Ecosyste.ms: Papers

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: almost 6 years ago

10.1111/jcmm.14163

LncRNA-mRNA competing endogenous RNA network depicts transcriptional regulation in ischaemia reperfusion injury
Cited by: 19
Author(s): Hongying Liu, Dan-Ping Xu, Xin Zhong, Dongsheng Xu, Geng Chen, Junbo Ge, Hua Li
Software Mentions: 4
Published: almost 6 years ago

10.1111/jcmm.15569

LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity
Cited by: 8
Author(s): Amandine Guérin, Delphine Martire, Eva Trenquier, Tom Lesluyes, Sébastien Sagnol, Marine Pratlong, Elise Lefebvre, Frédéric Chibon, Pascal de Santa Barbara, Sandrine Faure
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0166104

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
Cited by: 249
Author(s): Shoko Iwai, Thomas Weinmaier, Brian L. Schmidt, Donna G. Albertson, Neil J. Poloso, Karim Dabbagh, Todd Z. DeSantis
Software Mentions: 4
Published: about 8 years ago

10.1093/aobpla/ply013

Patterns of alternative splicing vary between species during heat stress
Cited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: over 6 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: over 12 years ago

10.1186/s12870-015-0661-8

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit
Cited by: 51
Author(s): Noam Chayut, Hui Yuan, Shachar Ohali, Ayala Meir, Yelena Yeselson, Vitaly Portnoy, Yi Zheng, Zhangjun Fei, Efraim Lewinsohn, Nurit Katzir, Arthur A. Schaffer, Shimon Gepstein, Joseph Burger, L i Li, Yaakov Tadmor
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: almost 10 years ago

10.1128/mSystems.00596-19

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12887-019-1564-x

Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation
Cited by: 22
Author(s): Najeeha Talat Iqbal, Sana Syed, Kamran Sadiq, Marium Khan, Junaid Iqbal, Z. Jennie, Fayaz Umrani, Sheraz Ahmed, Elizabeth A. Maier, Lee A. Denson, Yael Haberman, Monica McNeal, Kenneth D.R. Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A. Moskaluk, Ta‐Chiang Liu, Ömer H. Yılmaz, Donald E. Brown, Michael J. Barratt, Vanderlene L. Kung, Jeffrey I. Gordon, Sean R. Moore, Syed Asad Ali
Software Mentions: 4
Published: over 5 years ago

10.1186/s40104-021-00626-7

NORHA, a novel follicular atresia-related lncRNA, promotes porcine granulosa cell apoptosis via the miR-183-96-182 cluster and FoxO1 axis
Cited by: 16
Author(s): Yao Wang, Zengxiang Pan, Xiaohong Du, Jinbi Zhang, Honglin Liu, Qifa Li
Software Mentions: 4
Published: about 3 years ago

10.1126/sciadv.abf7346

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome
Cited by: 4
Author(s): Seung Kyoon Kim, Xihui Liu, Jong-Min Park, Dahun Um, Gokhul Kilaru, Cheng Ming Chiang, Min-Hee Kang, Kimberly M. Huber, Keunsoo Kang, Tae Kyung Kim
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 10 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225658

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses
Cited by: 15
Author(s): Dominika Borowska, Richard Kuo, Richard Bailey, Kellie Watson, Pete Kaiser, Lonneke Vervelde, Mark P. Stevens
Software Mentions: 4
Published: almost 5 years ago

10.3390/insects9040185

Differential Gene Expression in Red Imported Fire Ant (Solenopsis invicta) (Hymenoptera: Formicidae) Larval and Pupal Stages
Cited by: 11
Author(s): Margaret L. Allen, Joshua H. Rhoades, Michael E. Sparks, Michael J. Grodowitz
Software Mentions: 4
Published: almost 6 years ago

10.1172/jci.insight.143289

LncRNA DRAIR is downregulated in diabetic monocytes and modulates inflammatory phenotype via epigenetic mechanisms
Cited by: 15
Author(s): Marpadga A. Reddy, Vishnu Amaram, Sadhan Das, Vinay Singh Tanwar, Rituparna Ganguly, Mei Wang, Linda Lanting, Lingxiao Zhang, Maryam Abdollahi, Zhuo Chen, Xiwei Wu, Sridevi Devaraj, Rama Natarajan
Software Mentions: 4
Published: over 3 years ago

