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: about 12 years ago
3 dependent packages
0 downloads

Papers Mentioning STAR 5,759

10.3389/fgene.2018.00683
Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells
Cited by: 2
Author(s): Maxime Bodak, Jian Yu, Constance Ciaudo
Software Mentions: 2
Published: almost 6 years ago
10.3389/fgene.2019.00586
Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids
Cited by: 15
Author(s): Mark F. Richardson, Kylie Munyard, Larry Croft, Theo R. Allnutt, Felicity C. Jackling, Fahad Alshanbari, Matthew Jevit, Gus A. Wright, Rhys Cransberg, Ahmed Tibary, Polina L. Perelman, Belinda Appleton, Terje Raudsepp
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2018.00647
Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions
Cited by: 21
Author(s): Elvezia Maria Paraboschi, Giulia Cardamone, Giulia Soldà, Stefano Duga, Rosanna Asselta
Software Mentions: 2
Published: almost 6 years ago
10.3389/fgene.2020.601003
The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean
Cited by: 8
Author(s): Na Zhao, Xiaoyang Ding, Taotao Lian, Meng Wang, Yan Tong, Di Liang, Qi An, Shutao Sun, Scott A. Jackson, Liu B, Chunming Xu
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2021.683959
Camk2a-Cre and Tshz3 Expression in Mouse Striatal Cholinergic Interneurons: Implications for Autism Spectrum Disorder
Cited by: 3
Author(s): Xavier Caubit, Elise Arbeille, Dorian Chabbert, Florence Desprez, Imane Messak, Ahmed Fatmi, Bianca Habermann, Paolo Gubellini, Laurent Fasano
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2019.00889
Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra)
Cited by: 17
Author(s): Han Ming Gan, Mun Hua Tan, Christopher M. Austin, Craig D. H. Sherman, Yen Ting Wong, Jan M. Strugnell, Mark Gervis, Luke McPherson, Adam D. Miller
Software Mentions: 2
Published: about 5 years ago
10.3389/fgene.2019.00230
Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle
Cited by: 22
Author(s): Pâmela Almeida Alexandre, Marina Naval-Sánchez, Laércio R. Porto-Neto, José Bento Sterman Ferraz, Antônio Reverter, Heidge Fukumasu
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2021.714152
Pri smORF Peptides Are Wide Mediators of Ecdysone Signaling, Contributing to Shape Spatiotemporal Responses
Cited by: 2
Author(s): Azza Dib, Jennifer Zanet, Alexandra Mancheno-Ferris, Mélanie Gallois, Damien Markus, Philippe Valenti, Simon Marques-Prieto, Serge Plaza, Yuji Kageyama, Yuji Kageyama, Hélène Chanut-Delalande, François Payre
Software Mentions: 2
Published: about 3 years ago
10.3389/fgene.2021.651298
Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance
Cited by: 4
Author(s): Sin Gi Park, Eonji Noh, Su Ryun Choi, Boram Choi, In Gang Shin, Seung il Yoo, Dong Jin Lee, Shuaifei Ji, Hae Suk Kim, Yoon Jung Hwang, Jung Sun Kim, Jacqueline Batley, Yong Pyo Lim, David Edwards, Chang Pyo Hong
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.676935
Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene
Cited by: 1
Author(s): Elena N. Pushkova, George S. Krasnov, Valentina A. Lakunina, Roman O. Novakovskiy, Liubov V. Povkhova, Ekaterina M. Dvorianinova, А. Д. Бениаминов, Maria S. Fedorova, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, Alexey A. Dmitriev, Nataliya V. Melnikova
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2019.00150
Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques
Cited by: 4
Author(s): Eric Reed, Elizabeth Moses, Xiaohui Xiao, Gang Liu, Joshua D. Campbell, Catalina Perdomo, Stefano Monti
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2020.562855
Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size
Cited by: 2
Author(s): Xiaodong Zheng, Jin Cheng, Wenjuan Qin, Nyamsuren Balsai, Xuan-Jian Shang, Mengting Zhang, Hongquan Chen
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2020.00474
Bulked Segregant RNA-Seq Reveals Distinct Expression Profiling in Chinese Wheat Cultivar Jimai 23 Responding to Powdery Mildew
Cited by: 10
