3 years ago
10.1186/s13073-020-00741-6
Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patientCited by: 93
Author(s): Hye Won Lee, Wingyan Chung, Hae‐Ock Lee, Da Eun Jeong, Areum Jo, Ji Hyun Lim, Jeong Hee Hong, Do‐Hyun Nam, Byong Chang Jeong, Se Hoon Park, Kyeung Min Joo, Woong-Yang Park
Software Mentions: 7
Published: about 4 years ago
10.1186/s13073-019-0657-3
A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseasesCited by: 67
Author(s): Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Àlex Arenas, B. Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan‐Erik Karlsson, Mattias Köpsén, Eun Jung Lee, Antonio Lentini, Xinxiu Li, Mattias Magnusson, David Martínez-Enguita, Andreas Matussek, Colm E. Nestor, Samuel Schäfer, Oliver Seifert, Ceylan Sonmez, Henrik Stjernman, Andreas Tjärnberg, Simon Wu, Karin Åkesson, Alexander K Shalek, Margaretha Stenmarker, Huan Zhang, Mika Gustafsson, Mikael Benson
Software Mentions: 7
Published: almost 5 years ago
10.1186/s13059-021-02309-y
Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathwaysCited by: 11
Author(s): Carrie Kovalak, Scott Donovan, Alicia A. Bicknell, Mihir Metkar, Melissa J. Moore
Software Mentions: 7
Published: about 3 years ago
10.1186/s13059-021-02372-5
Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1Cited by: 11
Author(s): Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Francesca Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf, Juan Valcárcel
Software Mentions: 7
Published: about 3 years ago
10.3390/cells9020458
Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice SitesCited by: 25
Author(s): Karl Frey, Boas Pucker
Software Mentions: 7
Published: over 4 years ago
10.1186/s13040-016-0099-z
SePIA: RNA and small RNA sequence processing, integration, and analysisCited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: about 8 years ago
10.1186/1471-2105-16-S13-S7
Enhancing cancer clonality analysis with integrative genomicsCited by: 6
Author(s): Erich A. Peterson, Michael Bauer, Shweta S. Chavan, Cody Ashby, Niels Weinhold, Christoph Heuck, Gareth J. Morgan, Donald J. Johann
Software Mentions: 7
Published: over 8 years ago
10.1007/s00572-020-01001-6
Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptomeCited by: 6
Author(s): Christina Paparokidou, Jonathan R. Leake, David J. Beerling, Stephen A. Rolfe
Software Mentions: 7
Published: over 3 years ago
10.1016/j.stem.2020.11.015
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental HematopoiesisCited by: 152
Author(s): Anna Maria Ranzoni, Andrea Tangherloni, Ivan Berest, Simone G. Riva, Brynelle Myers, Paulina M. Strzelecka, Jiarui Xu, Elisa Panada, Irina Mohorianu, Judith B. Zaugg, Ana Cvejic
Software Mentions: 7
Published: over 3 years ago
10.1186/s12859-016-1274-4
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipelineCited by: 95
Author(s): Qian Qin, Shenglin Mei, Qiu Liang Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Xu Han, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long, X. Shirley Liu
Software Mentions: 7
Published: over 7 years ago
10.1093/molbev/msz154
Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome ParasitesCited by: 51
Author(s): Roy N. Platt, Marina McDew-White, Winka Le Clec’h, Frédéric D. Chevalier, Fiona Allan, Aidan M. Emery, Amadou Garba, Amina Amadou Hamidou, M. Shaali, Joanne P. Webster, David Rollinson, Bonnie L. Webster, Timothy J. Anderson
Software Mentions: 7
Published: almost 5 years ago
10.1038/s41422-019-0168-1
Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fateCited by: 64
Author(s): Rui Gao, Xingqun Liang, Sirisha Cheedipudi, Julio Cordero, Xiyi Jiang, Qingquan Zhang, Luca Caputo, Stefan Günther, Carsten Kuenne, Yongcheng Ren, Shoumo Bhattacharya, Xuejun Yuan, Guillermo Barreto, Yihan Chen, Thomas Braun, Sylvia M. Evans, Yunfu Sun, Gergana Dobreva
Software Mentions: 7
Published: about 5 years ago
10.1186/s12864-018-4835-2
Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)Cited by: 15
Author(s): Julien Richard Albert, Takao Koike, Hamid Younesy, Iain Thompson, Aaron B. Bogutz, Mehdi Karimi, Matthew C. Lorincz
Software Mentions: 7
Published: almost 6 years ago
10.1186/s13059-020-02156-3
STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cellsCited by: 42
Author(s): Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne, Hendrik Marks, Hendrik G. Stunnenberg, Wout Megchelenbrink
Software Mentions: 7
Published: over 3 years ago
10.1016/j.devcel.2017.07.002
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence TranscriptionCited by: 59
Author(s): Alper Akay, Tomás Di Domenico, Kin Man Suen, Amena Nabih, Guillermo E. Parada, Mark Larance, Ragini Medhi, Ahmet C. Berkyurek, Xinlian Zhang, Christopher J. Wedeles, Konrad L. M. Rudolph, Jan Engelhardt, Martin Hemberg, Ping Ma, Angus I. Lamond, Julie M. Claycomb, Eric A. Miska
Software Mentions: 7
Published: almost 7 years ago
10.1186/s12864-021-07735-7
Non-coding RNAs in the interaction between rice and Meloidogyne graminicolaCited by: 11
Author(s): Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz‐Ferrer, Carolina Escobar, Tim De Meyer, Tina Kyndt
Software Mentions: 7
Published: almost 3 years ago
10.1186/s12864-021-07593-3
Dense time-course gene expression profiling of the Drosophila melanogaster innate immune responseCited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: about 3 years ago
10.3390/genes11101165
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq DataCited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: over 3 years ago
10.1186/s13059-020-02087-z
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotoleranceCited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: almost 4 years ago
10.3390/microorganisms8101528
Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid BacteriaCited by: 14
Author(s): Mathilde Lebas, Peggy Garault, Daniel Carrillo, Francisco M. Codoñer, Muriel Derrien
Software Mentions: 7
Published: over 3 years ago
10.3390/genes11040400
Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host PlantCited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: about 4 years ago
10.1534/g3.120.401579
High-Quality Assemblies for Three Invasive Social Wasps from the <i>Vespula</i> GenusCited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: over 3 years ago
10.1534/g3.119.0011
Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode <i>Auanema rhodensis</i>Cited by: 31
Author(s): Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, André Pires-daSilva
Software Mentions: 7
Published: about 5 years ago
10.1016/j.celrep.2020.107694
A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during AgingCited by: 24
Author(s): Qi Zhou, Qianfen Wan, Yuxi Jiang, Jin Liu, Qiang Li, Li Sun
Software Mentions: 7
Published: about 4 years ago
10.1016/j.virol.2021.03.019
Zika virus infection during pregnancy protects against secondary infection in the absence of CD8+ cellsCited by: 3
Author(s): Blake Schouest, Brandon J Beddingfield, Margaret H. Gilbert, Rudolf P. Bohm, Faith Schiro, Pyone P. Aye, Antonito T. Panganiban, Diogo M. Magnani, Nicholas J. Maness
Software Mentions: 7
Published: almost 3 years ago
10.1186/s13059-021-02321-2
Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approachCited by: 23
Author(s): Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher, Edda G. Schulz
Software Mentions: 7
Published: about 3 years ago
10.1016/j.celrep.2019.12.057
Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem CellsCited by: 118
Author(s): James Rhodes, Angelika Feldmann, Benjamín Hernández-Rodríguez, Noèlia Díaz, Jill M. Brown, Nadezda A. Fursova, Neil P. Blackledge, Praveen Prathapan, Paula Dobrinić, Miles K. Huseyin, Aleksander Szczurek, Kai Kruse, K Nasmyth, Veronica J. Buckle, Juan M. Vaquerizas, Robert J. Klose
Software Mentions: 7
Published: over 4 years ago