10.1038/s41438-020-00416-8

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles
Cited by: 66
Author(s): Muhammad Umer, Luqman Bin Safdar, Haileslassie Gebremeskel, Shengjie Zhao, Pingli Yuan, Huiling Zhu, Mohamed Omar Kaseb, Muhammad Anees, Xingrong Lu, Nan He, Chengsheng Gong, Wenge Liu
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: about 9 years ago

10.1038/s41438-021-00531-0

Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Cited by: 28
Author(s): Chen Hong-guo, Xiangling Zeng, Jie Yang, Xuan Cai, Yumin Shi, Rencheng Zheng, Zhenqi Wang, Junyi Liu, Xiao Su Yi, Siwei Xiao, Qiang Fu, Jingjing Zou, Caiyun Wang
Software Mentions: 4
Published: over 3 years ago

10.1111/imb.12688

Jekyll or Hyde? The genome (and more) of <i>Nesidiocoris tenuis</i>, a zoophytophagous predatory bug that is both a biological control agent and a pest
Cited by: 11
Author(s): Kim Ferguson, Sako Visser, Martina Dalíková, Irena Provazníková, Alberto Urbaneja, František Marec, John H. Werren, Bas J. Zwaan, Bart A. Pannebakker, Eveline C. Verhulst
Software Mentions: 4
Published: almost 4 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: about 3 years ago

10.1126/sciadv.abg5982

Single-cell analyses unravel cell type–specific responses to a vitamin D analog in prostatic precancerous lesions
Cited by: 9
Author(s): Mohamed A. Abu el Maaty, Élise Grelet, Céline Keime, Anna‐Isavella Rerra, Justine Gantzer, C. Emprou, Julie Terzic, Régis Lutzing, Jean‐Marc Bornert, Gilles Laverny, Daniel Metzger
Software Mentions: 4
Published: over 3 years ago

10.1038/srep46553

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism
Cited by: 60
Author(s): Ling Yin, Yunhe An, Junjie Qu, Xinlong Li, Yali Zhang, Ian B. Dry, Huijuan Wu, Jiang Lu
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: almost 9 years ago

10.1016/j.heliyon.2020.e03493

Efficient differentiation and purification of human induced pluripotent stem cell-derived endothelial progenitor cells and expansion with the use of inhibitors of ROCK, TGF-β, and GSK3β
Cited by: 9
Author(s): Hiromasa Aoki, Misaki Yamashita, Tadahiro Hashita, Koichi Ogami, Shin‐ichi Hoshino, Takahiro Iwao, Tamihide Matsunaga
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giaa036

Chromosome-level reference genome of the jellyfish Rhopilema esculentum
Cited by: 16
Author(s): Yunfeng Li, Lei Gao, Yongjia Pan, Meilin Tian, Yulong Li, Chongbo He, Ying Dong, Yamin Sun, Zunchun Zhou
Software Mentions: 4
Published: over 4 years ago

10.3390/antiox9050402

Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione
Cited by: 1
Author(s): Qihao Guo, Linlin Cui, Weijun Sun, Li Feng, Hao Huang, Xueming Zhao, Huabin Zhu, Weihua Du
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giy101

The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation
Cited by: 56
Author(s): Conghui Liu, Yan Zhang, Yingxue Ren, Hengchao Wang, Shuqu Li, Fan Jiang, Lei Yin, Xi Qiao, Guojie Zhang, Wanqiang Qian, Bo Liu, Wei Fan
Software Mentions: 4
Published: over 6 years ago

10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Cited by: 49
Author(s): Yu Xing, Yang Liu, Qing Zhang, Xinghua Nie, Yamin Sun, Zhiyong Zhang, Huchen Li, Kefeng Fang, Guangpeng Wang, Hongwen Huang, Ton Bisseling, Qingqin Cao, Ling Qin
Software Mentions: 4
Published: about 5 years ago

