10.1186/s12872-021-02211-2

Identification of key miRNAs and mRNAs related to coronary artery disease by meta-analysis
Cited by: 3
Author(s): Long Liu, Jingze Zhang, Mei Yi Wu, Haiming Xu
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.23219

Co-expression analysis revealed PTCH1-3'UTR promoted cell migration and invasion by activating miR-101-3p/SLC39A6 axis in non-small cell lung cancer: implicating the novel function of PTCH1
Cited by: 21
Author(s): Xuechao Wan, Zhe Kong, Kaili Chu, Chuanyou Yi, Jian Hu, Rui Qin, Chunxia Zhao, Fangqiu Fu, Hai Wu, Yao Li, Yan Huang
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12885-021-08030-0

An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma
Cited by: 8
Author(s): Wei Zheng, Chaoying Chen, Jianghao Yu, Chengfeng Jin, Tie-Mei Han
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-018-4176-1

Integrated genomic analysis identifies clinically relevant subtypes of renal clear cell carcinoma
Cited by: 27
Author(s): Peng Wu, Jiali Liu, Shimei Pei, Changpeng Wu, Kai Yang, Shupeng Wang, Song Wu
Software Mentions: 1
Published: over 8 years ago

10.1186/s40064-016-3385-9

Discovery of the molecular mechanisms of the novel chalcone-based Magnaporthe oryzae inhibitor C1 using transcriptomic profiling and co-expression network analysis
Cited by: 3
Author(s): Hui Chen, Xiaoyun Wang, Hong Jin, Rui Li, Taiping Hou
Software Mentions: 1
Published: about 10 years ago

10.1186/1752-0509-8-S2-S7

Pathway network inference from gene expression data
Cited by: 26
Author(s): Ignacio Ponzoni, María José Nueda, Sonia Tarazona, Stefan Götz, David Montaner, Julieta Sol Dussaut, Joaquín Dopazo, Ana Conesa
Software Mentions: 1
Published: over 12 years ago

10.1186/s12918-015-0165-z

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data
Cited by: 10
Author(s): Ricardo de Matos Simoes, Sabine Dalleau, Kate E. Williamson, Frank Emmert‐Streib
Software Mentions: 1
Published: over 11 years ago

10.1186/1756-0500-5-265

Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes
Cited by: 24
Author(s): Ioannis Michalopoulos, Georgios A. Pavlopoulos, Apostolos Malatras, Alexandros Karelas, Myrto Kostadima, Reinhard Schneider, Σοφία Κοσσίδα
Software Mentions: 1
Published: over 14 years ago

10.1186/s13104-019-4559-7

A seed germination transcriptomic study contrasting two soybean genotypes that differ in terms of their tolerance to the deleterious impacts of elevated temperatures during seed fill
Cited by: 14
Author(s): Jason D. Gillman, Jessica J. Biever, Songqing Ye, William G. Spollen, Scott A. Givan, Zhen Lyu, Trupti Joshi, James R. Smith, Felix B. Fritschi
Software Mentions: 1
Published: about 7 years ago

10.1186/1753-6561-5-S2-S3

Nonlinear gene cluster analysis with labeling for microarray gene expression data in organ development
Cited by: 7
Author(s): Martin Ehler, Vinodh N. Rajapakse, Barry R. Zeebèrg, Brian P. Brooks, Jacob D. Brown, Wojciech Czaja, Robert F. Bonner
Software Mentions: 1
Published: over 15 years ago

10.18632/oncotarget.26554

Integrative system genetic analysis reveals mRNA-lncRNA network associated with mouse spontaneous lung cancer susceptibility
Cited by: 2
Author(s): Yanzhao Zhou, Ming You
Software Mentions: 1
Published: almost 8 years ago

10.1155/2021/5546032

A Comprehensive Prognostic and Immunological Analysis of a New Three-Gene Signature in Hepatocellular Carcinoma
Cited by: 7
Author(s): Jun Liu, Jianjun Lu, Wenli Li
Software Mentions: 1
Published: over 5 years ago

10.1177/1758835920937904

Development and validation of a hypoxia-related gene signature to predict overall survival in early-stage lung adenocarcinoma patients
Cited by: 36
Author(s): Jing Sun, Tianyu Zhao, Di Zhao, Xin Qi, Xuanwen Bao, Run Shi, Chuan Su
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12885-017-3413-3

Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration
Cited by: 24
Author(s): Princy Parsana, Sarah R. Amend, James R. Hernandez, Kenneth J. Pienta, Alexis Battle
Software Mentions: 1
Published: over 9 years ago

10.1186/s12919-016-0009-x

Using gene expression data to identify causal pathways between genotype and phenotype in a complex disease: application to Genetic Analysis Workshop 19
Cited by: 3
Author(s): Holly F. Ainsworth, Heather J. Cordell
Software Mentions: 1
Published: about 10 years ago