10.1016/j.cmet.2018.04.013
The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and DiabetesCited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: about 6 years ago
10.26508/lsa.202101080
Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changesCited by: 9
Author(s): Melissa Bothe, René Buschow, Sebastiaan H. Meijsing
Software Mentions: 7
Published: almost 3 years ago
10.1186/s40478-020-01020-6
Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitisCited by: 7
Author(s): Sharon Melamed, Roy Avraham, Deborah E. Rothbard, Noam Erez, Tomer Israely, Ziv Klausner, Anthony H. Futerman, Nir Paran, Einat B. Vitner
Software Mentions: 7
Published: almost 4 years ago
10.3389/fonc.2019.00523
Comprehensive Gene Expression Analysis in NMIBC Using RNA-seq Reveals New Therapy StrategiesCited by: 11
Author(s): Xiaoliang Chen, Fuquan Jiang, Jia Chen, Ming Liu, Yong-Hao Nan, Licheng Qu, Qingkuo Kong, Fangfang Hou, Wenshan Luo, Wanli Na, Xin Jin, Jiufeng Tan
Software Mentions: 7
Published: almost 5 years ago
10.1242/dev.178590
Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body planCited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: over 5 years ago
10.1038/s41419-021-04067-y
Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: almost 3 years ago
10.1186/s12864-021-07489-2
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue cultureCited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: about 3 years ago
10.1038/s41418-021-00751-w
Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomasCited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: over 3 years ago
10.26508/lsa.201800085
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cellsCited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: about 6 years ago
10.1371/journal.ppat.1009130
Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profilesCited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: over 3 years ago
10.1016/j.isci.2021.102870
Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritanceCited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: almost 3 years ago
10.3389/fgene.2019.00309
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric FunctionsCited by: 26
Author(s): Simon A. Hardwick, Samuel D. Bassett, Dominik C. Kaczorowski, James Blackburn, Kirston Barton, Nenad Bartoniček, Shaun Carswell, Hagen Tilgner, Clement T. Loy, Glenda M. Halliday, Tim R. Mercer, Martin A. Smith, John S. Mattick
Software Mentions: 7
Published: about 5 years ago
10.7554/eLife.22631
The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cellsCited by: 184
Author(s): Hamish W King, Robert J. Klose
Software Mentions: 7
Published: about 7 years ago
10.7554/eLife.63194
Evolutionary dynamics of transposable elements in bdelloid rotifersCited by: 21
Author(s): Reuben W. Nowell, Christopher G. Wilson, Pedro Almeida, Philipp H. Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodríguez, Irina R. Arkhipova, Timothy G. Barraclough
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-019-6349-y
Molecular evolution and expression of opsin genes in Hydra vulgarisCited by: 16
Author(s): Aide Macias-Muñoz, Rabi Murad, A Mortazavi
Software Mentions: 7
Published: over 4 years ago
10.1016/j.ccell.2020.08.016
Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast CancerCited by: 35
Author(s): Susana Ros, Alan J. Wright, Paula D’Santos, De‐En Hu, Robin Hesketh, Yaniv Lubling, Dimitra Georgopoulou, Giulia Lerda, Dominique‐Laurent Couturier, Pedram Razavi, Rapahel Pelossof, Ankita Batra, Elizabeth Mannion, David Y. Lewis, Alistair Martin, Richard D. Baird, Mafalda Oliveira, Leonora W. de Boo, Sabine C. Linn, Maurizio Scaltriti, Oscar M. Rueda, Alejandra Bruna, Carlos Caldas, Kevin M. Brindle
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pone.0201830
Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease riskCited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: almost 6 years ago