Author(s): Tong Zhu, Liru Wu, Huagang He, Jiancheng Song, Mengshu Jia, Liancheng Liu, Xiaolu Wang, Ran Han, Liping Niu, Wei Du, Xu Zhang, Wenrui Wang, Liang Xiao, Haosheng Li, Jing Liu, Hongxing Xu, Cheng Liu, Pengtao Ma
Software Mentions: 2
Published: over 4 years ago
10.3389/fgene.2019.00643
Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus)
Cited by: 20
Author(s): Ashley Byrne, Megan A. Supple, Roger Volden, Kristin L. Laidre, Beth Shapiro, Christopher Vollmers
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2020.535622
The FpPPR1 Gene Encodes a Pentatricopeptide Repeat Protein That Is Essential for Asexual Development, Sporulation, and Pathogenesis in Fusarium pseudograminearum
Cited by: 2
Author(s): Limin Wang, Shunpei Xie, Yinshan Zhang, Ruijiao Kang, Mengjuan Zhang, Min Wang, Haiyang Li, Linlin Chen, Hongxia Yuan, Shengli Ding, Liang Shen, Honglian Li
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2020.552490
Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction
Cited by: 11
Author(s): Flaviana Marzano, Mariano Francesco Caratozzolo, Arianna Consiglio, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Domenica D’Elia, Apollonia Tullo, Domenico Catalano
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2018.00379
SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin
Cited by: 7
Author(s): Kentaro Ohkuni, Nagesh Pasupala, Jennifer L Peek, Grace Lauren Holloway, Gloria D. Sclar, Reuben Levy-Myers, Richard E. Baker, Munira A. Basrai, Oliver Kerscher
Software Mentions: 2
Published: about 6 years ago
10.3389/fgene.2019.00710
Transcriptome Analysis Reveals Differential Expression of Genes Regulating Hepatic Triglyceride Metabolism in Pekin Ducks During Dietary Threonine Deficiency
Cited by: 9
Author(s): Yong Jiang, Ming Xie, Wenlei Fan, Jiajia Xue, Zhengkui Zhou, Jing Tang, Chen Guo-hong, Shuisheng Hou
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2019.00500
Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells
Cited by: 25
Author(s): Emma Jonasson, Salim Ghannoum, Emma Persson, Jan Ch Karlsson, Thomas Kroneis, Erik Larsson, Göran Landberg, Anders Ståhlberg
Software Mentions: 2
Published: over 5 years ago
10.3389/fgene.2021.657330
Transcriptional Profiling of Porcine HCC Xenografts Provides Insights Into Tumor Cell Microenvironment Signaling
Cited by: 3
Author(s): Shovik S. Patel, Amitha Sandur, Mohammed El-Kebir, Ron C. Gaba, Lawrence B. Schook, Kyle M. Schachtschneider
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.606285
Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks
Cited by: 7
Author(s): Maud Fagny, Marieke L. Kuijjer, Maike Stam, Johann Joets, Olivier Turc, Julien Rozière, Stéphanie Pateyron, Anthony Venon, Clémentine Vitte
Software Mentions: 2
Published: almost 4 years ago
10.3389/fimmu.2019.00816
Comparative Transcriptomic Analysis Identifies a Range of Immunologically Related Functional Elaborations of Lymph Node Associated Lymphatic and Blood Endothelial Cells
Cited by: 34
Author(s): Stella J. Berendam, Alexander F. Koeppel, Nicole R. Godfrey, Sherin J. Rouhani, Amber N. Woods, Anthony B. Rodriguez, J. David Peske, Kara L. Cummings, Stephen D. Turner, Víctor H. Engelhard
Software Mentions: 2
Published: over 5 years ago
10.3389/fimmu.2020.00453
Tissue-Specific Factors Differentially Regulate the Expression of Antigen-Processing Enzymes During Dendritic Cell Ontogeny
Cited by: 9
Author(s): Karim Mahiddine, Chervin Hassel, Claire Murat, Maeva Girard, Sylvie Guerder
Software Mentions: 2
Published: over 4 years ago
10.3389/fimmu.2017.01352
Human Primary Macrophages Derived In Vitro from Circulating Monocytes Comprise Adherent and Non-Adherent Subsets with Differential Expression of Siglec-1 and CD4 and Permissiveness to HIV-1 Infection
Cited by: 12
Author(s): Ousman Jobe, Jiae Kim, Eric Tycksen, Sayali Onkar, Nelson L. Michael, Carl R. Alving, Mangala Rao
Software Mentions: 2
Published: about 7 years ago
10.3389/fimmu.2021.625649
Complement-Opsonized HIV Modulates Pathways Involved in Infection of Cervical Mucosal Tissues: A Transcriptomic and Proteomic Study
Cited by: 2
