10.1186/s12870-020-02715-7

Comparative cellular, physiological and transcriptome analyses reveal the potential easy dehulling mechanism of rice-tartary buckwheat (Fagopyrum Tararicum)
Cited by: 10
Author(s): Hongyou Li, Chaoxin Wu, Qiuyu Lv, Taoxiong Shi, Qijiao Chen
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-016-0804-6

Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance
Cited by: 53
Author(s): Daniel Hopper, Ryan Ghan, Karen Schlauch, Grant R. Cramer
Software Mentions: 1
Published: about 9 years ago

10.1186/s12870-021-02986-8

Discovery of genes involved in anthocyanin biosynthesis from the rind and pith of three sugarcane varieties using integrated metabolic profiling and RNA-seq analysis
Cited by: 11
Author(s): Ni Yang, Haimei Chen, Di Liu, Lihui Zeng, Pinghua Chen, Chang Liu
Software Mentions: 1
Published: about 4 years ago

10.1038/s41398-019-0492-8

Postmortem transcriptional profiling reveals widespread increase in inflammation in schizophrenia: a comparison of prefrontal cortex, striatum, and hippocampus among matched tetrads of controls with subjects diagnosed with schizophrenia, bipolar or major depressive disorder
Cited by: 107
Author(s): Thomas A. Lanz, Veronica Reinhart, Mark J. Sheehan, Stacey J. Sukoff Rizzo, Susan E. Bove, Larry C. James, Dmitri Volfson, David A. Lewis, Robin J. Kleiman
Software Mentions: 1
Published: about 6 years ago

10.1186/s13023-016-0475-2

Common disease signatures from gene expression analysis in Huntington’s disease human blood and brain
Cited by: 26
Author(s): Eleni Mina, Willeke van Roon-Mom, Kristina Hettne, Erik W. van Zwet, Jelle J. Goeman, Christian Néri, Peter A.C. ’t Hoen, Barend Mons, Marco Roos
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41398-019-0486-6

Dysregulation of a specific immune-related network of genes biologically defines a subset of schizophrenia
Cited by: 21
Author(s): Svenja V. Trossbach, Laura Hecher, David Schafflick, René Deenen, Ovidiu Popa, Tobias Lautwein, Sarah K. Tschirner, Karl Köhrer, Karin Fehsel, Irina Papazova, Berend Malchow, Alkomiet Hasan, Georg Winterer, Aurore Schmitt, Gerd Meyer zu Hörste, Peter Falkai, Carsten Korth
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-020-02578-y

Scion genotypes exert long distance control over rootstock transcriptome responses to low phosphate in grafted grapevine
Cited by: 15
Author(s): Antoine Gautier, Noé Cochetel, Isabelle Merlin, Cyril Hévin, Virginie Lauvergeat, Philippe Vivin, Alain Mollier, Nathalie Ollat, Sarah Jane Cookson
Software Mentions: 1
Published: almost 5 years ago

10.18632/aging.104075

Weighted gene correlation network analysis identifies microenvironment-related genes signature as prognostic candidate for Grade II/III glioma
Cited by: 3
Author(s): Yong Li, Gang Deng, Huikai Zhang, Yangzhi Qi, Lun Gao, Yinqiu Tan, Ping Hu, Yixuan Wang, Baohui Liu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-021-03206-z

Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses
Cited by: 27
Author(s): Weixin Hu, Qiaoyu Ren, Yali Chen, Guoliang Xu, Yexiong Qian
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41398-019-0584-5

Gene network analysis reveals a role for striatal glutamatergic receptors in dysregulated risk-assessment behavior of autism mouse models
Cited by: 9
Author(s): Oded Oron, Dmitriy Getselter, Shahar Shohat, Eli Reuveni, Iva Lukić, Sagiv Shifman, Evan Elliott
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12870-021-02879-w

Genome-wide analysis and expression profile of the bZIP gene family in poplar
Cited by: 48
Author(s): Kai Zhao, Ching Song, Wenjing Yao, Zihao Cheng, Boru Zhou, Tingbo Jiang
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-020-2314-9

Transcriptome co-expression network analysis identifies key genes and regulators of ripening kiwifruit ester biosynthesis
Cited by: 20
Author(s): Aidi Zhang, Qiuyun Zhang, Jianzhao Li, Hansheng Gong, Xinguang Fan, Yanqing Yang, Xiaofen Liu, Yin X
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-018-2433-6

A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
Cited by: 41
Author(s): Gualter Silva Pereira, Antônio Augusto Franco Garcia, Gabriel Rodrigues Alves Margarido
Software Mentions: 1
Published: over 6 years ago