10.1093/gigascience/giy049

Population genomic data reveal genes related to important traits of quail
Cited by: 23
Author(s): Yan Wu, Yaolei Zhang, Zhuocheng Hou, Guangyi Fan, Jinsong Pi, Shuai Sun, Chen Jiang, Huaqiao Liu, Xiao Du, Jie Shen, Gang Hu, Wenbin Chen, Angelo Pan, Yin PingPing, Xiaoli Chen, Yuejin Pu, Zhonghu He, Zhen-Hua Liang, Jianbo Jian, Hao Zhang, Bin Wu, Jing Sun, Jianwei Chen, Hu Tao, Ting Yang, Hong‐Wei Xiao, Huan Yang, Chuanwei Zheng, Mingzhou Bai, Xiaodong Fang, David W. Burt, Wen Wang, Qingyi Li, Xun Xu, Chengfeng Li, Huanming Yang, Jian Wang, Ning Yang, Xin Liu, Junzheng Du
Software Mentions: 4
Published: over 6 years ago

10.1093/gigascience/gix109

Genome sequence of the small brown planthopper, Laodelphax striatellus
Cited by: 90
Author(s): Jiachen Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yan-Yuan Bao, Wan Zhao, Wei Wang, Hong Liang, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Luo Li, Jianping Yu, Le Kang, Feng Cui
Software Mentions: 4
Published: about 7 years ago

10.1093/gigascience/giz136

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Cited by: 20
Author(s): Joeri S. Strijk, Damien Daniel Hinsinger, Fengping Zhang, Kaihua Cao
Software Mentions: 4
Published: about 5 years ago

10.1038/s41438-018-0073-7

Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV
Cited by: 39
Author(s): Tian Wang, Zhiqi Deng, Xi Zhang, Hongzheng Wang, Yu Wang, Xiuying Liu, Songyu Liu, Feng Xu, Tao Li, Daqi Fu, Beiwei Zhu, Yunbo Luo, Hongliang Zhu
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0120385

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize
Cited by: 58
Author(s): Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-15-636

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome
Cited by: 30
Author(s): Alejandro Padrón, Alvaro Molina-Cruz, Mariam Quiñones, José M. C. Ribeiro, Urvashi N. Ramphul, Janneth Rodrigues, Kui Shen, Ashley Haile, José L. Ramirez, Carolina Barillas‐Mury
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.27786

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response
Cited by: 29
Author(s): Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0093846

The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs
Cited by: 104
Author(s): Lei Shi, Zhe Zhang, Angela M Yu, Wei Wang, Zhi Wei, Ehtisham Akhter, Kelly Maurer, Patrícia Costa-Reis, Li Song, Michelle Petri, Kathleen E. Sullivan
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0102398

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
Cited by: 51
Author(s): Yaron S.N. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard Corbett, Yisu Li, Johnson Pang, P. Yussanne, Steven J.M. Jones, İnanç Birol
Software Mentions: 4
Published: over 10 years ago

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: over 10 years ago

10.1186/s13073-014-0059-5

A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD
Cited by: 21
Author(s): Peter K. Davidsen, John Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Víctor I. Peinado, C. González, Josep Roca, Stuart Egginton, Joan Albert Barberà, Francesco Falciani
Software Mentions: 4
Published: over 10 years ago

10.1186/s13742-015-0046-9

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Cited by: 118
Author(s): Vikas Gupta, April D Estrada, Ivory C. Blakley, Robert W. Reid, Ketan Patel, Mason D. Meyer, Stig Uggerhøj Andersen, Allan Brown, Mary Ann Lila, Ann E. Loraine
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41438-020-00432-8

Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)
Cited by: 9
Author(s): Yin Liang, Shanshan Wang, Chang Zhao, Xinwei Ma, Yiyong Zhao, Jing Shao, Yuebo Li, Honglian Li, Song Hong‐wei, Hong Mā, Hao Li, Bingbing Zhang, Liangsheng Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-020-01973-w

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Cited by: 27
Author(s): Xin Liu, Yong Chen, Yuannyu Zhang, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pntd.0001409

