Ecosyste.ms: Papers

10.1186/1471-2164-15-337

Transcriptome differences between two sister desert poplar species under salt stress
Cited by: 36
Author(s): Jian Zhang, Jiexiong Feng, Jing Lü, Yongzhi Yang, Xu Zhang, Dongshi Wan, Jianquan Liu
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-015-1670-6

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites
Cited by: 31
Author(s): Jason S. Cumbie, Maria G. Ivanchenko, Molly Megraw
Software Mentions: 3
Published: over 9 years ago

10.3389/fimmu.2019.00180

Sex Differences in Older Adults' Immune Responses to Seasonal Influenza Vaccination
Cited by: 53
Author(s): Emily A. Voigt, Inna G. Ovsyannikova, Richard B. Kennedy, Diane E. Grill, Krista M. Goergen, Daniel J. Schaid, Gregory A. Poland
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-017-4147-y

An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta
Cited by: 30
Author(s): Xiaolong Cao, Haobo Jiang
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2019.00100

The Long Non-coding RNA NRIR Drives IFN-Response in Monocytes: Implication for Systemic Sclerosis
Cited by: 52
Author(s): Barbara Mariotti, Nila Hendrika Servaas, Marzia Rossato, Nicola Tamassia, Marco A. Cassatella, Marta Cossu, Lorenzo Beretta, Maarten van der Kroef, Timothy R D J Radstake, Flavia Bazzoni
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0147229

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing
Cited by: 30
Author(s): James A. Stapleton, Jeongwoon Kim, John Hamilton, Ming Wu, Luiz Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R. Burton, C. Titus Brown, Christina Chan, C. Robin Buell, Timothy A. Whitehead
Software Mentions: 3
Published: about 9 years ago

10.3389/fimmu.2020.00661

Neutrophil Extracellular Trap Induced Dendritic Cell Activation Leads to Th1 Polarization in Type 1 Diabetes
Cited by: 40
Author(s): Zuzana Paračková, Irena Zentsová, Petra Vrabcová, Adam Klocperk, Zdenĕk Šumnı́k, Štěpánka Průhová, Lenka Petruželková, Robert Häsler, Anna Šedivá
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2018.01666

Dynamic Interplay of Innate and Adaptive Immunity During Sterile Retinal Inflammation: Insights From the Transcriptome
Cited by: 8
Author(s): Riccardo Natoli, Elizabeth A. Mason, Haihan Jiao, Aaron Chuah, Hardip R. Patel, Nilisha Fernando, Krisztina Valter, Christine A. Wells, Jan Provis, Matt Rutar
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5953-1

Systematic evaluation of RNA-Seq preparation protocol performance
Cited by: 26
Author(s): Hsueh-Ping Chao, Yueping Chen, Yoko Takata, Mary W. Tomida, Kevin Lin, Jason Kirk, Melissa S. Simper, Carol Mikulec, Joyce E. Rundhaug, Susan M. Fischer, Taiping Chen, Dean G. Tang, Yue Lu, Jianjun Shen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0197548

ILDR2 has a negligible role in hepatic steatosis
Cited by: 0
Author(s): Elizabeth J. Millings, Maria Caterina De Rosa, Sarah Fleet, Kazuhisa Watanabe, Richard Rausch, Dieter Egli, Gen Li, Charles A. LeDuc, Yiying Zhang, Stuart G. Fischer, Rudolph L. Leibel
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: almost 12 years ago

10.3389/fimmu.2019.00280

Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway
Cited by: 49
Author(s): Jules Petit, Erin C. Bailey, Robert T. Wheeler, Carlos Alberto Ferreira de Oliveira, Maria Forlenza, G.F. Wiegertjes
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-021-08276-8

Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer
Cited by: 6
Author(s): Yichao Li, Sushila Jaiswal, Rupleen Kaur, Dana Alsaadi, Xiaoyu Liang, Frank A. Drews, Julie A. DeLoia, Thomas C. Krivak, Hanna M. Petrykowska, Valer Gotea, Lonnie R. Welch, Laura Elnitski
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0207497