10.1038/s41398-020-00907-1

Adult mouse hippocampal transcriptome changes associated with long-term behavioral and metabolic effects of gestational air pollution toxicity
Cited by: 20
Author(s): Amin Haghani, Richard G. Johnson, Nick Woodward, Jason I. Feinberg, Kristy Lewis, Christine Ladd‐Acosta, Nikoo Safi, Andrew E. Jaffe, Constantinos Sioutas, Hooman Allayee, Daniel B. Campbell, Heather E. Volk, Caleb E. Finch, Todd E. Morgan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41398-020-01007-w

Gene co-expression networks in peripheral blood capture dimensional measures of emotional and behavioral problems from the Child Behavior Checklist (CBCL)
Cited by: 2
Author(s): Jonathan Hess, Nicholas Nguyen, Jesse Suben, Ryan M Meath, Avery B. Albert, Sarah Van Orman, Kristin M. Anders, Patricia Forken, Cheryl Roe, Thomas G. Schulze, Stephen V. Faraone, Stephen J. Glatt
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12870-019-2186-z

Comparative physiological, metabolomic, and transcriptomic analyses reveal developmental stage-dependent effects of cluster bagging on phenolic metabolism in Cabernet Sauvignon grape berries
Cited by: 31
Author(s): Ruonan Sun, Guodong Cheng, Qiang Li, Yanrong Zhu, Xue Zhang, Yu Wang, Yuan He, Siyu Li, Lei He, Chen Wu, Qiu-Hong Pan, Chang‐Qing Duan, Jun Wang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-020-02798-2

Genome-wide identification and comprehensive analysis of NAC family genes involved in fruit development in kiwifruit (Actinidia)
Cited by: 15
Author(s): Dongfeng Jia, Zhiqiang Jiang, Haihui Fu, Lu Chen, Guanglian Liao, Yanqun He, Chunhui Huang, Xiaobiao Xu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-020-02785-7

Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao
Cited by: 15
Author(s): Jiawei Zhou, Siqi Chen, Wen-jiao Shi, Rakefet David‐Schwartz, Sutao Li, Fulin Yang, Zhan-xi Lin
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-020-02437-w

Long non-coding RNAs in the alkaline stress response in sugar beet (Beta vulgaris L.)
Cited by: 11
Author(s): Chunlei Zou, Yübo Wang, Bin Wang, Dan Liú, Lei Liu, Zhongtao Gai, Caifeng Li
Software Mentions: 1
Published: about 5 years ago

10.1186/s12870-019-1898-4

The R2R3-MYB transcription factor PaMYB10 is involved in anthocyanin biosynthesis in apricots and determines red blushed skin
Cited by: 46
Author(s): Wanpeng Xi, Jing Feng, Yu Liu, Shikui Zhang, Guohua Zhao
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-021-03152-w

Full-length transcriptome profiling reveals insight into the cold response of two kiwifruit genotypes (A. arguta) with contrasting freezing tolerances
Cited by: 12
Author(s): Shi Sun, Miaomiao Lin, Xiujuan Qi, Jinyong Chen, Hongcang Gu, Yunpeng Zhong, Lei Sun, Muhammad Abid, Danfeng Bai, Chun-Gen Hu, Jinbao Fang
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41398-021-01536-y

Genome-wide DNA methylation and gene expression analyses in monozygotic twins identify potential biomarkers of depression
Cited by: 28
Author(s): Weijing Wang, Weilong Li, Yili Wu, Xiaocao Tian, Haiping Duan, Shuxia Li, Qihua Tan, Dongfeng Zhang
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12870-017-1170-8

Comprehensive transcriptome analysis reveals distinct regulatory programs during vernalization and floral bud development of orchardgrass (Dactylis glomerata L.)
Cited by: 26
Author(s): Guangyan Feng, Linkai Huang, Ji Li, Jianping Wang, Lei Xu, Ling Pan, Xinxin Zhao, Xia Wang, Ting Huang, Xinquan Zhang
Software Mentions: 1
Published: over 7 years ago

10.1007/s12975-020-00869-y

Molecular Correlates of Hemorrhage and Edema Volumes Following Human Intracerebral Hemorrhage Implicate Inflammation, Autophagy, mRNA Splicing, and T Cell Receptor Signaling
Cited by: 21
Author(s): Marc Durocher, Bodie Knepp, Alan Yee, Glen C. Jickling, Fernando Rodríguez Rodríguez, Kwan Ng, Xinhua Zhan, Farah Hamade, Eva Ferino, Hajar Amini, Paulina Carmona-Mora, Heather Hull, Bradley P. Ander, Frank R. Sharp, Boryana Stamova
Software Mentions: 1
Published: over 4 years ago