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: almost 13 years ago

10.1186/s13059-021-02444-6

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network
Cited by: 12
Author(s): Zhonghua Du, Wei Xue, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Yang Wang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen, Ilkay Celik, Yanbo Zhu, Zi Yan, Changhao Fu, Shanshan Liu, Benzheng Jiao, Zhuo Wang, Hui Zhang, Günhan Gülsoy, Jianjun Luo, Baoming Qin, Sujun Gao, Philipp Kapranov, Miguel A. Esteban, Songling Zhang, Wei Li, Ferhat Ay, Runsheng Chen, Andrew R. Hoffman, Jiuwei Cui, Ji-Fan Hu
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0181061

Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq
Cited by: 22
Author(s): Chunbao Zhang, Chunjing Lin, Fuyou Fu, Xiaofang Zhong, Bao Peng, Hao Yan, Jingyong Zhang, Weilong Zhang, Pengnian Wang, Xiaoyang Ding, Wei Zhang, Limei Zhao
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-15-899

Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
Cited by: 40
Author(s): Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, G. L. Cao, Jinxin Wang, Ziyin Yang, Ying Ge, Mingxing Chu
Software Mentions: 4
Published: about 10 years ago

10.1186/s12859-015-0460-0

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
Cited by: 20
Author(s): Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-019-1686-3

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Cited by: 71
Author(s): Lin Zeng, Xiaolong Tu, He Dai, Fengming Han, LU Bing-she, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiaolong Li, Lili Ji, David M. Irwin, Zhou Hong, Min Liu, Hongkun Zheng, Ali Esmailizadeh, Dong‐Dong Wu
Software Mentions: 4
Published: over 5 years ago

10.1093/gbe/evy188

Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: about 6 years ago

10.1186/s13059-018-1416-2

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Cited by: 135
Author(s): Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0007743

Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development
Cited by: 19
Author(s): Arporn Wangwiwatsin, Anna V. Protasio, Shona Wilson, Christian Owusu, Nancy Holroyd, Mandy Sanders, Jacqueline A. Keane, Michael J. Doenhoff, Gabriel Rinaldi, Matthew Berriman
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2018.07.026

Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming
Cited by: 16
Author(s): Carl Ward, Giacomo Volpe, Pierre Cauchy, Anetta Ptasińska, Ruba Almaghrabi, Daniel Blakemore, Monica Nafria, Doris Kestner, Jon Frampton, George J. Murphy, Yosef Buganim, Keisuke Kaji, Paloma García
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2618-1

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 8 years ago

10.1016/j.celrep.2020.107748

Chromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes
Cited by: 20
Author(s): Sarah L Bevington, Sky T. H. Ng, Graham J. Britton, Peter Keane, David C. Wraith, Peter N. Cockerill
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-2950-5

The influence of trematode parasite burden on gene expression in a mammalian host
Cited by: 9
Author(s): Bhagya K. Wijayawardena, Dennis J. Minchella, J. Andrew DeWoody
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-017-1290-3

A tandem simulation framework for predicting mapping quality
Cited by: 14
Author(s): Ben Langmead
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-018-1551-9

Alternative polyadenylation factors link cell cycle to migration
Cited by: 21
Author(s): Mithun Mitra, Elizabeth L. Johnson, Vinay Swamy, Lois E Nersesian, David C. Corney, David G. Robinson, Daniel Taylor, Aaron M. Ambrus, David Jelínek, Wei Wang, Sandra Batista, Hilary A. Coller
Software Mentions: 4
Published: about 6 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-00267-9

Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis
Cited by: 12
Author(s): Anthony R. Soltis, Shmulik Motola, Santiago Vérnia, Christopher Ng, Norman J. Kennedy, Simona Dalin, Bryan J. Matthews, Roger J. Davis, Ernest Fraenkel
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: almost 11 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms221910403

MMP14 Contributes to HDAC Inhibition-Induced Radiosensitization of Glioblastoma
Cited by: 1
Author(s): Yuchuan Zhou, Hongxia Liu, Zheng Wang, Qianping Chen, Songling Hu, Yan Pan, Yang Bai, Jianghong Zhang, Chunlin Shao
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-016-0932-1