Response of Tribolium castaneum to dietary mannitol, with remarks on its possible nutritive effects
Cited by: 8
Author(s): Shingo Kikuta
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1006108

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
Cited by: 148
Author(s): Raúl Castanera, Leticia López-Varas, Alessandra Borgognone, Kurt LaButti, Alla Lapidus, Jeremy Schmutz, Jane Grimwood, Gúmer Pérez, Antonio G. Pisabarro, Igor V. Grigoriev, Jason E. Stajich, Lucı́a Ramı́rez
Software Mentions: 3
Published: over 8 years ago

10.1186/s13068-015-0407-8

Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus
Cited by: 65
Author(s): Marie Couturier, David Navarro, Didier Chevret, Bernard Henrissat, François Piumi, Francisco J. Ruíz-Dueñas, Ángel T. Martı́nez, Igor V. Grigoriev, Robert Riley, Anna Lipzen, Jean‐Guy Berrin, Emma R. Master, Marie‐Noëlle Rosso
Software Mentions: 3
Published: about 9 years ago

10.1186/s13068-019-1506-8

Transcriptomic and proteomic responses to very low CO2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica
Cited by: 40
Author(s): Li Wei, Mohamed El Hajjami, Chen Shen, Wuxin You, Yandu Lu, Jing Li, Xiaoyan Jing, Qiang Hu, Wenxu Zhou, Ansgar Poetsch, Jian Xu
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.01368

APRIL Induces a Novel Subset of IgA+ Regulatory B Cells That Suppress Inflammation via Expression of IL-10 and PD-L1
Cited by: 56
Author(s): Cynthia M. Fehres, Nathalie O. van Uden, Nataliya Yeremenko, Leticia Fernández, Gabriela Salinas, Leonie M. van Duivenvoorde, Bertrand Huard, Jacques Morel, Hergen Spits, Michael Hahne, Dominique Baeten
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-015-0208-0

A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production
Cited by: 22
Author(s): Bang Wang, Pengli Cai, Wenliang Sun, Jingen Li, Chaoguang Tian, Yanhe Ma
Software Mentions: 3
Published: about 10 years ago

10.1186/s13068-020-01810-z

Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress
Cited by: 17
Author(s): Peilin Chen, Jing Chen, Min Sun, Haidong Yan, Guangyan Feng, Bingchao Wu, Xinquan Zhang, Xiaoshan Wang, Linkai Huang
Software Mentions: 3
Published: over 4 years ago

10.1155/2016/3791214

A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data
Cited by: 17
Author(s): Manuel Galli, Italo Zoppis, Gabriele De Sio, Clizia Chinello, Fabio Pagni, Fulvio Magni, Giancarlo Mauri
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-021-07450-3

A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum
Cited by: 5
Author(s): Maricel Podio, Carolina Colono, Lorena Adelina Siena, Juan Pablo Amelio Ortiz, Silvina Claudia Pessino
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-4856-x

Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen
Cited by: 25
Author(s): Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zhuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Zhilong Bie, Yuan Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13068-017-0700-9

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments
Cited by: 17
Author(s): Paul Daly, Jolanda M. van Munster, Martin Blythe, Roger Ibbett, Matthew Kokolski, Sanyasi Gaddipati, Erika Lindquist, Vasanth Singan, Kerrie Barry, Anna Lipzen, Chew Yee Ngan, Young-Mo Kim, Leanne Jade G. Chan, Steven T. Pullan, Stéphane Delmas, Paul Ravi Waldron, Igor V. Grigoriev, Gregory A. Tucker, Blake A. Simmons, David B. Archer
Software Mentions: 3
Published: about 8 years ago

10.1186/s13068-017-0825-x

Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters
Cited by: 73
Author(s): Wan-Chen Li, Chien‐Hao Huang, Chia-Ling Chen, Yu-Chien Chuang, Shu-Yun Tung, Ting-Fang Wang
Software Mentions: 3
Published: over 7 years ago