Author(s): Cecilia Svanberg, Rada Ellegård, Elisa Crisci, Mohammad Khalid, Ninnie Borendal Wodlin, Maria Svenvik, Sofia Nyström, Kenzie Birse, Adam Burgener, Esaki M. Shankar, Marie Larsson
Software Mentions: 2
Published: over 3 years ago
10.3389/fimmu.2017.01807
Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
Cited by: 48
Author(s): Alex Rubinsteyn, Julia Kodysh, Isaac Hodes, Sebastien Mondet, Bülent Arman Aksoy, John P. Finnigan, Nina Bhardwaj, Jeff Hammerbacher
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2021.711545
The Differential Growth Inhibition of Phytophthora spp. Caused by the Rare Sugar Tagatose Is Associated With Species-Specific Metabolic and Transcriptional Changes
Cited by: 9
Author(s): Abdessalem Chahed, Valentina Lazazzara, Marco Moretto, Andrea Nesler, Paola E. Corneo, Essaïd Ait Barka, I. Pertot, Gerardo Puopolo, Michele Perazzolli
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2019.00429
Comparative Description of the Expression Profile of Interferon-Stimulated Genes in Multiple Cell Lineages Targeted by HIV-1 Infection
Cited by: 17
Author(s): Hirofumi Aso, Jumpei Ito, Yoshio Koyanagi, Kei Sato
Software Mentions: 2
Published: over 5 years ago
10.3389/fmicb.2021.724345
Blood Meals With Active and Heat-Inactivated Serum Modifies the Gene Expression and Microbiome of Aedes albopictus
Cited by: 2
Author(s): Arley Calle-Tobón, Andrés F. Holguin-Rocha, C Mark Moore, Meagan Rippee-Brooks, Paula Rozo-López, Jania Harrod, Soheila Fatehi, Guillermo Rúa‐Uribe, Yoonseong Park, Berlin Londoño-Rentería
Software Mentions: 2
Published: about 3 years ago
10.3389/fmicb.2020.568805
Single-Cell Transcriptomics Reveals That Metabolites Produced by Paenibacillus bovis sp. nov. BD3526 Ameliorate Type 2 Diabetes in GK Rats by Downregulating the Inflammatory Response
Cited by: 1
Author(s): Zhenyi Qiao, Xiaohua Wang, Huanchang Zhang, Jin Han, Huafeng Feng, Zhengjun Wu
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmicb.2018.01281
The BCGΔBCG1419c Vaccine Candidate Reduces Lung Pathology, IL-6, TNF-α, and IL-10 During Chronic TB Infection
Cited by: 22
Author(s): Mario Alberto Flores-Valdéz, César Pedroza-Roldán, Michel de Jesús Aceves-Sánchez, Eliza J.R. Peterson, Nitin S. Baliga, Rogelio Hernández-Pando, JoLynn Troudt, Elizabeth Creissen, Linda Izzo, Helle Bielefeldt‐Ohmann, Thomas Bickett, Angelo A. Izzo
Software Mentions: 2
Published: over 6 years ago
10.3389/fmicb.2021.676693
SARS-CoV-2-Host Chimeric RNA-Sequencing Reads Do Not Necessarily Arise From Virus Integration Into the Host DNA
Cited by: 12
Author(s): Anastasiya Kazachenka, George Kassiotis
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.00397
Binding of Phage-Encoded FlaGrab to Motile Campylobacter jejuni Flagella Inhibits Growth, Downregulates Energy Metabolism, and Requires Specific Flagellar Glycans
Cited by: 13
Author(s): Jessica Sacher, Asif Shajahan, James Butcher, Robert T. Patry, Annika Flint, David R. Hendrixson, Alain Stintzi, Parastoo Azadi, Christine M. Szymanski
Software Mentions: 2
Published: over 4 years ago
10.3389/fmicb.2015.00764
Integrated inference and evaluation of host–fungi interaction networks
Cited by: 45
Author(s): Christian W. Remmele, Christian H. Luther, Johannes Balkenhol, Thomas Dandekar, Tobias Müller, Marcus Dittrich
Software Mentions: 2
Published: over 9 years ago
10.3389/fmicb.2018.01457
Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?
Cited by: 16
Author(s): Caroline Poyntner, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 2
Published: over 6 years ago
10.3389/fmicb.2020.01688
Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections
Cited by: 16
Author(s): Fatemah Sadeghpour Heravi, Martha Zakrzewski, Karen Vickery, Matthew Malone, Honghua Hu
Software Mentions: 2
Published: over 4 years ago
10.3389/fmolb.2021.640779
CXCR2 May Serve as a Useful Index of Disease Activity in Interstitial Lung Disease Associated With Primary Sjögren’s Syndrome
Cited by: 0
Author(s): Xiaoyu Zhu, Saisai Lu, Lixia Zhu, Mengjiao Yu, Tingting Wei, Xiongzhao Zhu, Dan Chen, Chengshui Chen
Software Mentions: 2
Published: over 3 years ago