Single-cell analysis of long non-coding RNAs in the developing human neocortex
Cited by: 291
Author(s): Siyuan John Liu, Tomasz J. Nowakowski, Alex A. Pollen, Jan H. Lui, Max A. Horlbeck, Frank J. Attenello, Daniel He, Jonathan S. Weissman, Arnold R. Kriegstein, Aaron A. Diaz, Daniel A. Lim
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-016-1088-8

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Cited by: 214
Author(s): Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung‐Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher P. Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stéphanie Haddad, Yi Han, Daniel Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, D. R. Lance, Chien Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba Reddy Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Anandasankar Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard L. Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George D. Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-018-5115-x

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-015-2270-1

Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis
Cited by: 66
Author(s): Wenli Li, Amy Turner, Praful Aggarwal, Andrea Matter, Erin Storvick, Donna K. Arnett, Ulrich Broeckel
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12859-015-0859-7

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Cited by: 9
Author(s): Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D’Esposito
Software Mentions: 4
Published: almost 9 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.1186/s12862-017-0902-6

Transcriptomic insights into the genetic basis of mammalian limb diversity
Cited by: 19
Author(s): Jennifer Maier, Marcelo Rivas‐Astroza, Jenny Deng, Anna Dowling, Paige Oboikovitz, Xiaoyi Cao, Richard R. Behringer, Chris J. Cretekos, John J. Rasweiler, Sheng Zhong, Karen E. Sears
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.9093

Collecting duct carcinoma of the kidney is associated with<i>CDKN2A</i>deletion and<i>SLC</i>family gene up-regulation
Cited by: 44
Author(s): Jianmin Wang, Antonios Papanicolau‐Sengos, Sreenivasulu Chintala, Lei Wei, Biao Liu, Qiang Hu, Kiersten Marie Miles, Jeffrey M. Conroy, Sean T. Glenn, Manuela Costantini, Cristina Magi‐Galluzzi, Sabina Signoretti, Toni K. Choueiri, Michele Gallucci, Steno Sentinelli, Vito Michele Fazio, Maria Luana Poeta, Song Liu, Carl Morrison, Роберто Пили
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-015-0746-6

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: about 9 years ago

10.1101/mcs.a002444

Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient
Cited by: 15
Author(s): Christopher A. Miller, Sonika Dahiya, Tiandao Li, Robert S. Fulton, Matthew D. Smyth, Gavin P. Dunn, Joshua B. Rubin, Elaine R. Mardis
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-015-0825-8

Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells
Cited by: 26
Author(s): Christelle Etard, Olivier Armant, Urmas Roostalu, Victor Gourain, Marco Ferg, Uwe Strähle
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1006959

Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish
Cited by: 12
Author(s): Catherine Scahill, Zsofia Digby, Ian Sealy, Sonia Wojciechowska, Richard White, John Collins, Derek L. Stemple, Till Bartke, Marie E. Mathers, E. Elizabeth Patton, Elisabeth M Busch-Nentwich
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-15-845

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data
Cited by: 66
Author(s): Kunshan Zhang, Kefei Huang, Yuan Luo, Siguang Li
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pbio.3000382

LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation
Cited by: 19
Author(s): Caitlin M. Braitsch, D. Berfin Azizoglu, Yadanar Htike, Haley R. Barlow, Ulrike Schnell, Christopher Chaney, Thomas J. Carroll, Ben Z. Stanger, Ondine Cleaver
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-016-1146-2

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Cited by: 148
Author(s): Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2105-16-S17-S10

SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data
Cited by: 3
Author(s): Chong Chu, Li X, Yufeng Wu
Software Mentions: 4
Published: almost 9 years ago

10.1534/g3.119.400777

<i>rmtA</i>-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence in<i>Aspergillus flavus</i>
Cited by: 5
Author(s): Timothy Satterlee, Sarah Entwistle, Yanbin Yin, J. W. Cary, Matthew D. Lebar, Liliana Losada, Ana M. Calvo
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-019-5709-y

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data
Cited by: 53
Author(s): Hamid Beiki, Haibo Li, Jinrong Huang, Nancy Manchanda, D. Nonneman, Timothy P. L. Smith, James M. Reecy, Christopher K. Tuggle
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400152