10.1042/BSR20191139

Comprehensive analysis of long noncoding RNA and mRNA in five colorectal cancer tissues and five normal tissues
Cited by: 4
Author(s): Zhenxu Zhou, Xiaoming Chen, Yuqi Zhang, Peng Liu, Xiangyang Xue, Guoxin Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12885-015-1955-9

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Cited by: 51
Author(s): Katayoon Kasaian, Sam M. Wiseman, Blair Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Software Mentions: 3
Published: about 9 years ago

10.3382/ps/pez354

Transcriptomic analysis of early B-cell development in the chicken embryo
Cited by: 6
Author(s): Nikhil Nuthalapati, J. D. Evans, Robert L. Taylor, S. L. Branton, Bindu Nanduri, G. T. Pharr
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-12-293

RNA-seq: technical variability and sampling
Cited by: 250
Author(s): Lauren M. McIntyre, Kenneth K. Lopiano, Alison M. Morse, V. Amin, Ann L. Oberg, Linda J. Young, Sergey V. Nuzhdin
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2020.00910

The Effector Repertoire of the Hop Downy Mildew Pathogen Pseudoperonospora humuli
Cited by: 8
Author(s): Savithri Purayannur, Liliana Cano, Megan J. Bowman, Kevin L. Childs, David H. Gent, Lina M. Quesada‐Ocampo
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.719201

Genome-Wide Transcription Analysis of Electroacupuncture Precondition-Induced Ischemic Tolerance on SD Rat With Ischemia–Reperfusion Injury
Cited by: 2
Author(s): Shunjun Fu, Min Yu, Houxi Xu, Qing Liu, Xiaoxiao Li, Yaling Wang, Yonglin Chen, Ling-Ling Meng, Yu Qiu, Xianwen Jing, Chenchen Liu, Lu Shen
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-13-S8-S11

DFI: gene feature discovery in RNA-seq experiments from multiple sources
Cited by: 5
Author(s): Hatice Gülçin Özer, Jeffrey D. Parvin, Kun Huang
Software Mentions: 3
Published: about 13 years ago

10.3389/fgene.2021.654146

MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean
Cited by: 3
Author(s): Chunbao Zhang, Fuyou Fu, Chunjing Lin, Xiaoyang Ding, Jingyong Zhang, Hao Yan, Pengnian Wang, Wei Zhang, Bao Peng, Limei Zhao
Software Mentions: 3
Published: almost 4 years ago

10.3390/biom9080364

Identification of SWI2/SNF2-Related 1 Chromatin Remodeling Complex (SWR1-C) Subunits in Pineapple and the Role of Pineapple SWR1 COMPLEX 6 (AcSWC6) in Biotic and Abiotic Stress Response
Cited by: 9
Author(s): Bello Hassan Jakada, Mohammad Aslam, Beenish Fakher, Joseph G. Greaves, Zeyun Li, Weimin Liu, Linyi Lai, Oyekunle Adenike Ayoade, Yan Cheng, Shijiang Cao, Gang Li, Jer‐Ming Hu, Yuan Qin
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-13-721

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
Cited by: 75
Author(s): Tingting Lu, Chuanrang Zhu, Lu Gui, Yunli Guo, Yan Zhou, Zhiyong Zhang, Yan Zhao, Wenjun Li, Ying Lu, Weihua Tang, Qi Feng, Bin Han
Software Mentions: 3
Published: about 13 years ago

10.1186/1471-2105-14-S11-S8

Assessing the impact of human genome annotation choice on RNA-seq expression estimates
Cited by: 41
Author(s): Po-Yen Wu, John H. Phan, May D. Wang
Software Mentions: 3
Published: over 11 years ago

10.1038/srep33342

Metabolic engineering of cottonseed oil biosynthesis pathway via RNA interference
Cited by: 29
Author(s): Zhongping Xu, Jingwen Li, Xiaoping Guo, Shuangxia Jin, Xianlong Zhang
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2018.00291