10.1186/s12870-020-02513-1

Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam)
Cited by: 6
Author(s): Zhen Qin, Fuyun Hou, Aixian Li, Shuxu Dong, Chengxing Huang, Zhang Li-ming
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-016-0952-6

A NMF based approach for integrating multiple data sources to predict HIV-1–human PPIs
Cited by: 17
Author(s): Sumanta Ray, Sanghamitra Bandyopadhyay
Software Mentions: 1
Published: over 9 years ago

10.1186/s12870-019-1900-1

Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance
Cited by: 10
Author(s): Huixia Jia, Zening Jin, Jianbo Li, Peng Sun, Yahong Zhang, Xuebing Xin, Mengzhu Lu, Jianjun Hu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s40360-019-0288-8

Identification of novel candidate indicators for assessing zinc status during pregnancy in mice from microarray data
Cited by: 0
Author(s): Wei Xu, Hongyan Wu, Shang Liu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12883-021-02156-1

Identification of upregulated NF-κB inhibitor alpha and IRAK3 targeting lncRNA following intracranial aneurysm rupture-induced subarachnoid hemorrhage
Cited by: 8
Author(s): Wei Leng, Dan Fan, Zhong Ren, Qiaoying Li
Software Mentions: 1
Published: about 4 years ago

10.1186/s12866-020-01939-9

Targeting the honey bee gut parasite Nosema ceranae with siRNA positively affects gut bacteria
Cited by: 12
Author(s): Qiang Huang, Jay D. Evans
Software Mentions: 1
Published: almost 5 years ago

10.1186/1755-8794-6-4

Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer’s disease
Cited by: 55
Author(s): Andrew J. Levine, Jeremy A. Miller, Paul Shapshak, Benjamin B. Gelman, Elyse J. Singer, Charles H. Hinkin, Deborah Commins, Susan Morgello, Igor Grant, Steve Horvath
Software Mentions: 1
Published: over 12 years ago

10.1128/mSystems.00036-16

RNA Sequencing-Based Genome Reannotation of the Dermatophyte <i>Arthroderma benhamiae</i> and Characterization of Its Secretome and Whole Gene Expression Profile during Infection
Cited by: 30
Author(s): Van Du T. Tran, Niccolò De Coi, Marc Feuermann, Emanuel Schmid‐Siegert, Elena-Tatiana Băguţ, Bernard Mignon, Patrice Waridel, Corinne Peter, Sylvain Pradervand, Marco Pagni, Michel Monod
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-15-S15-S3

Gene differential coexpression analysis based on biweight correlation and maximum clique
Cited by: 35
Author(s): Chun-Hou Zheng, Yandan Lin, Shengjun Wen, Zhan-Li Sun
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-017-1946-8

A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer’s disease progression
Cited by: 19
Author(s): Sumanta Ray, Sk Md Mosaddek Hossain, Lutfunnesa Khatun, Anirban Mukhopadhyay
Software Mentions: 1
Published: over 7 years ago

10.1186/s12920-021-01012-y

Multivariate transcriptome analysis identifies networks and key drivers of chronic lymphocytic leukemia relapse risk and patient survival
Cited by: 2
Author(s): Tiara Griffen, Eric B. Dammer, Courtney D. Dill, Kaylin Carey, Corey Young, Sha’Kayla Nunez, Adaugo Q. Ohandjo, Steven M. Kornblau, James W. Lillard
Software Mentions: 1
Published: about 4 years ago

10.1186/s12920-021-00890-6

Identification of monocyte-associated genes as predictive biomarkers of heart failure after acute myocardial infarction
Cited by: 11
Author(s): Qixin Chen, Qijin Yin, Junxian Song, Chuan‐Fen Liu, Chang Seop Hong, Sufang Li
Software Mentions: 1
Published: over 4 years ago

10.1186/s12920-019-0608-2

A new method for mining information of co-expression network based on multi-cancers integrated data
Cited by: 4
Author(s): Mi-Xiao Hou, Ying-Lian Gao, Jin-Xing Liu, Junliang Shang, Rong Zhu, Shasha Yuan
Software Mentions: 1
Published: over 5 years ago

10.1186/1755-8794-4-5

Incorporating higher-order representative features improves prediction in network-based cancer prognosis analysis
Cited by: 18
Author(s): Shuangge Ma, Michael R. Kosorok, Jian Huang, Ying Dai
Software Mentions: 1
Published: over 14 years ago