10.7150/thno.48064

ROS production and mitochondrial dysfunction driven by PU.1-regulated NOX4-p22^phox activation in Aβ-induced retinal pigment epithelial cell injury
Cited by: 18
Author(s): Junran Sun, Jieqiong Chen, Tong Li, Peng Huang, Jie Li, Mengxi Shen, Min Gao, Yang Sun, Jian Liang, Xiaomeng Li, Yimin Wang, Yushu Xiao, Xiang Shi, Yifan Hu, Jing Feng, Huixun Jia, Te Liu, Xiaodong Sun
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2229-12-245

OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize
Cited by: 46
Author(s): Christian Colmsee, Martin Mascher, Tobias Czauderna, Anja Hartmann, Urte Schlüter, Nina Zellerhoff, J. E. Schmitz, Andrea Bräutigam, Thea R. Pick, Philipp Alter, Manfred Gahrtz, Sandra A. Witt, Alisdair R. Fernie, Frederik Börnke, Holger Fahnenstich, Marcel Bucher, Thomas Dresselhaus, Andreas P.M. Weber, Falk Schreiber, Uwe Scholz, Uwe Sonnewald
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12885-021-07817-5

Comprehensive analysis of ceRNA network related to lincRNA in glioblastoma and prediction of clinical prognosis
Cited by: 3
Author(s): Guangdong Liu, Danian Liu, Jingjing Huang, Jianxin Li, Chuang Wang, Shiqiang Ge, Haidong Gong
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-021-08066-2

A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer
Cited by: 15
Author(s): Xun Liu, Bobo Chen, Jiahui Chen, Shung Shung Sun
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-018-1544-6

Canopy attachment position influences metabolism and peel constituency of European pear fruit
Cited by: 20
Author(s): Sara Serra, Nathanael Sullivan, James P. Mattheis, Stefano Musacchi, David R. Rudell
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-14-365

Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma
Cited by: 22
Author(s): Chao Wu, Jun Zhu, Xuegong Zhang
Software Mentions: 1
Published: almost 13 years ago

10.1089/pancan.2020.0007

Gene Expression Network Analysis of Precursor Lesions in Familial Pancreatic Cancer
Cited by: 13
Author(s): Ming Tan, Ove B. Schaffalitzky de Muckadell, Maiken Thyregod Jøergensen
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-020-02606-x

Transcriptome analysis provides new insights into the transcriptional regulation of methyl jasmonate-induced flavonoid biosynthesis in pear calli
Cited by: 34
Author(s): Apekshika T Premathilake, Junbei Ni, Jiemin Shen, Songling Bai, Yuanwen Teng
Software Mentions: 1
Published: about 6 years ago

10.1186/s12870-020-02569-z

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Cited by: 31
Author(s): Yinghua Pan, He Liang, Lijun Gao, Gaoxing Dai, Weiwei Chen, Yang Xiao-ling, Dongjin Qing, Ju Gao, Hao Wu, Juan Huang, Weiyong Zhou, Chengcui Huang, Yuntao Liang, Gaofeng Deng
Software Mentions: 1
Published: about 6 years ago

10.1038/tp.2015.118

Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients
Cited by: 46
Author(s): Aaron Topol, James English, Erin Flaherty, Prashanth Rajarajan, Brigham J. Hartley, Siddharth Gupta, Fiona Desland, Shijia Zhu, Troy Goff, Lawrence Friedman, Judith L. Rapoport, Dan P. Felsenfeld, Gerard Cagney, Alan Mackay‐Sim, Jeffrey N. Savas, Bruce J. Aronow, Gang Fang, B Zhang, David Cotter, Kristen J. Brennand
Software Mentions: 1
Published: about 11 years ago

10.1186/s12870-020-02442-z

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton
Cited by: 23
Author(s): Kashif Shahzad, Xuexian Zhang, Liping Guo, Ting Qi, Lisheng Bao, Meng Zhang, Bingbing Zhang, Hailin Wang, Huini Tang, Xin Qiao, Juanjuan Feng, Jianyong Wu, Chaozhu Xing
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-019-2192-1

Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots
Cited by: 40
Author(s): Guowen Cui, Hua Chai, Hang Yin, Mei Yang, Guofu Hu, Mingying Guo, Rugeletu Yi, Pan Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1038/tp.2016.245

Peripheral blood gene expression profiles linked to monoamine metabolite levels in cerebrospinal fluid
Cited by: 13
Author(s): Jurjen J. Luykx, Loes Olde Loohuis, M Neeleman, Eric Strengman, Steven C. Bakker, Eef G.W.M. Lentjes, Paul Borgdorff, Eric P.A. van Dongen, Peter Bruins, René S. Kahn, Steve Horvath, Simone de Jong, Roel A. Ophoff
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12870-021-03133-z

Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon
Cited by: 10
Author(s): Qingyou Zheng, Wenxing Chen, Man Luo, Lingfei Xu, Qinglin Zhang, Zhitian Luo
Software Mentions: 1
Published: over 5 years ago