10.3389/fnmol.2021.659681
The Perils of Navigating Activity-Dependent Alternative Splicing of Neurexins
Cited by: 8
Author(s): Kifayathullah Liakath‐Ali, Thomas C. Südhof
Software Mentions: 2
Published: over 3 years ago
10.3389/fnmol.2017.00009
Quantitative Nucleotide Level Analysis of Regulation of Translation in Response to Depolarization of Cultured Neural Cells
Cited by: 13
Author(s): Jasbir S. Dalal, Chengran Yang, Darshan Sapkota, Allison M. Lake, David R. O’Brien, Joseph D. Dougherty
Software Mentions: 2
Published: almost 8 years ago
10.3389/fnmol.2018.00104
Altered Gene-Regulatory Function of KDM5C by a Novel Mutation Associated With Autism and Intellectual Disability
Cited by: 52
Author(s): Christina N Vallianatos, Clara Farrehi, Michael J. Friez, Margit Burmeister, Catherine E. Keegan, Shigeki Iwase
Software Mentions: 2
Published: over 6 years ago
10.3389/fnmol.2019.00318
Transcriptome Analysis of Pineal Glands in the Mouse Model of Alzheimer’s Disease
Cited by: 6
Author(s): Kwang Il Nam, Gil-Sang Yoon, Young‐Kook Kim, Jeong Sup Song
Software Mentions: 2
Published: almost 5 years ago
10.3389/fnana.2019.00023
Uncovering the Functional Link Between SHANK3 Deletions and Deficiency in Neurodevelopment Using iPSC-Derived Human Neurons
Cited by: 29
Author(s): Guofu Huang, Shuting Chen, Xiaoxia Chen, Jiajun Zheng, Zhuoran Xu, Abolfazl Doostparast Torshizi, Siyi Gong, Qingpei Chen, Xiaokuang Ma, Jianan Yu, Libing Zhou, Shenfeng Qiu, Kai Wang, Lingling Shi
Software Mentions: 2
Published: over 5 years ago
10.3389/fnins.2020.00280
Gene Expression Dynamics at the Neurovascular Unit During Early Regeneration After Cerebral Ischemia/Reperfusion Injury in Mice
Cited by: 19
Author(s): Roxane-Isabelle Kestner, Franziska Mayser, Rajkumar Vutukuri, Lena Hansen, Stefan Günther, R. Brunkhorst, Kavi Devraj, Waltraud Pfeilschifter
Software Mentions: 2
Published: over 4 years ago
10.3389/fnins.2019.01139
Impairment of Membrane Repolarization Accompanies Axon Transport Deficits in Glaucoma
Cited by: 13
Author(s): Rachel A. Fischer, Michael L Risner, Abigail L. Roux, Lauren K. Wareham, Rebecca M. Sappington
Software Mentions: 2
Published: about 5 years ago
10.3389/fnins.2020.00900
Pyneal: Open Source Real-Time fMRI Software
Cited by: 5
Author(s): Jeff MacInnes, R. Alison Adcock, Andrea Stocco, Chantel S. Prat, Rajesh P. N. Rao, Kathryn C. Dickerson
Software Mentions: 2
Published: about 4 years ago
10.3389/fnins.2019.01032
Enriched Environmental Conditions Modify the Gut Microbiome Composition and Fecal Markers of Inflammation in Parkinson’s Disease
Cited by: 16
Author(s): Yogesh Singh, Mohamed El-Hadidi, Jakob Admard, Zinah Wassouf, Julia M. Schulze‐Hentrich, Ursula Kohlhofer, Leticia Quintanilla-Martı́nez, Daniel H. Huson, Olaf Rieß, Nicolas Casadei
Software Mentions: 2
Published: about 5 years ago
10.3389/fnins.2021.636969
Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells
Cited by: 5
Author(s): Ángeles Arzalluz-Luque, José Luis Cabrera, Heli Skottman, Alberto Benguría, Arantxa Bolinches-Amorós, Nicolás Cuenca, Vincenzo Lupo, Ana Dopazo, Sonia Tarazona, Bárbara Delás, Miguel Carballo, Beatriz Pascual, Imma Hernán, Slaven Erceg, Dunja Lukovic
Software Mentions: 2
Published: over 3 years ago
10.3389/fnut.2021.590978
Mainstreaming Local Food Species for Nutritional and Livelihood Security: Insights From Traditional Food Systems of Adi Community of Arunachal Pradesh, India
Cited by: 3
Author(s): Ranjay K. Singh, Rakesh Bhardwaj, Anamika Singh, Temin Payum, Kumar Arvind, Anshuman Singh, L. Wangchu, Sanjay Kumar Upadhyay
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2021.667995
RNA-Sequencing Reveals Heat Shock 70-kDa Protein 6 (HSPA6) as a Novel Thymoquinone-Upregulated Gene That Inhibits Growth, Migration, and Invasion of Triple-Negative Breast Cancer Cells
Cited by: 17
Author(s): Shiyi Shen, Chunli Wei, Junjiang Fu
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2021.641187
A Zebrafish Model of Metastatic Colonization Pinpoints Cellular Mechanisms of Circulating Tumor Cell Extravasation
Cited by: 6