10.1186/s12920-016-0171-z

Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses
Cited by: 30
Author(s): Niamh M. Troy, Elysia M. Hollams, Patrick G. Holt, Anthony Bosco
Software Mentions: 1
Published: over 9 years ago

10.1128/mSystems.00499-20

Dietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life Undernutrition
Cited by: 3
Author(s): Kylynda C. Bauer, Kelsey E. Huus, Eric Brown, Tahereh Bozorgmehr, Charisse Petersen, Mihai Cirstea, Sarah E. Woodward, John J. McCoy, Jeong Ki Hun, Reinald Pamplona, Victòria Ayala, B. Brett Finlay
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-020-03861-3

LC-N2G: a local consistency approach for nutrigenomics data analysis
Cited by: 1
Author(s): Xiangnan Xu, Samantha M. Solon-Biet, Alistair M. Senior, David Raubenheimer, Stephen J. Simpson, Luigi Fontana, Samuel Mueller, Jean Yee Hwa Yang
Software Mentions: 1
Published: over 4 years ago

10.1186/s40246-021-00350-3

Identification of subgroups along the glycolysis-cholesterol synthesis axis and the development of an associated prognostic risk model
Cited by: 4
Author(s): Enchong Zhang, Yijing Chen, Shurui Bao, Xueying Hou, Jing Hu, Oscar Yong Nan Mu, Yi Song, Liping Shan
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-020-3418-9

Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington’s disease mice
Cited by: 5
Author(s): Lucile Mégret, Satish S. Nair, Julia Dancourt, Jeff Aaronson, Jim Rosinski, Christian Néri
Software Mentions: 1
Published: over 5 years ago

10.1186/s12920-018-0407-1

Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis
Cited by: 32
Author(s): Pengfei Xu, Jian Yang, Junhui Liu, Yang Xue, Jianming Liao, Fanen Yuan, Yang Xu, Baohui Liu
Software Mentions: 1
Published: over 6 years ago

10.1186/s40246-016-0071-5

Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia
Cited by: 33
Author(s): Garima Kushwaha, Mikhail G. Dozmorov, Jonathan D. Wren, Jing Qiu, Huidong Shi, Dong Xu
Software Mentions: 1
Published: about 9 years ago

10.1093/hmg/ddv166

Spatiotemporal dynamics of the postnatal developing primate brain transcriptome
Cited by: 32
Author(s): Trygve E. Bakken, Jeremy A. Miller, Rui Luo, Amy Bernard, Jeffrey Bennett, Chang Kyu Lee, Darren Bertagnolli, Neelroop N. Parikshak, Kimberly A. Smith, Susan M. Sunkin, David G. Amaral, Daniel H. Geschwind, Ed Lein
Software Mentions: 1
Published: about 10 years ago

10.1186/s12859-019-3089-6

A robustness metric for biological data clustering algorithms
Cited by: 6
Author(s): Yuping Lu, Charles Phillips, Michael A. Langston
Software Mentions: 1
Published: over 5 years ago

10.1186/s12920-020-0702-5

Gene co-expression networks are associated with obesity-related traits in kidney transplant recipients
Cited by: 4
Author(s): Rosario B. Jaime-Lara, Abhrarup Roy, Yupeng Wang, Ansley Grimes Stanfill, Ann K. Cashion, Paule V. Joseph
Software Mentions: 1
Published: over 5 years ago

10.1093/hmg/ddaa132

Serum biomarkers associated with baseline clinical severity in young steroid-naïve Duchenne muscular dystrophy boys
Cited by: 14
Author(s): Utkarsh J. Dang, Michael Ziemba, Paula R. Clemens, Yetrib Hathout, Laurie S. Conklin, Cinrg Vamorolone, Investigators, Eric P. Hoffman
Software Mentions: 1
Published: about 5 years ago

10.1186/s40478-015-0203-5

Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis
Cited by: 436
Author(s): Inge R. Holtman, Divya Raj, Jeremy A. Miller, W. Schaafsma, Zhuoran Yin, Nieske Brouwer, Paul D. Wes, Thomas Møller, Marie Orre, Willem Kamphuis, Elly M. Hol, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 1
Published: about 10 years ago

10.1161/HYPERTENSIONAHA.118.12409

<i>Camk2n1</i> Is a Negative Regulator of Blood Pressure, Left Ventricular Mass, Insulin Sensitivity, and Promotes Adiposity
Cited by: 13
Author(s): Neza Alfazema, Marjorie Barrier, Sophie Marion de Procé, Robert Menzies, Roderick Nicholas Carter, Kevin Stewart, Ana García Díaz, Ben Moyon, Zoë Webster, Christopher Bellamy, Mark J. Arends, Roland H Stimson, Nicholas M. Morton, Timothy J. Aitman, Philip Coan
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12920-015-0098-9

Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia
Cited by: 39
Author(s): Mariana Maschietto, Ana Carolina Tahira, Renato Puga, Leandro Lima, Daniel Mariani, Bruna Paulsen, Paulo Belmonte-de-Abreu, Henrique Cursino Vieira, Ana Cristina Victorino Krepischi, Dirce Maria Carraro, Joana Almeida Palha, Stevens K. Rehen, Helena Brentani
Software Mentions: 1
Published: about 10 years ago

10.1186/1755-8794-7-51

Genetic network identifies novel pathways contributing to atherosclerosis susceptibility in the innominate artery
Cited by: 9
Author(s): Jody Albright, Pamela M. Quizon, Aldons J. Lusis, Brian J. Bennett
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12916-020-01741-4

Postpartum plasma metabolomic profile among women with preeclampsia and preterm delivery: implications for long-term health
Cited by: 10
Author(s): Xiumei Hong, Boyang Zhang, Liming Liang, Yan Zhang, Yuelong Ji, Guoying Wang, Hongkai Ji, Clary B. Clish, Irina Burd, Colleen Pearson, Barry Zuckerman, Frank B. Hu, Xiaobin Wang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-018-4999-9

Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)
Cited by: 57
Author(s): Yuling Tai, Liu Chun, Shijie Yu, Hua Yang, Jun Sun, Chunxiao Guo, Bei Huang, Zhaoye Liu, Yuan Yang, Enhua Xia, Chaoling Wei, Xiaochun Wan
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41396-018-0342-3

Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
Cited by: 43
Author(s): Ivan D. Mateus, Frédéric G. Masclaux, Consolée Aletti, Edward C. Rojas, Romain Savary, Cindy Dupuis, Ian R. Sanders
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2015.00829

Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach
Cited by: 16
Author(s): Wenchuan Xie, Junfeng Huang, Yang Liu, Rao Jianan, Da Luo, Miao He
Software Mentions: 1
Published: almost 10 years ago

10.3389/fpls.2020.528108

Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis
Cited by: 5
Author(s): Shuangshuang Qin, Kunhua Wei, Zhan-Hu Cui, Ying Liang, Mingjie Li, Li Gu, Chuyun Yang, Xiaolei Zhou, Linxuan Li, Wei Xü, Can Liu, Miao Jin, Zhongyi Zhang
Software Mentions: 1
Published: almost 5 years ago

10.3389/fpls.2020.604849

Network Analysis Combining Proteomics and Metabolomics Reveals New Insights Into Early Responses of Eucalyptus grandis During Rust Infection
Cited by: 11
Author(s): Alline Sekiya, Felipe Garbelini Marques, Thiago Falda Leite, Thaís Regiani Cataldi, Fabrício Edgar de Moraes, Ana Lúcia Mendes Pinheiro, Mônica Teresa Veneziano Labate, Carlos Alberto Labate
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2020.616338

Interspecific Variation in the Unsaturation Level of Seed Oils Were Associated With the Expression Pattern Shifts of Duplicated Desaturase Genes and the Potential Role of Other Regulatory Genes
Cited by: 3
Author(s): Mengli Wang, Lexuan Gao, Gengyun Li, Chengchuan Zhou, Jinjing Jian, Zhen Xing, Yuguo Wang, Wenju Zhang, Song Zhang, Yonghong Hu, Ji Hyun Yang
Software Mentions: 1
Published: over 4 years ago

10.1038/s41396-019-0472-2

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection
Cited by: 54
Author(s): Bethany Kolody, John P. McCrow, Lisa Zeigler Allen, Frank O. Aylward, Kristina M. Fontanez, Ahmed Moustafa, Mohammad Moniruzzaman, Francisco P. Chávez, Christopher A. Scholin, Eric E. Allen, Alexandra Z. Worden, Edward F. DeLong, Andrew E. Allen
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-021-07714-y

Transcriptomic insights into the effects of CytCo, a novel nematotoxic protein, on the pine wood nematode Bursaphelenchus xylophilus
Cited by: 4
Author(s): Ye Chen, Xiang Zhou, Kai Guo, Sha-Ni Chen, Xiu Su
Software Mentions: 1
Published: about 4 years ago