10.3389/fmolb.2020.565530
Cross-Sectional Transcriptional Analysis of the Aging Murine HeartCited by: 4
Author(s): Matthew Greenig, Andrew Melville, Derek Huntley, Mark Isalan, Michał Mielcarek
Software Mentions: 7
Published: over 3 years ago
10.1186/s12967-021-02936-w
TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models RepositoryCited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: almost 3 years ago
10.3389/fgene.2019.00400
NormExpression: An R Package to Normalize Gene Expression Data Using Evaluated MethodsCited by: 10
Author(s): Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Haishuo Ji, Hua Wang, Gustavo Glusman, Max Robinson, Lin Liu, Jishou Ruan, Shan Gao
Software Mentions: 7
Published: about 5 years ago
10.7554/eLife.69975
Notch-induced endoplasmic reticulum-associated degradation governs mouse thymocyte β−selectionCited by: 8
Author(s): Xia Liu, Jingjing Yu, Longyong Xu, Katharine Umphred-Wilson, Fanglue Peng, Yao Ding, Brendan M Barton, Xiangdong Lv, Michael Y Zhao, Shengyi Sun, Yuning Hong, Ling Qi, Stanley Adoro, Xi Chen
Software Mentions: 7
Published: almost 3 years ago
10.7554/eLife.56689
Genome streamlining in a minute herbivore that manipulates its host plantCited by: 30
Author(s): Robert Greenhalgh, Wannes Dermauw, Joris J. Glas, Stéphane Rombauts, Nicky Wybouw, Jainy Thomas, Juan M. Alba, Ellen J. Pritham, Saioa Legarrea, René Feyereisen, Yves Van de Peer, Thomas Van Leeuwen, Richard M. Clark, Merijn R. Kant
Software Mentions: 7
Published: over 3 years ago
10.1186/s12915-021-01062-9
Exposure to ethanol leads to midfacial hypoplasia in a zebrafish model of FASD via indirect interactions with the Shh pathwayCited by: 12
Author(s): Alfire Sidik, Groves Dixon, Desirè M. Buckley, Hannah G. Kirby, Suwan Sun, Johann K. Eberhart
Software Mentions: 7
Published: almost 3 years ago
10.1093/bfgp/ely003
The impact of single-cell RNA sequencing on understanding the functional organization of the immune systemCited by: 15
Author(s): Péter Végh, Muzlifah Haniffa
Software Mentions: 7
Published: about 6 years ago
10.3389/fgene.2021.664424
Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and TissuesCited by: 5
Author(s): Eliah Overbey, Theros T Ng, Pietro Catini, Lisa Griggs, Paul A. Stewart, Suzana Tkalčić, R. David Hawkins, Yvonne Drechsler
Software Mentions: 7
Published: almost 3 years ago
10.7554/eLife.61138
The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle functionCited by: 15
Author(s): Zachary Clemens, Sruthi Sivakumar, Abish Pius, Amrita Sahu, Sunita Shinde, Hikaru Mamiya, Nathaniel Luketich, Jian Cui, Purushottam D. Dixit, Joerg D. Hoeck, Sebastian Kreuz, Michael Franti, Aaron Barchowsky, Fabrisia Ambrosio
Software Mentions: 7
Published: about 3 years ago
10.1186/s12864-021-07509-1
Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasisCited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: about 3 years ago
10.1093/bib/bbx143
Bioinformatics for precision oncologyCited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: over 6 years ago
10.3389/fgene.2020.00396
Single-Cell Transcriptomic Analysis Reveals Mitochondrial Dynamics in Oocytes of Patients With Polycystic Ovary SyndromeCited by: 34
Author(s): Lingbin Qi, Boxuan Liu, Xian Chen, Qiwei Liu, Wanqiong Li, Bo Lv, Xiaoyu Xu, Lu Wang, Qiao Zeng, Jinfeng Xue, Zhigang Xue
Software Mentions: 7
Published: about 4 years ago
10.7554/eLife.66788
An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinomaCited by: 11
Author(s): Rediet Zewdu, Elnaz Mirzaei Mehrabad, Kelley Ingram, Pengshu Fang, Katherine L Gillis, Soledad A. Camolotto, Grace Orstad, Alex Jones, Michelle C. Mendoza, Benjamin T. Spike, Eric L. Snyder
Software Mentions: 7
Published: about 3 years ago
10.7554/eLife.59654
HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitnessCited by: 19