Author(s): Tyler A. Allen, Mark M. Cullen, Nathan Hawkey, Hiroyasu Mochizuki, Lan Nguyễn, Elyse Schechter, Luke B. Borst, Jeffrey A. Yoder, Jennifer A. Freedman, Steven R. Patierno, Ke Cheng, William C. Eward, Jason A. Somarelli
Software Mentions: 2
Published: about 3 years ago
10.3389/fonc.2021.650891
Autophagy-Related Three-Gene Prognostic Signature for Predicting Survival in Esophageal Squamous Cell Carcinoma
Cited by: 9
Author(s): Heyang Cui, Yongjia Weng, Ning Ding, Cheng Chen, Longlong Wang, Yong Zhou, Ling Zhang, Yongping Cui, Weimin Zhang
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2014.00007
Current Challenges in the Bioinformatics of Single Cell Genomics
Cited by: 38
Author(s): Ning Liu, Geng Li, Guibo Li, Yong Hou, Yin Tong, Jiankui He
Software Mentions: 2
Published: almost 11 years ago
10.3389/fonc.2021.684351
High-Throughput In Vitro Gene Expression Profile to Screen of Natural Herbals for Breast Cancer Treatment
Cited by: 4
Author(s): Ling Kui, Qinghua Kong, Xiaonan Yang, Yunbing Pan, Zetan Xu, Shouling Wang, Jian Chen, Kunhua Wei, Xiaolei Zhou, Xuebo Yang, Tingqin Wu, Anthati Mastan, Yao Liu, Jun Miao
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2020.547392
Apoptosis in Cancer Cells Is Induced by Alternative Splicing of hnRNPA2/B1 Through Splicing of Bcl-x, a Mechanism that Can Be Stimulated by an Extract of the South African Medicinal Plant, Cotyledon orbiculata
Cited by: 13
Author(s): Tshepiso Jan Makhafola, Mzwandile Mbele, Kiren Yacqub-Usman, Amy Hendren, Daisy B. Haigh, Zoe Blackley, Mervin Meyer, Nigel P. Mongan, David O. Bates, Zodwa Dlamini
Software Mentions: 2
Published: about 4 years ago
10.3389/fonc.2019.01305
Expanding the Transcriptome of Head and Neck Squamous Cell Carcinoma Through Novel MicroRNA Discovery
Cited by: 14
Author(s): Leigha D. Rock, Brenda C. Minatel, Erin A. Marshall, Florian Guisier, Adam P. Sage, Mateus Camargo Barros-Filho, Greg L. Stewart, Cathie Garnis, Wan L. Lam
Software Mentions: 2
Published: about 5 years ago
10.3389/fonc.2021.631021
High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer
Cited by: 13
Author(s): Anson T. Ku, Jacob Fredsøe, Karina D. Sørensen, Michael Borre, Mikael Evander, Thomas Laurell, Hans Lilja, Yvonne Ceder
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2021.667495
The Deubiquitinase USP39 Promotes ESCC Tumorigenesis Through Pre-mRNA Splicing of the mTORC2 Component Rictor
Cited by: 7
Author(s): Yuan Zhao, Huiwu Geng, Gang Liu, Qiang Ji, Xiaomin Cheng, Xinying Li, Wei Liu, Rick F. Thorne, Renquan Zhang, Xiaoying Li
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2020.593989
Systematically Characterizing A-to-I RNA Editing Neoantigens in Cancer
Cited by: 18
Author(s): Chi Zhou, Zhiting Wei, Liye Zhang, Zhaoyi Yang, Qi Liu
Software Mentions: 2
Published: almost 4 years ago
10.3389/fonc.2021.656132
Ginsenoside Rh7 Suppresses Proliferation, Migration and Invasion of NSCLC Cells Through Targeting ILF3-AS1 Mediated miR-212/SMAD1 Axis
Cited by: 5
Author(s): Xiangbo Chen, Wenguang Liu, Liu B
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2021.650673
Establishment of an Immune Cell Infiltration Score to Help Predict the Prognosis and Chemotherapy Responsiveness of Gastric Cancer Patients
Cited by: 26
Author(s): Quan Jiang, Jie Sun, Hao Chen, Chen Ding, Zhaoqing Tang, Yuanyuan Ruan, Fenglin Liu, Yihong Sun
Software Mentions: 2
Published: over 3 years ago
10.3389/fonc.2020.598394
Polyvinyl Alcohol Carbazate as a Polymer-Based Antitumoral Agent
Cited by: 0
Author(s): Felix Sellberg, Robin Fröbom, Christian Binder, Erik Berglund, David Berglund
Software Mentions: 2
Published: almost 4 years ago
10.3389/fonc.2020.01771
Immune Checkpoint Blockade Improves Chemotherapy in the PyMT Mammary Carcinoma Mouse Model
Cited by: 4
Author(s): Evelyn Sirait‐Fischer, Catherine Olesch, Annika F. Fink, Matthias Berkefeld, Arnaud Huard, Tobias Schmid, Kunio Takeda, Bernhard Brüne, Andreas Weigert
Software Mentions: 2
Published: about 4 years ago
10.3389/fonc.2020.01012
Dual-mTOR Inhibitor Rapalink-1 Reduces Prostate Cancer Patient-Derived Xenograft Growth and Alters Tumor Heterogeneity