10.3389/fpls.2021.705321

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense
Cited by: 9
Author(s): Zhonghua Tu, Yu-Fang Shen, Shaoying Wen, Huanhuan Liu, Lingmin Wei, Huogen Li
Software Mentions: 1
Published: about 4 years ago

10.3389/fpls.2021.624319

Grafting Delays Watermel on Fruit Ripening by Altering Gene Expression of ABA Centric Phytohormone Signaling
Cited by: 5
Author(s): Sheng Guo, Honghe Sun, Jiaxing Tian, Guoyu Zhang, Guoyi Gong, Yi Ren, Jie Zhang, Maoying Li, Haiying Zhang, Haizhen Li, Yong Xu
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2017.00092

De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues
Cited by: 19
Author(s): Shi-Fang Wu, Jing Liu, Guoju Chen, Hancai Chen, Bihao Cao, Changming Chen
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-021-07368-w

De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress
Cited by: 22
Author(s): Pan Zhang, Tianqi Duo, Fengdan Wang, Xunzhong Zhang, Zouzhuan Yang, Guofu Hu
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2014.00565

Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores
Cited by: 38
Author(s): Heidi M. Appel, Howard W. Fescemyer, Jürgen Ehlting, David J. Weston, Erin MacNeal Rehrig, Trupti Joshi, Dong Xu, Jöerg Bohlmann, Jack C. Schultz
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-15-1056

Metabolic and co-expression network-based analyses associated with nitrate response in rice
Cited by: 40
Author(s): Viktoriya Coneva, Caitlin M. A. Simopoulos, José A. Casaretto, Ashraf El-Kereamy, David Guevara, Jonathan Cohn, Tong Zhu, Lining Guo, Danny Alexander, Yong‐Mei Bi, Paul D. McNicholas, Steven J. Rothstein
Software Mentions: 1
Published: over 10 years ago

10.3389/fpls.2017.01371

Phenotypic and Comparative Transcriptome Analysis of Different Ploidy Plants in Dendrocalamus latiflorus Munro
Cited by: 11
Author(s): Guirong Qiao, Mingying Liu, Kunlin Song, Haiying Li, Haiming Yang, Yafang Yin, Renying Zhuo
Software Mentions: 1
Published: almost 8 years ago

10.3389/fpls.2018.00137

A Systems Biology Study in Tomato Fruit Reveals Correlations between the Ascorbate Pool and Genes Involved in Ribosome Biogenesis, Translation, and the Heat-Shock Response
Cited by: 9
Author(s): Rebecca Stevens, Piérre Baldet, Jean‐Paul Bouchet, Mathilde Causse, Catherine Deborde, Claire Deschodt, Mireille Faurobert, Cécile Garchery, Virginie Garcia, Hélène Gautier, Barbara Gouble, Mickaël Maucourt, Annick Moing, David L. Page, J. Petit, Jean‐Luc Poëssel, Vincent Truffault, Christophe Rothan
Software Mentions: 1
Published: over 7 years ago

10.3389/fphys.2019.00662

Analysis of Genes Involved in Ulcerative Colitis Activity and Tumorigenesis Through Systematic Mining of Gene Co-expression Networks
Cited by: 28
Author(s): Wu Shi, Rongjun Zou, Minglei Yang, Lei Mai, Jiangnan Ren, Ji Wen, Zhaoshi Liu, Renxu Lai
Software Mentions: 1
Published: about 6 years ago

10.3389/fphys.2019.00275

Identification of the Biomarkers and Pathological Process of Osteoarthritis: Weighted Gene Co-expression Network Analysis
Cited by: 36
Author(s): Hao Gu, Min Yang, Jia Guo, Zhang Chao, Lu-Lu Lin, Yang Liu, Renxiong Wei
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2021.668736

Comparison of Transcriptional Response of C3 and C4 Plants to Drought Stress Using Meta-Analysis and Systems Biology Approach
Cited by: 7
Author(s): Ahmad Tahmasebi, Ali Niazi‎
Software Mentions: 1
Published: about 4 years ago

10.3389/fphys.2018.01841

Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus–A Co-expression Network Based Analysis
Cited by: 7
Author(s): Amnah Siddiqa, Elisa Cirillo, Samar Tareen, Amjad Ali, Martina Kutmon, Lars Eijssen, Jamil Ahmad, Chris T. Evelo, Susan L. Coort
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2018.01139

The Galling Truth: Limited Knowledge of Gall-Associated Volatiles in Multitrophic Interactions
Cited by: 13
Author(s): Renée M. Borges
Software Mentions: 1
Published: almost 7 years ago

