bioconductor: GENIE3 | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 years ago

10.1038/s41422-020-00453-x

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration
Cited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: over 3 years ago

10.7554/eLife.58993

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
Cited by: 23
Author(s): Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung
Software Mentions: 12
Published: about 4 years ago

10.3389/fgene.2021.655536

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
Cited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 3 years ago

10.1186/s12915-019-0709-6

Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment
Cited by: 31
Author(s): Hang Ruan, Yingnan Liao, Zongna Ren, Lin Mao, Fang Yao, Yu Peng, Youqiong Ye, Zhao Zhang, Shengli Li, Hanshi Xu, Jiewei Liu, Lixia Diao, Bingying Zhou, Leng Han, Li Wang
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41422-021-00467-z

Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses
Cited by: 44
Author(s): Jian He, Yan Jing, Jianfang Wang, Liangyu Zhao, Xin Qian, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Software Mentions: 10
Published: over 3 years ago

10.1126/sciadv.abc3781

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
Cited by: 21
Author(s): Maria Litovchenko, Antonio C. A. Meireles-Filho, Michael Frochaux, R. Bevers, Alessio Prunotto, Ane Martín Anduaga, Brian Hollis, Vincent Gardeux, Virginie Braman, Julie Russeil, Sebastián Kadener, Matteo Dal Peraro, Bart Deplancke
Software Mentions: 10
Published: over 3 years ago

10.1534/g3.120.401436

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat
Cited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: about 4 years ago

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pcbi.1008223

Causal network inference from gene transcriptional time-series response to glucocorticoids
Cited by: 15
Author(s): Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1009029

G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Cited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: over 3 years ago

10.1186/s12864-021-07659-2

Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite
Cited by: 15
Author(s): Océane Cassan, Sophie Lèbre, Antoine Martin
Software Mentions: 8
Published: over 3 years ago

10.17179/excli2015-168

Data- and knowledge-based modeling of gene regulatory networks: an update.
Cited by: 24
Author(s): Jörg Linde, Sylvie Schulze, Sebastian Henkel, Reinhard Guthke
Software Mentions: 8
Published: almost 10 years ago

10.1093/database/baz046

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data
Cited by: 621
Author(s): Oscar Franzén, Li‐Ming Gan, Johan Björkegren
Software Mentions: 8
Published: almost 6 years ago

10.3233/JAD-170011

Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data
Cited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: about 7 years ago

10.1038/s41422-018-0053-3

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis
Cited by: 162
Author(s): Xiaoying Fan, Ji Dong, Shaobo Zhong, Wei Yuan, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao, Wei Wang, Jie Yan, Xiaoqun Wang, Jie Qiao, Fuchou Tang
Software Mentions: 8
Published: over 6 years ago

10.1186/s12859-016-1235-y

BTR: training asynchronous Boolean models using single-cell expression data
Cited by: 62
Author(s): Chee Lim, Huange Wang, Steven Woodhouse, Nir Piterman, Lorenz Wernisch, Jasmin Fisher, Berthold Göttgens
Software Mentions: 8
Published: about 8 years ago

10.1038/s41422-020-00412-6

Single-cell transcriptomic atlas of primate cardiopulmonary aging
Cited by: 76
Author(s): Shuai Ma, Shuhui Sun, Jiaming Li, Yanling Fan, Jing Qu, Liang Sun, Si Wang, Yiyuan Zhang, Shanshan Yang, Zunpeng Liu, Zeming Wu, Sheng Zhang, Qiaoran Wang, Ai Zheng, Shuguang Duo, Yang Yu, Juan Carlos Izpisúa Belmonte, Piu Chan, Qi Zhou, Moshi Song, Weiqi Zhang, Guang Hui Liu
Software Mentions: 7
Published: about 4 years ago

10.1186/s12864-020-07338-8

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
Cited by: 10
Author(s): Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulín, Petri Auvinen
Software Mentions: 7
Published: almost 4 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-87234-7

Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model
Cited by: 9
Author(s): Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 7
Published: over 3 years ago