Cited by: 19
Author(s): Federico La Manna, Marta De Menna, Nikhil Patel, Sofia Karkampouna, Maria Rosaria De Filippo, Irena Klima, Peter Kloen, Lijkele Beimers, George N. Thalmann, Rob C.M. Pelger, Estela Jacinto, Marianna Kruithof-de Julio
Software Mentions: 2
Published: over 4 years ago
10.3389/fped.2020.618553
Technical Considerations and Protocol Optimization for Neonatal Salivary Biomarker Discovery and Analysis
Cited by: 6
Author(s): Elizabeth Yen, Tomoko Kaneko-Tarui, Jill L. Maron
Software Mentions: 2
Published: almost 4 years ago
10.3389/fphar.2020.00952
Hypo-Osmotic Loading Induces Expression of IL-6 in Nucleus Pulposus Cells of the Intervertebral Disc Independent of TRPV4 and TRPM7
Cited by: 8
Author(s): Aleksandra Sadowska, Birsen Altinay, Wolfgang Hitzl, Stephen J. Ferguson, Karin Wuertz‐Kozak
Software Mentions: 2
Published: over 4 years ago
10.3389/fphar.2018.00431
GPCRomics: GPCR Expression in Cancer Cells and Tumors Identifies New, Potential Biomarkers and Therapeutic Targets
Cited by: 101
Author(s): Paul A. Insel, Krishna Sriram, Shu Z. Wiley, Andrea Wilderman, Trishna Katakia, Thalia McCann, Hiroshi Yokouchi, Lingzhi Zhang, Ross Corriden, Dongling Liu, Michael E. Feigin, Randall French, Andrew M. Lowy, Fiona Murray
Software Mentions: 2
Published: over 6 years ago
10.3389/fphar.2020.604404
Subacute Toxicity Study of Nicotinamide Mononucleotide via Oral Administration
Cited by: 6
Author(s): Yingnan You, Yang Gao, Han Wang, Jingshu Li, Xiang Zhang, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 2
Published: almost 4 years ago
10.3390/genes12081132
Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma
Cited by: 21
Author(s): Emel Rothzerg, Xuan Dung Ho, Jiake Xu, David Wood, Aare Märtson, Sulev Kõks
Software Mentions: 2
Published: over 3 years ago
10.3390/genes12091416
Papaya (Carica papaya L.) Flavour Profiling
Cited by: 12
Author(s): Zhou Zi-wei, Rebecca Ford, Ido Bar, Chutchamas Kanchana-udomkan
Software Mentions: 2
Published: about 3 years ago
10.1038/s41436-020-0766-9
Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance
Cited by: 88
Author(s): Diana Baralle, Jenny Lord, M. Lyon, Adam C. Gunning, Hugh Kelly, Penelope Cibin, Eleanor G. Seaby, Kerry Spiers-Fitzgerald, Jed Lye, Sian Ellard, N. Simon Thomas, David J. Bunyan, Andrew G.L. Douglas, Diana Baralle, Splicing
Software Mentions: 2
Published: over 4 years ago
10.1038/s41436-018-0137-y
TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants
Cited by: 40
Author(s): Jennifer N. Dines, Katie Golden‐Grant, Amy J. LaCroix, Alison M. Muir, Dianne Laboy Cintrón, Kirsty McWalter, Megan T. Cho, Angela Sun, J. Lawrence Merritt, Jenny Thies, Dmitriy Niyazov, Barbara K. Burton, Katherine Kim, Leah Fleming, Rachel Westman, Peter Karachunski, Joline Dalton, Alice Basinger, Can Fıçıcıoğlu, Ingo Helbig, Manuela Pendziwiat, Hiltrud Muhle, Katherine L. Helbig, Almuth Caliebe, René Santer, Kolja Becker, Sharon F. Suchy, Ganka Douglas, Francisca Millan, Amber Begtrup, Kristin G. Monaghan, Heather C Mefford
Software Mentions: 2
Published: over 5 years ago
10.1038/s41436-021-01204-y
Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype
Cited by: 3
Author(s): Satyamaanasa Polubothu, Davide Zecchin, Lara Al-Olabi, Daniël A. Lionarons, Mark Harland, Stuart Horswell, Anna Thomas, Lilian Hunt, Nathan Wlodarchak, Paula Aguilera, Sarah Brand, Dale Bryant, Cristina Carrera, Hui Chen, Greg Elgar, Catherine A. Harwood, Michael Howell, Lionel Larue, Sam Loughlin, Jeffrey R. MacDonald, Josep Malvehy, Sara Martin Barberan, Vanessa Martins da Silva, Miriam Molina, Deborah Morrogh, Dale Moulding, Jérémie Nsengimana, Alan Pittman, J.A. Puig‐Butillé, Kiran Parmar, Neil J. Sebire, Stephen W. Scherer, Paulina Stadnik, Philip Stanier, Gemma Tell, Regula Waelchli, Mehdi Zarrei, Susana Puig, Véronique Bataille, Yongna Xing, Eugene Healy, Gudrun E. Moore, Wei-Li Di, Julia Newton-Bishop, Julian Downward, Veronica A. Kinsler
Software Mentions: 2
Published: about 3 years ago
10.1186/gb-2014-15-1-r15
