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: bioconductor: ballgown

https://packages.ecosyste.ms/registries/bioconductor.org/packages/ballgown

Flexible, isoform-level differential expression analysis
1 version
Latest release: about 1 year ago
3 dependent packages
133,475 downloads total

Papers Mentioning ballgown 21

10.3390/ijms20061510

Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR)
Cited by: 48
Author(s): Marta Majewska, Aleksandra Lipka, Łukasz Paukszto, J Jastrzebski, Karol Szeszko, Marek Gowkielewicz, Ewa Lepiarczyk, Marcin Jóźwik, Mariusz Majewski
Software Mentions: 10
Published: over 5 years ago

10.1186/s12859-016-1323-z

variancePartition: interpreting drivers of variation in complex gene expression studies
Cited by: 390
Author(s): Gabriel E. Hoffman, Eric E. Schadt
Software Mentions: 9
Published: almost 8 years ago

10.1371/journal.pone.0236226

Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response
Cited by: 10
Author(s): Fatemeh Gholizadeh, Ghader Mirzaghaderi
Software Mentions: 7
Published: about 4 years ago

10.3390/cells10071576

Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model
Cited 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: over 3 years ago

10.1038/s41598-021-89938-2

Improved methods for RNAseq-based alternative splicing analysis
Cited by: 20
Author(s): Rebecca F. Halperin, Apurva M. Hegde, Jessica D. Lang, Elizabeth A. Raupach, Christophe Legendre, Winnie S. Liang, Patricia LoRusso, Aleksandar Sekulić, Jeffrey A. Sosman, Jeffrey M. Trent, Sampathkumar Rangasamy, Patrick Pirrotte, Nicholas J. Schork
Software Mentions: 6
Published: over 3 years ago

10.1002/ece3.6422

Evidence of capacitation in the parasitoid wasp, Nasonia vitripennis, and its potential role in sex allocation
Cited by: 0
Author(s): Alun R. C. Jones, Eamonn B. Mallon
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2018.00477

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma
Cited by: 122
Author(s): Li Zhang, Chenkai Lv, Yichen Jin, Ganqi Cheng, Yibao Fu, Dongsheng Yuan, Yiran Tao, Yongli Guo, Xin Ni, Tieliu Shi
Software Mentions: 3
Published: about 6 years ago

10.1186/s13287-021-02256-2

EIF5A2 enhances stemness of epithelial ovarian cancer cells via a E2F1/KLF4 axis
Cited by: 9
Author(s): Kun Wang, Yiyang Wang, Yuanjian Wang, Shujie Liu, Chunyan Wang, Shuo Zhang, Tianli Zhang, Xinggang Yang
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.36898

Mitotic progression, arrest, exit or death relies on centromere structural integrity, rather than de novo transcription
Cited by: 16
Author(s): Marco Novais-Cruz, Maria Alba Abad, Wilfred F. J. van IJcken, Niels Galjart, A. Arockia Jeyaprakash, Hélder Maiato, Cristina Ferrás
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms221910589

Transcriptome and Proteome Analysis Revealed Key Pathways Regulating Final Stage of Oocyte Maturation of the Turkey (Meleagris gallopavo)
Cited by: 1
Author(s): Mariola Słowińska, Łukasz Paukszto, Laura Pardyak, J Jastrzebski, Ewa Liszewska, Joanna Bukowska, Krzysztof Kozłowski, Jan Jankowski, Barbara Bilińska, Andrzej Ciereszko
Software Mentions: 2
Published: about 3 years ago

10.3390/ijms19082201

Transcriptome Analysis Reveals Multiple Hormones, Wounding and Sugar Signaling Pathways Mediate Adventitious Root Formation in Apple Rootstock
Cited by: 45
Author(s): Ké Li, Yongqi Liang, Libo Xing, Jiangping Mao, Zhen Liu, Feng Dong, Meng Yuan, Mingyu Han, Caiping Zhao, Liang Bao, Dong Zhang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20061479