Transcriptome Analyses Reveal Adult Metabolic Syndrome With Intrauterine Growth Restriction in Pig Models
Cited by: 21
Author(s): Linyuan Shen, Mailin Gan, Shunhua Zhang, Jideng Ma, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Jinyong Wang, Xuewei Li, Lianqiang Che, Li Zhu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-019-5681-6

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma
Cited by: 11
Author(s): Noah Berlow, Rikhi Rikhi, Mathew Geltzeiler, Jinu Abraham, Matthew N. Svalina, Lara E. Davis, Erin Wise, Maria Mancini, Jonathan Noujaim, Atiya Mansoor, Michael J. Quist, Kevin Matlock, Martin Goros, Brian Hernandez, Yee Cheen Doung, Khin Thway, Tomohide Tsukahara, Jun Nishio, Elaine Huang, Susan D. Airhart, Carol J. Bult, Regina Gandour‐Edwards, Robert G. Maki, Robin L. Jones, Joel E. Michalek, Milan Milovancev, Souparno Ghosh, Ranadip Pal, Charles Keller
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0174236

Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors
Cited by: 7
Author(s): Niels van Tol, Martijn Rolloos, Johan E. Pinas, Christiaan V. Henkel, Dieuwertje Augustijn, Paul J. J. Hooykaas, Bert J. van der Zaal
Software Mentions: 3
Published: almost 8 years ago

10.1038/srep40049

The molecular sensory machinery of a Chagas disease vector: expression changes through imaginal moult and sexually dimorphic features
Cited by: 41
Author(s): José Manuel Latorre-Estivalis, Hugh M. Robertson, Kimberly K. O. Walden, Jerônimo C. Ruiz, Leilane Oliveira Gonçalves, Alessandra A. Guarneri, Marcelo G. Lorenzo
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0195132

RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population
Cited by: 15
Author(s): Shaohua Yang, Ying Wāng, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Yuan Jia, Wei Wang, Fu-Hu Cao, Guoqing Liu
Software Mentions: 3
Published: almost 7 years ago

10.18632/aging.202738

Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan
Cited by: 3
Author(s): Arman Ali Shah, Binghua Liu, Zhihuai Tang, Wang Wang, Wenjie Yang, Quanjun Hu, Yan Liu, Nianhui Zhang, Ke Liu
Software Mentions: 3
Published: almost 4 years ago

10.1155/2015/690873

Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data
Cited by: 7
Author(s): Guohua Wang, Yunlong Liu, Dongxiao Zhu, Gunnar W. Klau, Weixing Feng
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-017-00176-x

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
Cited by: 28
Author(s): Feinan Wu, Jie Yao
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-016-2453-4

Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2018.00340

Integrative Analyses of Transcriptome Sequencing Identify Functional miRNAs in the Chicken Embryo Fibroblasts Cells Infected With Reticuloendotheliosis Virus
Cited by: 6
Author(s): Jie Zhai, Chang Gao, Lisheng Fu, Long Jiang, Shengyuan Dang, Shangen Zheng
Software Mentions: 3
Published: over 6 years ago

10.1038/srep31150

Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay
Cited by: 99
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0200692

Identification and characterization of circRNAs in Pyrus betulifolia Bunge under drought stress
Cited by: 25
Author(s): Jinxing Wang, Jing Lin, Hong Wang, Yong Li, Qiyun Yang, Hui Li, Chang YouHong
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/1705387

Ammonia Exposure Induced Cilia Dysfunction of Nasal Mucosa in the Piglets
Cited by: 3
Author(s): Qiankun Wang, Mengyao Wang, Chun Liu, Liurong Huang, Yun Gao, Mei Yu, Zhao Song, Xiaoping Li
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.00701

Chromosome Level Genome Assembly of Andrographis paniculata
Cited by: 11
Author(s): Ying Liang, Shanshan Chen, Kunhua Wei, Zijiang Yang, Shengchang Duan, Yihui Du, Peng Qu, Miao Jin, Wei Chen, Yang Dong
Software Mentions: 3
Published: over 4 years ago