Differential protein occupancy profiling of the mRNA transcriptome
Cited by: 69
Author(s): Markus Schueler, Mathias Munschauer, Lea H. Gregersen, Ana Finzel, Alexander Loewer, Weiwei Chen, Markus Landthaler, Christoph Dieterich
Software Mentions: 2
Published: almost 11 years ago
10.1186/s13059-015-0684-3
Scalable microfluidics for single-cell RNA printing and sequencing
Cited by: 111
Author(s): Sugata Bose, Zhenmao Wan, A. J. H. Carr, Abbas H. Rizvi, G. Vieira, Dana Pe’er, Peter A. Sims
Software Mentions: 2
Published: over 9 years ago
10.1186/s13059-015-0762-6
Tools and best practices for data processing in allelic expression analysis
Cited by: 290
Author(s): Stephane E. Castel, Ami Levy‐Moonshine, Pejman Mohammadi, Eric Banks, Tuuli Lappalainen
Software Mentions: 2
Published: about 9 years ago
10.1186/s13059-015-0853-4
Meta-analysis of RNA-seq expression data across species, tissues and studies
Cited by: 115
Author(s): Peter H. Sudmant, Maria S. Alexis, Christopher B. Burge
Software Mentions: 2
Published: almost 9 years ago
10.1186/s13059-016-1054-5
Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection
Cited by: 94
Author(s): Rieza Aprianto, Jelle Slager, Siger Holsappel, Jan‐Willem Veening
Software Mentions: 2
Published: about 8 years ago
10.1186/s13059-017-1237-8
CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion
Cited by: 136
Author(s): Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill E. Moore, Xiao‐Ou Zhang, Chun‐Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Özata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng, Wen Xue
Software Mentions: 2
Published: over 7 years ago
10.1186/s13059-017-1363-3
Intergenic disease-associated regions are abundant in novel transcripts
Cited by: 38
Author(s): Nenad Bartoniček, Michael B. Clark, Xiu Cheng Quek, James R. Torpy, Antonia L. Pritchard, Jesper L.V. Mååg, Brian Gloss, Joanna Crawford, Ryan J. Taft, Nicholas K. Hayward, Grant W. Montgomery, John S. Mattick, Tim R. Mercer, Marcel E. Dinger
Software Mentions: 2
Published: almost 7 years ago
10.1186/s13059-018-1497-y
Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries
Cited by: 73
Author(s): Seung-Hoon Baek, Kyung Choi, Goon-Bo Kim, Hee‐Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kyung‐Il Chang, Joohwan Kim, Jeong‐Hwan Mun
Software Mentions: 2
Published: about 6 years ago
10.1186/s13059-018-1504-3
Predicting microRNA targeting efficacy in Drosophila
Cited by: 82
Author(s): Vikram Agarwal, Alexander O. Subtelny, Prathapan Thiru, Igor Ulitsky, David P. Bartel
Software Mentions: 2
Published: about 6 years ago
10.1186/s13059-018-1571-5
Simulation-based benchmarking of isoform quantification in single-cell RNA-seq
Cited by: 23
Author(s): Jennifer Westoby, Marcela Sjöberg-Herrera, Anne C. Ferguson-Smith, Martin Hemberg
Software Mentions: 2
Published: about 6 years ago
10.1186/s13059-019-1670-y
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
Cited by: 167
Author(s): Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery, Rob Patro
Software Mentions: 2
Published: over 5 years ago
10.1186/s13059-019-1910-1
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
Cited by: 734
Author(s): Sam Kovaka, Aleksey V. Zimin, Geo Pertea, Roham Razaghi, Steven L. Salzberg, Mihaela Pertea
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13059-019-1919-5
The somatic mutation landscape of the human body
Cited by: 76
Author(s): Pablo E. García-Nieto, Ashby J. Morrison, Hunter B. Fraser
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13059-020-02033-z
Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients
Cited by: 4
Author(s): Daniel Spakowicz, Shaoke Lou, Brian Barron, José L. Gómez, Tianxiao Li, Qing Liu, Nicole Grant, Xiting Yan, Rebecca Hoyd, George M. Weinstock, Geoffrey Chupp, Mark Gerstein
Software Mentions: 2
Published: over 4 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/s13059-020-02085-1
Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance
Cited by: 53
Author(s): Christine E. Eyler, Hironori Matsunaga, Volker Hovestadt, Samantha J. Vantine, Peter van Galen, B Bernstein