Transcriptome Analysis Reveals Cotton (Gossypium hirsutum) Genes That Are Differentially Expressed in Cadmium Stress Tolerance
Cited by: 29
Author(s): Mingge Han, Xuke Lu, John Z. Yu, Xiugui Chen, Xiaoge Wang, Waqar Afzal Malik, Junjuan Wang, Delong Wang, Shuai Wang, Lixue Guo, Chao Chen, Ruifeng Cui, Xiaoming Yang, Wuwei Ye
Software Mentions: 2
Published: over 5 years ago

10.1016/j.omtn.2019.10.033

Systematic Transcriptome and Regulatory Network Analyses Reveal the Hypoglycemic Mechanism of Dendrobium fimbriatum
Cited by: 9
Author(s): Qiong Zhang, Jing Li, Mei Luo, Gui-Yan Xie, Weiwei Zeng, Yuxin Wu, Yanhong Zhu, Xiangliang Yang, An‐Yuan Guo
Software Mentions: 2
Published: over 4 years ago

10.1186/s13072-019-0278-5

MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy)methylation and gene expression to maintain a neoplastic phenotype in T-ALL
Cited by: 20
Author(s): Candace J. Poole, Atul Lodh, Jeong Hyeon Choi, Jan van Riggelen
Software Mentions: 2
Published: over 5 years ago

10.1186/s13041-021-00829-z

RNA-seq co-expression network analysis reveals anxiolytic behavior of mice with Efnb2 knockout in parvalbumin+ neurons
Cited by: 1
Author(s): Ying Sun, Le Ma, Jianhua Chen, Weidi Wang, Shi-Yu Peng, Ying Cheng, Yu Zhang, Jinghong Chen, Peijun Ju
Software Mentions: 2
Published: over 3 years ago

10.1038/sdata.2017.24

Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas
Cited by: 178
Author(s): Zheng Zhao, Fengyan Meng, Wen Wang, Zheng Wang, Chuanbao Zhang, Tao Jiang
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.8801

Integrative analysis reveals pathways associated with sex reversal in <i>Cynoglossus semilaevis</i>
Cited by: 4
Author(s): Zhan Ye, Weifeng Wang, Yaqun Zhang, Liping Wang, Yu Hua Cui, Hengde Li
Software Mentions: 1
Published: over 4 years ago

10.3389/fimmu.2021.570425

Peroxisome Proliferator-Activated Receptor-δ Deficiency in Microglia Results in Exacerbated Axonal Injury and Tissue Loss in Experimental Autoimmune Encephalomyelitis
Cited by: 8
Author(s): Ellinore R Doroshenko, Paulina C. Drohomyrecky, Annette Gower, Heather Whetstone, Lindsay S. Cahill, Milan Ganguly, Shoshana Spring, Tae Joon Yi, John G. Sled, Shannon Dunn
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-017-08738-9

Analyses of Long Non-Coding RNA and mRNA profiling using RNA sequencing in chicken testis with extreme sperm motility
Cited by: 40
Author(s): Yifan Liu, Yanyan Sun, Yunlei Li, Hao Bai, Fuguang Xue, Songshan Xu, Hong Xu, Lei Shi, Ning Yang, Jilan Chen
Software Mentions: 1
Published: about 7 years ago

10.1155/2020/5747923

Long Noncoding RNAs Coregulated by Annexin A7 and JNK in Hepatocellular Carcinoma Cells Identified by Whole-Genome Expression Profiling
Cited by: 1
Author(s): Qi Deng, Lianhong Li, Yanling Jin
Software Mentions: 1
Published: over 4 years ago

10.1111/tpj.14626

Dormancy cycling: translation‐related transcripts are the main difference between dormant and non‐dormant seeds in the field
Cited by: 28
Author(s): Gonda Buijs, Afke Vogelzang, Harm Nijveen, Leónie Bentsink
Software Mentions: 1
Published: over 4 years ago