10.1155/2015/146250

An Association Rule Mining Approach to Discover lncRNAs Expression Patterns in Cancer Datasets
Cited by: 7
Author(s): Paolo Cremaschi, Roberta Carriero, Stefania Astrologo, Caterina Colì, Antonella Lisa, Silvia Parolo, Silvia Bione
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-34015-4

ERK1/2-dependent gene expression in the bovine ovulating follicle
Cited by: 15
Author(s): Yasmin Schuermann, Monique Tomazele Rovani, Bernardo Garziera Gasperin, Rogério Ferreira, Juliana Germano Ferst, Ejimedo Madogwe, Paulo Bayard Dias Gonçalves, Vilceu Bordignon, Raj Duggavathi
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-38233-8

Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.)
Cited by: 7
Author(s): Upasna Chettry, Nikhil K. Chrungoo, Kirti Kulkarni
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-41294-y

CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer
Cited by: 3
Author(s): Woochang Hwang, Stefano Calza, M. Silvestri, Yudi Pawitan, Youngjo Lee
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.00837

Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level
Cited by: 5
Author(s): David Botero, Jonathan M. Monk, María Juliana Rodríguez Cubillos, Andrés Rodríguez Cubillos, Mariana Restrepo, Vivian Bernal-Galeano, Alejandro Reyes, Andrés Barrios, Bernhard Ø. Palsson, Silvia Restrepo, Adriana Bernal
Software Mentions: 3
Published: over 4 years ago

10.1155/2020/6798590

Disease-Associated Circular RNAs: From Biology to Computational Identification
Cited by: 12
Author(s): Min Tang, Ling Kui, Guanyi Lu, Wenqiang Chen
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-018-5037-7

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species
Cited by: 80
Author(s): Colin Kern, Ying Wang, James L. Chitwood, Ian F Korf, Mary E. Delany, Hans H. Cheng, Juan F. Medrano, Alison L. Van Eenennaam, Catherine W. Ernst, Pablo J. Ross, Huaijun Zhou
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.630290

Environmentally Driven Color Variation in the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus, 1758) Is Associated With Differential Methylation of CpGs in Pigment- and Biomineralization-Related Genes
Cited by: 5
Author(s): Pierre‐Louis Stenger, Chin‐Long Ky, Céline Reisser, Céline Cosseau, Christoph Grunau, Mickaël Mège, Serge Planes, Jérémie Vidal-Dupiol
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0165823

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem
Cited by: 37
Author(s): Bilal A. Padder, Kelvin Kamfwa, Halima E. Awale
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2019.00116

Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium
Cited by: 14
Author(s): Yupeng Cui, Jianjiang Ma, Guoyuan Liu, Nuohan Wang, Wenfeng Pei, Man Wu, Xingli Li, Jinfa Zhang, Jie-Ae Yu
Software Mentions: 3
Published: almost 6 years ago

10.3390/biology10090885

Metabolic Regulation of Sugar Assimilation for Lipid Production in Aspergillus oryzae BCC7051 through Comparative Transcriptome Perspective
Cited by: 5
Author(s): Tayvich Vorapreeda, Bhimabol Khongto, Chinae Thammarongtham, Tanawut Srisuk, Kobkul Laoteng
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0177814

ANK1 is up-regulated in laser captured microglia in Alzheimer’s brain; the importance of addressing cellular heterogeneity
Cited by: 35
Author(s): Diego Mastroeni, Shobana Sekar, Jennifer Nolz, Elaine Delvaux, Katie Lunnon, Jonathan Mill, Winnie S. Liang, Paul D. Coleman
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2014.00043

Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
Cited by: 12
Author(s): Andreia J. Amaral, Francisco Brito, Tamar Chobanyan, S. Yoshikawa, Takakazu Yokokura, David Van Vactor, Margarida Gama‐Carvalho
Software Mentions: 3
Published: almost 11 years ago