Software Mentions: 2
Published: over 4 years ago
10.1186/s40104-021-00560-8
Feeding a Saccharomyces cerevisiae fermentation product improves udder health and immune response to a Streptococcus uberis mastitis challenge in mid-lactation dairy cows
Cited by: 13
Author(s): Mario Vailati-Riboni, Dennis D. Coleman, Vincenzo Lopreiato, Abdulrahman S. Alharthi, Ryan Bucktrout, Emad Abdel-Hamied, Ismael Martínez-Cortés, Yu Liang, Erminio Trevisi, I. Yoon, JuanJuan Loor
Software Mentions: 2
Published: over 3 years ago
10.1186/s40781-018-0177-5
Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology
Cited by: 3
Author(s): Shanti Choudhary, Wenli Li, Derek M. Bickhart, Ramneek Verma, R. S. Sethi, Chandra Sekhar Mukhopadhyay, Ratan K. Choudhary
Software Mentions: 2
Published: over 6 years ago
10.1007/s13353-020-00603-2
European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients
Cited by: 15
Author(s): Szymon Hryhorowicz, Adam Ustaszewski, Marta Kaczmarek-Ryś, Emilia Lis, Michał Witt, Andrzej Pławski, Ewa Ziętkiewicz
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.jaut.2017.03.004
B cells expressing the IgA receptor FcRL4 participate in the autoimmune response in patients with rheumatoid arthritis
Cited by: 49
Author(s): Khaled Amara, Elizabeth Clay, Lorraine Yeo, Daniel Ramsköld, Julia Spengler, Natalie Sippl, J. A. Cameron, Lena Israelsson, Philip J. Titcombe, Caroline Grönwall, Ilfita Sahbudin, Andrew Filer, Karim Raza, Vivianne Malmström, Dagmar Scheel‐Toellner
Software Mentions: 2
Published: over 7 years ago
10.1128/JB.00780-18
Refining the Pneumococcal Competence Regulon by RNA Sequencing
Cited by: 33
Author(s): Jelle Slager, Rieza Aprianto, Jan‐Willem Veening
Software Mentions: 2
Published: over 5 years ago
10.1074/jbc.RA118.006271
Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200
Cited by: 36
Author(s): Karine Choquet, Diane Forget, Elisabeth Meloche, Marie‐Josée Dicaire, Geneviève Bernard, Adeline Vanderver, Raphael Schiffmann, Marc R. Fabian, Martin Teichmann, Benoit Coulombe, Bernard Brais, Claudia L. Kleinman
Software Mentions: 2
Published: over 5 years ago
10.1074/jbc.RA120.013206
An aberrantly sustained emergency granulopoiesis response accelerates postchemotherapy relapse in MLL1-rearranged acute myeloid leukemia in mice
Cited by: 2
Author(s): Hao Wang, Chirag Shah, Liping Hu, Weiqi Huang, Leonidas C. Platanias, Elizabeth A. Eklund
Software Mentions: 2
Published: over 4 years ago
10.1074/jbc.RA120.015152
Genome editing demonstrates that the −5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment
Cited by: 12
Author(s): Puja Agrawal, Steven Blinka, Kirthi Pulakanti, Michael Reimer, Cary Stelloh, Alison E. Meyer, Sridhar Rao
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.jbc.2021.100386
Two distinct trophectoderm lineage stem cells from human pluripotent stem cells
Cited by: 38
Author(s): Adam Mischler, Victoria Karakis, Jessica Mahinthakumar, Celeste K. Carberry, Adriana San-Miguel, Julia E. Rager, Rebecca C. Fry, Balaji M. Rao
Software Mentions: 2
Published: almost 4 years ago
10.1074/jbc.RA120.014126
Glycosyltransferase ST6Gal-I promotes the epithelial to mesenchymal transition in pancreatic cancer cells
Cited by: 32
Author(s): Colleen M. Britain, Nikita Bhalerao, Austin D. Silva, Asmi Chakraborty, Donald J. Buchsbaum, Michael R. Crowley, David K. Crossman, Yvonne J. K. Edwards, Susan L. Bellis
Software Mentions: 2
Published: almost 4 years ago
10.1074/jbc.RA120.014682
ABHD5 suppresses cancer cell anabolism through lipolysis-dependent activation of the AMPK/mTORC1 pathway
Cited by: 11
Author(s): Guohua Chen, Guoli Zhou, Aaron Lotvola, James G. Granneman, Jian Wang
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.jbc.2021.100882
PRPF19 regulates p53-dependent cellular senescence by modulating alternative splicing of MDM4 mRNA
Cited by: 21
Author(s): Kimiyoshi Yano, Ryou‐u Takahashi, Bunsyo Shiotani, Junko Abe, Tomoki Shidooka, Yuki Sudo, Yusuke Yamamoto, Shisei Kan, Hiroki Sakagami, Hidetoshi Tahara
Software Mentions: 2
Published: over 3 years ago