10.1016/j.ccell.2020.06.004

Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma
Cited by: 86
Author(s): Johannes Gojo, Bernhard Englinger, Li Jiang, Jens Martin Hübner, McKenzie Shaw, Olivia A. Hack, Sibylle Madlener, Dominik Kirchhofer, Ilon Liu, Jason W. Pyrdol, Volker Hovestadt, Emanuele Mazzola, Nathan D. Mathewson, Maria Trissal, Daniela Lötsch, Christian Dorfer, Christine Haberler, Angela Halfmann, Lisa Mayr, Andreas Peyrl, René Geyeregger, Benjamin Schwalm, Monica Mauermann, Kristian W. Pajtler, Till Milde, Marni E. Shore, Jack Geduldig, Kristine Pelton, Thomas Czech, Orr Ashenberg, Kai W. Wucherpfennig, Orit Rozenblatt-Rosen, Sanda Alexandrescu, Keith L. Ligon, Stefan M. Pfister, Aviv Regev, Irene Slavc, Walter Berger, Mario L. Suvà, Marcel Kool, Mariella G. Filbin
Software Mentions: 7
Published: over 4 years ago

10.18632/oncotarget.27808

Identification of novel prognostic markers of survival time in high-risk neuroblastoma using gene expression profiles
Cited by: 6
Author(s): Abdulazeez Giwa, Azeez Ayomide Fatai, Junaid Gamieldien, Alan Christoffels, Hocine Bendou
Software Mentions: 7
Published: almost 4 years ago

10.7150/thno.44306

Single-cell Transcriptome Profiling reveals Dermal and Epithelial cell fate decisions during Embryonic Hair Follicle Development
Cited by: 39
Author(s): Wei Ge, Shao-Jing Tan, Shan-He Wang, Lan Li, Xiaowen Sun, Wei Shen, Xin Wang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13073-021-00908-9

scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks
Cited by: 16
Author(s): Ting Jin, Peter Rehani, Mufang Ying, Jiawei Huang, Shuang Liu, Panagiotis Roussos, Daifeng Wang
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-016-3317-7

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data
Cited by: 32
Author(s): Yongli Hu, Takeshi Hase, Hui Peng Li, Shyam Prabhakar, Hiroaki Kitano, See Ket Ng, Samik Ghosh, Lionel Wee
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pone.0111661

How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?
Cited by: 18
Author(s): Djordje Djordjevic, Andrian Yang, Armella Zadoorian, Kevin Rungrugeecharoen, Joshua W. K. Ho
Software Mentions: 6
Published: almost 10 years ago

10.1038/s42003-020-01476-1

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
Cited by: 58
Author(s): Baijun Dong, Juju Miao, Yanqing Wang, Wenqin Luo, Zhongzhong Ji, Huadong Lai, Man Zhang, Xiaomu Cheng, Jinming Wang, Yuxiang Fang, Helen He Zhu, Chee Wai Chua, Liancheng Fan, Yao Zhu, Jiahua Pan, Jia Wang, Wei Xue, Wei‐Qiang Gao
Software Mentions: 6
Published: almost 4 years ago

10.3389/fpls.2019.00698

PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation
Cited by: 5
Author(s): Hongryul Ahn, Kyuri Jo, Dabin Jeong, Minwoo Pak, Jihye Hur, Wi Hoon Jung, Sun Kim
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.202718

TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cells
Cited by: 4
Author(s): Qizheng Han, Junhao Wang, Haihua Luo, Lei Li, Xinya Lu, Aihua Liu, Yongqiang Deng, Yong Jiang
Software Mentions: 6
Published: over 3 years ago

10.3389/fpls.2021.619062

Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance
Cited by: 5
Author(s): Weilin Cao, Li‐Ming Gan, Chenchen Wang, Xuan Zhao, Mingyu Zhang, Jinyan Du, Shumei Zhou, Changxiang Zhu
Software Mentions: 6
Published: over 3 years ago

10.3389/fnmol.2019.00316

Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis
Cited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12920-018-0413-3

Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature
Cited by: 20
Author(s): Dan Li, William Yang, Yifan Zhang, Jack Yang, Renchu Guan, Dong Xu, Mary Qu Yang
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12859-020-03707-y

A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count data
Cited by: 11
Author(s): Michael Sekula, Jeremy Gaskins, Susmita Datta
Software Mentions: 6
Published: about 4 years ago

10.1002/pld3.279

Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis
Cited by: 12
Author(s): Will E. Hinckley, Judy A. Brusslan
Software Mentions: 6
Published: almost 4 years ago