Author(s): Jessica Sy Ho, Federico Di Tullio, Megan Schwarz, Diana Low, Danny Incarnato, Tommaso Tabaglio, Jingxian Zhang, Heike Wollmann, Leilei Chen, Ömer An, Tim Chan, Alexander Hall Hickman, Simin Zheng, Vladimir Roudko, Sujun Chen, Alcida Karz, Musaddeque Ahmed, Housheng Hansen He, Benjamin Greenbaum, Salvatore Oliviero, Michela Serresi, Gaetano Gargiulo, Karen Mann, Eva Hernando, David J. Mulholland, Ivan Marazzi, Dave Keng Boon Wee, Ernesto Guccione
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pgen.1006402
Gene co-expression network connectivity is an important determinant of selective constraintCited by: 96
Author(s): Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K. Ingvarsson, Nathaniel R. Street, Torgeir R. Hvidsten
Software Mentions: 7
Published: about 7 years ago
10.12688/f1000research.17145.2
False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errorsCited by: 35
Author(s): Ashis Saha, Alexis Battle
Software Mentions: 7
Published: about 5 years ago
10.1371/journal.pgen.1009587
The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotencyCited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: about 3 years ago
10.7554/eLife.29312
Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesisCited by: 35
Author(s): Isabelle Bergiers, Tallulah Andrews, Özge Vargel Bölükbaşı, Andreas Buneß, Ewa Janosz, Natalia López-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin, Paul Collier, Bianka Baying, Vladimı́r Beneš, Martin Hemberg, Christophe Lancrin
Software Mentions: 7
Published: about 6 years ago
10.1186/s12864-021-07595-1
Dynamics of rumen gene expression, microbiome colonization, and their interplay in goatsCited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: about 3 years ago
10.3390/brainsci10020109
Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional ChangesCited by: 27
Author(s): Dar'ya Pozhidayeva, Sean P. Farris, Calla M Goeke, Evan Firsick, Kayla G. Townsley, Marina Guizzetti, Angela R. Ozburn
Software Mentions: 7
Published: over 4 years ago
10.12688/f1000research.11290.1
Gene length and detection bias in single cell RNA sequencing protocolsCited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: about 7 years ago
10.7554/eLife.34031
Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticityCited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: about 6 years ago
10.7554/eLife.51529
Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stabilityCited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.ppat.1005438
Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene ExpressionCited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 8 years ago
10.1016/j.ccell.2019.08.008
An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in CancerCited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.pone.0173115
Altered regulation and expression of genes by BET family of proteins in COPD patientsCited by: 11
Author(s): Rajneesh Malhotra, Nisha Kurian, Xin Zhou, Fang Jiang, Susan J. Monkley, Amy DeMicco, Ib Groth Clausen, Göran Dellgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg, Elisabeth Israelsson, Graham Belfield, Outi Vaarala
Software Mentions: 7
Published: over 7 years ago
10.1093/bib/bbz126
Systematic evaluation of differential splicing tools for RNA-seq studiesCited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: over 4 years ago
10.12688/f1000research.17916.1
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seqCited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: over 5 years ago
10.1534/g3.114.011759
Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform ExpressionCited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: almost 10 years ago
10.7554/eLife.51413
Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammationCited by: 190
Author(s): Ankit Jambusaria, Zhigang Hong, Lianghui Zhang, Shubhi Srivastava, Arundhati Jana, Péter T. Tóth, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 7
Published: over 4 years ago