10.1111/acel.13219

Immune checkpoint protein VSIG4 as a biomarker of aging in murine adipose tissue
Cited by: 18
Author(s): Brandon M. Hall, Anatoli S. Gleiberman, Evguenia Strom, Peter Krasnov, David Frescas, Slavoljub Vujcic, Olga V. Leontieva, Marina P. Antoch, V. R. Kogan, Igor Koman, Yi Zhu, Tamara Tchkonia, James L. Kirkland, Olga B. Chernova, Andrei V. Gudkov
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0180842

RNA sequencing to determine the contribution of kinase receptor transactivation to G protein coupled receptor signalling in vascular smooth muscle cells
Cited by: 15
Author(s): Danielle Kamato, Venkata Vijayanand Bhaskarala, Nitin Mantri, Tae Gyu Oh, Dora Ling, Reearna Janke, Wenhua Zheng, Peter J. Little, Narin Osman
Software Mentions: 3
Published: over 7 years ago

10.1038/cddis.2017.48

Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4
Cited by: 30
Author(s): Josefina Castex, Dominica Willmann, Toufike Kanouni, Laura Arrigoni, Yan Li, Marcel Friedrich, Michael Schleicher, Simon Wöhrle, Mark Pearson, Norbert Kraut, Michaël Méret, Thomas Manke, Eric Metzger, Roland Schüle, Thomas Günther
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0094270

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs
Cited by: 27
Author(s): Nicholas J. Schurch, Christian Callebaut, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G. Storey, Whi McLean, Sara J. Brown, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12915-018-0509-4

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes
Cited by: 39
Author(s): Yuichiro Hara, Miki Takeuchi, Yuka Kageyama, Kaori Tatsumi, Masahiko Hibi, Hiroshi Kanazawa, Shigehiro Kuraku
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 9 years ago

10.15252/embr.201949602

Coordinated control of adiposity and growth by anti‐anabolic kinase ERK7
Cited by: 6
Author(s): Kiran Hasygar, Onur Deniz, Ying Liu, Josef Gullmets, Riikka Hynynen, Hanna Ruhanen, Krista Kokki, Reijo Käkelä, Ville Hietakangas
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-15-35

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals
Cited by: 91
Author(s): Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0192362

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification
Cited by: 21
Author(s): C. N. Neeraja, Kalyani S. Kulkarni, P. Madhu Babu, D. N. Rao, K. Surekha, V. Ravindra Babu
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-3287-9

AnnoLnc: a web server for systematically annotating novel human lncRNAs
Cited by: 43
Author(s): Mei Hou, Xing Tang, Feng Tian, Fang-Yuan Shi, Fenglin Liu, Ge Gao
Software Mentions: 3
Published: over 8 years ago

10.15252/emmm.201708552

Comprehensive evaluation of coding region point mutations in microsatellite‐unstable colorectal cancer
Cited by: 9
Author(s): Johanna Kondelin, Kari Salokas, Lilli Saarinen, Kristian Ovaska, Heli Rauanheimo, Roosa‐Maria Plaketti, Jiri Hamberg, Xiaonan Liu, Leena Yadav, Alexandra E. Gylfe, Tatiana Cajuso, Ulrika A. Hänninen, Kimmo Palin, Heikki Ristolainen, Riku Katainen, Eevi Kaasinen, Tomas Tanskanen, Mervi Aavikko, Minna Taipale, Jussi Taipale, Laura Renkonen–Sinisalo, Anna Lepistö, Selja Koskensalo, Jan Böhm, Jukka–Pekka Mecklin∥, Halit Ongen, Emmanouil T. Dermitzakis, Outi Kilpivaara, Pia Vahteristo, Mikko Turunen, Sampsa Hautaniemi, Sari Tuupanen, Auli Karhu, Niko Välimäki, Markku Varjosalo, Esa Pitkänen, Lauri A. Aaltonen
Software Mentions: 3
Published: over 6 years ago