10.3389/fphys.2017.00822

Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis
Cited by: 102
Author(s): Moulun Luo, Yong Liu, Pengfei Wu, Dongxia Luo, Qun Sun, Han Zheng, Richard Hu, Stephen J. Pandol, Qingfeng Li, Yuan‐Ping Han, Yilan Zeng
Software Mentions: 1
Published: over 7 years ago

10.3389/fphys.2020.623190

Transcriptomic Coupling of PKP2 With Inflammatory and Immune Pathways Endogenous to Adult Cardiac Myocytes
Cited by: 11
Author(s): Marta Pérez-Hernández, Grecia M Marrón-Liñares, Florencia Schlamp, Adriana Heguy, Chantal J.M. van Opbergen, Valeria Mezzano, Mingliang Zhang, Feng-Xia Liang, Marina Cerrone, Mario Delmar
Software Mentions: 1
Published: over 4 years ago

10.3389/fphys.2017.00594

Murine Myocardial Transcriptome Analysis Reveals a Critical Role of COPS8 in the Gene Expression of Cullin-RING Ligase Substrate Receptors and Redox and Vesicle Trafficking Pathways
Cited by: 7
Author(s): Ammara Abdullah, Kathleen M. Eyster, Travis Bjordahl, Xiao Peng, Erliang Zeng, Xuejun Wang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-018-2193-3

Identification of common coexpression modules based on quantitative network comparison
Cited by: 4
Author(s): Yousang Jo, Sang-Hyun Kim, Doheon Lee
Software Mentions: 1
Published: about 7 years ago

10.3389/fphar.2020.00881

Integrated PPI- and WGCNA-Retrieval of Hub Gene Signatures Shared Between Barrett's Esophagus and Esophageal Adenocarcinoma
Cited by: 54
Author(s): Asma Sindhoo Nangraj, Gurudeeban Selvaraj, Satyavani Kaliamurthi, Aman Chandra Kaushik, William C. Cho, Dong Wei
Software Mentions: 1
Published: almost 5 years ago

10.3389/fphar.2021.474267

The Advantages of Connectivity Map Applied in Traditional Chinese Medicine
Cited by: 9
Author(s): Huimin Jiang, Cheng Hu, Meijuan Chen
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms22031020

DNA Methylation Analysis Identifies Patterns in Progressive Glioma Grades to Predict Patient Survival
Cited by: 13
Author(s): Jing Yin Weng, Nicole Salazar
Software Mentions: 1
Published: over 4 years ago

10.3389/fphar.2020.01112

Construction and Analysis of the Tumor-Specific mRNA–miRNA–lncRNA Network in Gastric Cancer
Cited by: 27
Author(s): Xiaohao Zheng, Xiaohui Wang, Li Zheng, Hao Zhao, Wenbin Li, Bingzhi Wang, Liyan Xue, Yantao Tian, Yibin Xie
Software Mentions: 1
Published: about 5 years ago

10.3389/fphar.2021.725341

An Integrated Metabolomic Study of Osteoporosis: Discovery and Quantification of Hyocholic Acids as Candidate Markers
Cited by: 13
Author(s): Dawei Deng, Pan Chen, Zeming Wu, Yanan Sun, Chang Liu, Hong Xiang, Peiyuan Yin, Dong Shang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2020.00224

Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses
Cited by: 11
Author(s): Lauriane Hennet, Angélique Berger, Noemí Trabanco, Emeline Ricciuti, Jean François Dufayard, Stéphanie Bocs, Denis Bastianelli, Laurent Bonnal, Sandrine Roques, Laura Rossini, Delphine Luquet, Nancy Terrier, David Pot
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2018.00450

Emerging Biomarkers in Bladder Cancer Identified by Network Analysis of Transcriptomic Data
Cited by: 44
Author(s): Matteo Giulietti, Giulia Occhipinti, Alessandra Righetti, Massimo Bracci, Alessandro Conti, Annamaria Ruzzo, Elisabetta Cerigioni, Tiziana Cacciamani, Giovanni Principato, Francesco Piva
Software Mentions: 1
Published: almost 7 years ago

10.3389/fpls.2020.01256

Transcriptome and Flavonoids Metabolomic Analysis Identifies Regulatory Networks and Hub Genes in Black and White Fruits of Lycium ruthenicum Murray
Cited by: 16
Author(s): Tingting Li, Yunfang Fan, Huan Qin, Guoli Dai, Guo‐Xiu Li, Yanlong Li, Jingjin Wang, Yue Yin, Fang Chen, Xiaoya Qin, Yang Cao, Lin Tang
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2020.00638