10.1038/tp.2016.291

Rare damaging variants in DNA repair and cell cycle pathways are associated with hippocampal and cognitive dysfunction: a combined genetic imaging study in first-episode treatment-naive patients with schizophrenia
Cited by: 4
Author(s): Zhenxing Yang, M Li, Xun Hu, Bo Xiang, Wei Deng, Q Wang, Y Wang, Liansheng Zhao, Xiaoyan Ma, Pak C. Sham, Georg Northoff, T Li
Software Mentions: 1
Published: over 9 years ago

10.1002/path.4467

Cancer‐associated fibroblasts predict poor outcome and promote periostin‐dependent invasion in oesophageal adenocarcinoma
Cited by: 148
Author(s): Tim Underwood, Annette Hayden, Mathieu Derouet, Edwin Garcia, Fergus Noble, Michael J. White, Steve Thirdborough, Abbie Mead, Nicholas J. Clemons, Massimiliano Mellone, Chudy Uzoho, John Primrose, Jeremy P. Blaydes, Gareth J. Thomas
Software Mentions: 1
Published: almost 12 years ago

10.1177/1759091419854627

Identification of the Molecular Events Involved in the Development of Prefrontal Cortex Through the Analysis of RNA-Seq Data From BrainSpan
Cited by: 2
Author(s): Hadi Najafi, Mohadeseh Naseri, Javad Zahiri, Mehdi Totonchi, Shahana Majid
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-019-2125-z

PI signal transduction and ubiquitination respond to dehydration stress in the red seaweed Gloiopeltis furcata under successive tidal cycles
Cited by: 10
Author(s): Shun Liu, Zi‐Min Hu, Quansheng Zhang, Xiaoqi Yang, Alan T. Critchley, Delin Duan
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-021-02961-3

Analysis of miRNA-mediated regulation of flowering induction in Lilium × formolongi
Cited by: 4
Author(s): Qian Zhang, Yuqian Zhao, Xue Gao, Guanqing Jia
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-017-1590-3

Preservation affinity in consensus modules among stages of HIV-1 progression
Cited by: 14
Author(s): Sk Md Mosaddek Hossain, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-016-1319-8

SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations
Cited by: 14
Author(s): Casey P. Shannon, Virginia Chen, Mandeep Takhar, Zsuzsanna Hollander, Robert Balshaw, Bruce M. McManus, Scott J. Tebbutt, Don D. Sin, Raymond T. Ng
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41398-018-0234-3

Identification and replication of RNA-Seq gene network modules associated with depression severity
Cited by: 33
Author(s): Trang T. Le, Jonathan Savitz, Hideo Suzuki, Masaya Misaki, T. Kent Teague, Bill C. White, Julie H. Marino, Graham B. Wiley, Patrick M. Gaffney, Wayne C. Drevets, Brett A. McKinney, Jerzy Bodurka
Software Mentions: 1
Published: about 8 years ago

10.1186/s12870-021-02952-4

Explore the gene network regulating the composition of fatty acids in cottonseed
Cited by: 7
Author(s): Lihong Ma, Xinqi Cheng, Chuan Wang, Xinyu Zhang, Fei Xue, Yanjun Li, Qian Zhu, Jie Sun, Feng Liu
Software Mentions: 1
Published: over 5 years ago

10.1515/med-2021-0286

A nomogram for predicting metabolic steatohepatitis: The combination of NAMPT, RALGDS, GADD45B, FOSL2, RTP3, and RASD1
Cited by: 4
Author(s): Shenling Liao, He He, Yuping Zeng, Yang Lin-de, Zhi Liu, Zhenmei An, Mei Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41398-018-0325-1

Dopamine perturbation of gene co-expression networks reveals differential response in schizophrenia for translational machinery
Cited by: 7
Author(s): Mark Z. Kos, Jubao Duan, Alan R. Sanders, Lucy Blondell, Eugene Drigalenko, Melanie A. Carless, Pablo V. Gejman, Harald H.H. Göring, Mgs
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-020-02460-x

The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences
Cited by: 7
Author(s): Shuaibin Lian, Yongjie Zhou, Zixiao Liu, Andong Gong, Lin Cheng
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-018-1497-9

Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis)
Cited by: 38
Author(s): Junyan Zhu, Xuewen Wang, Qingshan Xu, Sheng Zhao, Yuling Tai, Chaoling Wei
Software Mentions: 1
Published: almost 8 years ago

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: almost 6 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: over 10 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: over 5 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: over 7 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: about 10 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: over 7 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: about 6 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: almost 6 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: about 5 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: about 7 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 5 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 6 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: almost 8 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: over 6 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: about 6 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: almost 7 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: almost 6 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: almost 6 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: over 6 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: over 7 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: about 5 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: about 5 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: almost 9 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: almost 6 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: over 6 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 10 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: about 7 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 7 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: over 5 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: about 6 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 13 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: about 10 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: almost 12 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: almost 9 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: over 5 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 5 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: almost 7 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: almost 16 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 10 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: about 6 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: almost 6 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: about 5 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 6 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: almost 8 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: over 10 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: over 11 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: almost 7 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 6 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: over 6 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: over 11 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: about 7 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: over 11 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: about 12 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: about 6 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: about 8 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: almost 8 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: over 7 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: over 5 years ago