10.7150/thno.58433

Single-cell transcriptomic profiling provides insights into the toxic effects of Zearalenone exposure on primordial follicle assembly
Cited by: 20
Author(s): Yu Tian, Mingyu Zhang, Ai-Hong Zhao, Li Kong, Junjie Wang, Wei Shen, Lan Li
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-020-1949-z

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Cited by: 173
Author(s): Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai, Julio Sáez-Rodríguez
Software Mentions: 6
Published: over 4 years ago

10.1038/s41422-020-0374-x

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma
Cited by: 155
Author(s): Yu-Pei Chen, Jianhua Yin, Wenfei Li, Han-Jie Li, Dongping Chen, Cuijuan Zhang, Jiawei Lv, Yaqin Wang, Xiaomin Li, Junyan Li, Panpan Zhang, Ying‐Qin Li, Qing‐Mei He, Xiaojing Yang, Yuan Liu, Ling‐Long Tang, Guan-Qun Zhou, Yan‐Ping Mao, Wei Chen, Ke Xiong, Hongbo Zhang, Shida Zhu, Yong Hou, Ying Sun, Michael Dean, Ido Amit, Kui Wu, Dong-Ming Kuang, Guibo Li, Na Liu
Software Mentions: 6
Published: about 4 years ago

10.1016/j.csbj.2020.06.033

Integration of single-cell multi-omics for gene regulatory network inference
Cited by: 37
Author(s): Xinlin Hu, Yaohua Hu, Fanjie Wu, Ricky Wai Tak Leung, Jing Qin
Software Mentions: 5
Published: almost 5 years ago

10.1038/srep20533

Gene regulatory network inference using fused LASSO on multiple data sets
Cited by: 114
Author(s): Nooshin Omranian, Jeanne M. O. Eloundou-Mbebi, Bernd Mueller‐Roeber, Zoran Nikoloski
Software Mentions: 5
Published: over 8 years ago

10.1186/s12976-019-0103-7

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans
Cited by: 19
Author(s): Juan Castro, Iván Valdés, Laura González-García, Giovanna Danies, Silvia Cañas, Flávia Vischi Winck, Carlos Eduardo Ñústez, Silvia Restrepo, Diego Mauricio Riaño‐Pachón
Software Mentions: 5
Published: over 5 years ago

10.1186/s12920-016-0202-9

Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to psychiatric disorders
Cited by: 5
Author(s): Dongchul Kim, Min-Hee Kang, Ashis Kumer Biswas, Chun Yu Liu, Jean Gao
Software Mentions: 5
Published: about 8 years ago

10.3389/fimmu.2021.670574

Single-Cell Transcriptional Heterogeneity of Neutrophils During Acute Pulmonary Cryptococcus neoformans Infection
Cited by: 14
Author(s): M. Elizabeth Deerhake, Estefany Y. Reyes, Shengjie Xu-Vanpala, Mari L. Shinohara
Software Mentions: 5
Published: over 3 years ago

10.1242/dev.184143

A single cell transcriptome atlas of the developing zebrafish hindbrain
Cited by: 33
Author(s): Monica Tambalo, Richard Mitter, David Wilkinson
Software Mentions: 5
Published: almost 5 years ago

10.1093/jxb/eraa108

Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditions
Cited by: 16
Author(s): Tai‐Hsi Wu, Shalini Krishnamoorthi, Honzhen Goh, Richalynn Leong, Amy Catherine Sanson, Daisuke Urano
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2021.652623

Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis
Cited by: 2
Author(s): Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Wi Hoon Jung, Sun Kim
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1008156

Transcriptomic basis and evolution of the ant nurse-larval social interactome
Cited by: 14
Author(s): Michael Warner, Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 5
Published: over 5 years ago

10.3389/fcvm.2020.615161

Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic Hearts
Cited by: 21
Author(s): Lingfang Zhuang, Lin Lü, Ruiyan Zhang, Kang Chen, Xiaoxiang Yan
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-020-02210-0

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Cited by: 98
Author(s): Shuai He, Lin He Wang, Yang Liu, Yi Qi Li, Hai Tian Chen, Jing Xu, Peng Wan, Guo Wang Lin, Pan Wei, Bo Li, Xiaojun Xia, Dan Wang, Jin Xin Bei, Xiaoshun He, Zhiyong Guo
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12918-018-0547-0