10.1186/s12915-015-0159-8

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline
Cited by: 58
Author(s): Ho-Su Sin, Andrey V. Kartashov, Kazuteru Hasegawa, Artem Barski, Satoshi H. Namekawa
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: over 11 years ago

10.1186/1745-6150-9-15

Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets
Cited by: 6
Author(s): Lei Wang, Dequan Zhou, Jing Tu, Yan Wang, Lu Zhang
Software Mentions: 3
Published: over 10 years ago

10.3389/fimmu.2021.618807

Cyclic-di-GMP Induces STING-Dependent ILC2 to ILC1 Shift During Innate Type 2 Lung Inflammation
Cited by: 10
Author(s): Kellen Cavagnero, Jana Badrani, Luay H. Naji, Michael Amadeo, Anthea Leng, Lee Lacasa, Allyssa Strohm, Samantha Renusch, Suzanna Gasparian, Taylor Doherty
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41419-019-2137-5

The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA–RNA interactions in breast cancer
Cited by: 11
Author(s): Shouping Xu, Hongbo Liu, Lin Wan, Weijia Zhang, Qin Wang, Shumei Zhang, Shuai Shang, Yan Zhang, Da Pang
Software Mentions: 3
Published: about 5 years ago

10.1186/1745-6150-9-20

A new rhesus macaque assembly and annotation for next-generation sequencing analyses
Cited by: 150
Author(s): Aleksey V. Zimin, Adam Cornish, Mnirnal D Maudhoo, Robert Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T. Meehan, Kristin Wipfler, Steven E. Bosinger, Zachary P. Johnson, Gregory K. Tharp, Guillaume Marçais, Michael R. Roberts, Betsy Ferguson, Howard S. Fox, Todd J. Treangen, Steven L. Salzberg, James A. Yorke, Robert B. Norgren
Software Mentions: 3
Published: over 10 years ago

10.1093/bioinformatics/btt731

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
Cited by: 12
Author(s): Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Kaushik Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
Software Mentions: 3
Published: about 11 years ago

10.3389/fgene.2019.01040

Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat
Cited by: 10
Author(s): Yinghui Ling, Qi Zheng, Yunsheng Li, Menghua Sui, Hao Wu, Yunhai Zhang, Mingxing Chu, Yuehui Ma, Fugui Fang, Lei Xu
Software Mentions: 3
Published: over 5 years ago

10.1093/bioinformatics/btab171

<i>Ribo-ODDR</i>: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq
Cited by: 5
Author(s): Ferhat Alkan, Joana Silva, Eric Pintó Barberà, William J. Faller
Software Mentions: 3
Published: almost 4 years ago

10.1007/s00204-016-1879-4

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women
Cited by: 24
Author(s): Karin Engström, Tomasz K. Wojdacz, Francesco Marabita, Philip Ewels, Max Käller, Francesco Vezzi, Nicola Prezza, Joel Gruselius, Marie Vahter, Karin Broberg
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0234029

An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions
Cited by: 8
Author(s): Jie Shen, Meijun Guo, Yuguo Wang, Xiangyang Yuan, Shuqi Dong, Xi-e Song, Peng Guo
Software Mentions: 3
Published: over 4 years ago

10.1016/j.ebiom.2014.10.003

An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation
Cited by: 110
Author(s): Olga M. Pena, David G. Hancock, Ngan H. Lyle, Adam Linder, James A. Russell, Jianguo Xia, Christopher D. Fjell, John H. Boyd, Robert E. W. Hancock
Software Mentions: 3
Published: over 10 years ago