Identification Hub Genes in Colorectal Cancer by Integrating Weighted Gene Co-Expression Network Analysis and Clinical Validation in vivo and vitro
Cited by: 31
Author(s): Yihang Yuan, Ji Chen, Jue Wang, Ming Xu, Yunpeng Zhang, Peng Sun, Leilei Liang
Software Mentions: 1
Published: about 5 years ago

10.3389/fonc.2021.681280

N6-Methyladenosine RNA Demethylase FTO Promotes Gastric Cancer Metastasis by Down-Regulating the m6A Methylation of ITGB1
Cited by: 22
Author(s): Duo Wang, Xiujuan Qu, Wenqing Lü, Yizhe Wang, Yue Jin, Kezuo Hou, Bowen Yang, Ce Li, Jianfei Qi, Jiawen Xiao, Xiaofang Che, Yunpeng Liu
Software Mentions: 1
Published: about 4 years ago

10.3389/fonc.2019.01465

Prognostic Heterogeneity of MRE11 Based on the Location of Primary Colorectal Cancer Is Caused by Activation of Different Immune Signals
Cited by: 7
Author(s): Cheng Fan, Maria Kopsida, You-Bin Liu, Hong Zhang, Jingfang Gao, Gunnar Arbman, Siyuwei Cao, Yuan Li, Zong‐Guang Zhou, Xiao‐Feng Sun
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5098-7

Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density
Cited by: 36
Author(s): Amy Ellison, Tamsyn M. Uren Webster, Olivier Rey, Carlos García de Leániz, Sofía Consuegra, Pablo Orozco‐terWengel, Joanne Cable
Software Mentions: 1
Published: almost 7 years ago

10.3389/fonc.2021.591507

Identification of Ten Core Hub Genes as Potential Biomarkers and Treatment Target for Hepatoblastoma
Cited by: 8
Author(s): Rui Sun, Simin Li, Ke Zhao, Mei Diao, Long Li
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2016.00497

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System
Cited by: 67
Author(s): Collin M. Timm, Dale A. Pelletier, Sara Jawdy, Lee E. Gunter, Jeremiah A. Henning, Nancy L. Engle, Jayde A. Aufrecht, Emily Gee, Intawat Nookaew, Zamin K. Yang, Tse Yuan S Lu, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, David J. Weston
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-6418-2

De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)
Cited by: 8
Author(s): Ying Liu, Chunxia Zhang, Kebin Yang, Jingjing Shi, Yulong Ding, Zhimin Gao
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2021.679629

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)
Cited by: 6
Author(s): Yuan‐Jen Chang, Feifei Sun, Shufeng Sun, Lanfen Wang, Jing Wu, Zhendong Zhu
Software Mentions: 1
Published: about 4 years ago

10.3389/fonc.2020.592413

Ubiquitin-Like Modifier Activating Enzyme 1 as a Novel Diagnostic and Prognostic Indicator That Correlates With Ferroptosis and the Malignant Phenotypes of Liver Cancer Cells
Cited by: 29
Author(s): Yiru Shan, Guang Yang, Haixia Huang, Yehan Zhou, Xiangyu Hu, Qiuhong Lu, Peng Guo, Jun Hou, Li Cao, Fuhua Tian, Qi Pan
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2021.670490

Potential Impact of ALKBH5 and YTHDF1 on Tumor Immunity in Colon Adenocarcinoma
Cited by: 18
Author(s): Guanyu Yan, Yi An, Boyang Xu, Ningning Wang, Xiaodi Sun, Mingjun Sun
Software Mentions: 1
Published: about 4 years ago

10.3389/fonc.2021.647253

Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis
Cited by: 6
Author(s): Yaxin Hou, Junyi Hu, Lijie Zhou, Lilong Liu, Ke Chen, Xiong Yang
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms22042079

Dysfunctional Gut Microbiome Networks in Childhood IgE-Mediated Food Allergy
Cited by: 24
Author(s): Khui Hung Lee, Jing Guo, Yong Song, Amir Ariff, Michael O’Sullivan, Belinda J. Hales, Benjamin J. Mullins, Guicheng Zhang
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2021.641851

Identification of Key Functional Gene Signatures Indicative of Dedifferentiation in Papillary Thyroid Cancer
Cited by: 2
Author(s): Weihua Xu, Cuiwei Li, Ben Ma, Zhongxin Lu, Yuchen Wang, Hongyi Jiang, Yi Luo, Yichen Yang, Xiao Wang, Tian Liao, Qinghai Ji, Yu Wang, Wenjun Wei
Software Mentions: 1
Published: about 4 years ago