Early Developmental Stress Affects Subsequent Gene Expression Response to an Acute Stress in Atlantic Salmon: An Approach for Creating Robust Fish for Aquaculture?
Cited by: 23
Author(s): Nick Robinson, Hanne Johnsen, Hooman K. Moghadam, Øivind Andersen, Helge Tveiten
Software Mentions: 4
Published: over 5 years ago

10.1111/tpj.14299

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
Cited by: 46
Author(s): Xiaoming Wang, Siyuan Chen, Song Xue, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma
Software Mentions: 4
Published: over 5 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.118.200516

Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Cited by: 6
Author(s): Cathy Boscarino, Thomas Nalpathamkalam, Giovanna Pellecchia, Weili Li, Bhooma Thiruvahindrapuram, Daniele Merico
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.116.028324

Histone H1 Limits DNA Methylation in Neurospora crassa
Cited by: 18
Author(s): Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, Zachary A. Lewis
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.115.021550

Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response to<i>Fusarium graminearum</i>
Cited by: 33
Author(s): Thomas Nußbaumer, Benedikt Warth, Sapna Sharma, Christian Ametz, Christoph Bueschl, Alexandra Parich, Matthias Pfeifer, Gerald Siegwart, Barbara Steiner, Marc Lemmens, Rainer Schuhmacher, Hermann Buerstmayr, Klaus Mayer, Karl G. Kugler, Wolfgang Schweiger
Software Mentions: 4
Published: almost 9 years ago

10.1534/g3.115.020016

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer
Cited by: 20
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Yun-Gyeong Lee, Namshin Kim, Yong‐Kook Kang
Software Mentions: 4
Published: almost 9 years ago

10.1534/g3.116.033308

Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus <i>Mrakia psychrophila</i>
Cited by: 37
Author(s): Su Yao, Xianzhi Jiang, Wenping Wu, Manman Wang, Muhammad Imran Hamid, Meichun Xiang, Xingzhong Liu
Software Mentions: 4
Published: about 8 years ago

10.1093/function/zqaa004

The Mechanism of High-Output Cardiac Hypertrophy Arising From Potassium Channel Gain-of-Function in Cantú Syndrome
Cited by: 17
Author(s): Conor McClenaghan, Yan Huang, Scot J. Matkovich, Attila Kovács, Carla J. Weinheimer, Ronald A. Perez, Thomas J. Broekelmann, Theresa Harter, Jin-Moo Lee, Marı́a S. Remedi, Colin G. Nichols
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2021.630243

Identification of Key Gene Networks Associated With Cell Wall Components Leading to Flesh Firmness in Watermelon
Cited by: 11
Author(s): Muhammad Anees, Lei Gao, Muhammad Umer, Pingli Yuan, Huiling Zhu, Xingrong Lu, Nan He, Chengsheng Gong, Mohamed Omar Kaseb, Shengjie Zhao, Wenge Liu
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2016.01245

Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica
Cited by: 20
Author(s): Lulu Xie, Fēi Li, Shifan Zhang, Hui Zhang, Wei Qian, Pei-Rong Li, Shujiang Zhang, Rifei Sun
Software Mentions: 4
Published: over 8 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: almost 9 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: about 9 years ago

10.3389/fpls.2015.00718

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
Cited by: 20
Author(s): Itziar Frades, Kibrom B. Abreha, Estelle Proux‐Wéra, Åsa Lankinen, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: about 9 years ago

10.3389/fonc.2021.687629

A Non-Coding RNA Network Involved in KSHV Tumorigenesis
Cited by: 4
Author(s): Julián Naipauer, Martín E García Solá, Daria Salyakina, Santas Rosario, Siôn L. Williams, Omar A. Coso, Martı́n C. Abba, Enrique A. Mesri, Ezequiel Lacunza
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2019.00603

Analysis of Key Genes Involved in Potato Anthocyanin Biosynthesis Based on Genomics and Transcriptomics Data
Cited by: 13
Author(s): Nie Tengkun, Dongdong Wang, Xiaoyan Ma, Yue Chen, Qin Chen
Software Mentions: 4
Published: over 5 years ago