10.1186/s12915-017-0419-x

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Cited by: 95
Author(s): Muluneh Tamiru, Satoshi Natsume, Hiroki Takagi, Ben White, Hiroki Yaegashi, Mitsuru Shimizu, Kentaro Yoshida, Aiko Uemura, Kanta Oikawa, Akira Abe, Naoya Urasaki, Hideo Matsumura, Babil Pachakkil, Shinşuke Yamanaka, Ryo Matsumoto, Satoru Muranaka, Gezahegn Girma, Antonio Lopez-Montes, Melaku Gedil, Ranjana Bhattacharjee, Michael T. Abberton, P. Lava Kumar, Ismail Rabbi, Mai Tsujimura, Toru Terachi, Wilfried Haerty, Manuel Corpas, Sophien Kamoun, Günter Kahl, H. Takagi, Robert Asiedu, Ryohei Terauchi
Software Mentions: 3
Published: over 7 years ago

10.1186/s13040-021-00237-y

DASSI: differential architecture search for splice identification from DNA sequences
Cited by: 2
Author(s): Shabir Moosa, Abbes Amira, Sabri Boughorbel
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-15-148

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi
Cited by: 30
Author(s): Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben‐Dor
Software Mentions: 3
Published: about 11 years ago

10.1186/1741-7007-12-42

RNA-seq: impact of RNA degradation on transcript quantification
Cited by: 327
Author(s): Irene Gallego Romero, Athma A. Pai, Jenny Tung, Yoav Gilad
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-020-2309-6

A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy
Cited by: 6
Author(s): Deying Zeng, Jiantao Guan, Jiangtao Luo, Laibin Zhao, Yazhou Li, Wenshuai Chen, Lianquan Zhang, Shunzong Ning, Zhongwei Yuan, Aili Li, Youliang Zheng, Long Mao, Dengcai Liu, Ming Hao
Software Mentions: 3
Published: almost 5 years ago

10.1186/1746-6148-10-146

Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing
Cited by: 5
Author(s): Akira Mori, Kelly Kappen, A. C. Dilger, Kelly S. Swanson
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-021-07690-3

Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
Cited by: 0
Author(s): Bahiyah Azli, Sharanya Ravi, M. Hair-Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-017-4430-y

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes
Cited by: 38
Author(s): Deepak Kumar Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J. Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke, Marco Thines
Software Mentions: 3
Published: about 7 years ago

10.1242/dmm.030536

Comprehensive analysis of gene expression patterns in Friedreich's ataxia fibroblasts by RNA sequencing reveals altered levels of protein synthesis factors and solute carriers
Cited by: 34
Author(s): Marek Napierala, Yanjie Li, Yue Lu, Kevin Lin, Lauren Hauser, David R. Lynch, Марек Напиерала
Software Mentions: 3
Published: over 7 years ago

10.1186/1746-1596-9-142

NF-κB signaling and vesicle transport are correlated with the reactivation of the memory trace of morphine dependence
Cited by: 9
Author(s): Junyi Ye, Zhaoyang Yang, Candong Li, Meimei Cai, Daizhan Zhou, Qin Zhang, Wei Y, Ting Wang, Yun Liu
Software Mentions: 3
Published: over 10 years ago

10.15252/embj.201798783

Lmo2 expression defines tumor cell identity during T‐cell leukemogenesis
Cited by: 31
Author(s): Idoia García-Ramírez, Sanil Bhatia, Guillermo Rodríguez-Hernández, Inés González-Herrero, Carolin Walter, Sara González de Tena-Dávila, Salma Parvin, Oskar A. Haas, Wilhelm Woessmann, Martin Stanulla, Martin Schrappe, Martin Dugas, Yasodha Natkunam, Alberto Órfão, Verónica Domínguez, B. Pintado, Óscar Blanco, Diego Alonso-López, Javier De Las Rivas, Alberto Martín-Lorenzo, Rafael Jiménez, Francisco Javier García Criado, María Begoña García Cenador, Izidore S. Lossos, Carolina Vicente-Dueñas, Arndt Borkhardt, Julia Hauer, Isidro Sánchez-Garcı́a
Software Mentions: 3
Published: over 6 years ago

10.1186/s12918-016-0366-0

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
Cited by: 87
Author(s): Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng, Herbert M. Lachman
Software Mentions: 3
Published: over 8 years ago