BTNET : boosted tree based gene regulatory network inference algorithm using time-course measurement data
Cited by: 30
Author(s): Sungjoon Park, Jung Min Kim, Weon Ho Shin, Sung Won Han, Minji Jeon, Hyun Jin Jang, Ik Soon Jang, Jaewoo Kang
Software Mentions: 5
Published: over 6 years ago

10.3390/cells10082143

Single-Cell Transcriptomics Reveals Core Regulatory Programs That Determine the Heterogeneity of Circulating and Tissue-Resident Memory CD8+ T Cells
Cited by: 12
Author(s): Yao Chen, Jian Shen, Moujtaba Y. Kasmani, Paytsar Topchyan, Weiguo Cui
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0251666

PEPN-GRN: A Petri net-based approach for the inference of gene regulatory networks from noisy gene expression data
Cited by: 4
Author(s): Deepika Vatsa, Sumeet Agarwal
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-019-2749-x

Efficient proximal gradient algorithm for inference of differential gene networks
Cited by: 3
Author(s): Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D’Urso, Xiaodong Cai
Software Mentions: 5
Published: over 5 years ago

10.1186/s12870-018-1329-y

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
Cited by: 39
Author(s): Ji Huang, Jue-Fei Zheng, Hui Yuan, Karen M. McGinnis
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-96837-z

Partitioning of gene expression among zebrafish photoreceptor subtypes
Cited by: 20
Author(s): Yohsuke Ogawa, Joseph C. Corbo
Software Mentions: 4
Published: about 3 years ago

10.3389/fimmu.2021.739605

Prednisone Reprograms the Transcriptional Immune Cell Landscape in CNS Autoimmune Disease
Cited by: 3
Author(s): Lin He, Yuehan Gao, Lihui Xie, Rong Wang, Runping Duan, Zhaohuai Li, Binyao Chen, Lei Zhu, Xianggui Wang, Wenru Su
Software Mentions: 4
Published: about 3 years ago

10.1007/s13238-019-0648-6

Core transcriptional signatures of phase change in the migratory locust
Cited by: 26
Author(s): Pengcheng Yang, Hou Li, Xianhui Wang, Le Kang
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.6694

Integrated analysis reveals five potential ceRNA biomarkers in human lung adenocarcinoma
Cited by: 14
Author(s): Yu Liu, Deyao Xie, Zuhua He, Liangcheng Zheng
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0110134

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer
Cited by: 20
Author(s): Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Software Mentions: 4
Published: almost 10 years ago

10.3390/plants10020364

A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants
Cited by: 5
Author(s): Rachel M. McCoy, Russell Julian, Shoban R V Kumar, Rajeev Ranjan, Kranthi Varala, Ying Liu
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.14286

Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets
Cited by: 23
Author(s): Wen‐Xing Li, Kan He, Ling Tang, Shao‐Xing Dai, Gong‐Hua Li, Wen Lv, Yicheng Guo, Sanqi An, Guoying Wu, Dahai Liu, Jing‐Fei Huang
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pcbi.1003361

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks
Cited by: 33
Author(s): Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano
Software Mentions: 4
Published: almost 11 years ago

10.1038/srep20518

Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data
Cited by: 27
Author(s): Marilena M. Bourdakou, Emmanouil Athanasiadis, George M. Spyrou
Software Mentions: 4
Published: over 8 years ago

10.1172/jci.insight.141024

Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration
Cited by: 34
Author(s): Tianyi Chen, Seh–Hoon Oh, Simon Gregory, Xiling Shen, Anna Mae Diehl
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.6691

Leaf shape in Populus tremula is a complex, omnigenic trait
Cited by: 17
Author(s): Niklas Mähler, Bastian Schiffthaler, Kathryn M. Robinson, Barbara K Terebieniec, Matej Vučak, Chanaka Mannapperuma, Mark E.S. Bailey, Stefan Jansson, Torgeir R. Hvidsten, Nathaniel R. Street
Software Mentions: 4
Published: almost 4 years ago

10.1093/gigascience/gix078

fastBMA: scalable network inference and transitive reduction
Cited by: 6
Author(s): Ling‐Hong Hung, Kaiyuan Shi, Migao Wu, William Chad Young, Adrian E. Raftery, Ka Yee Yeung
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.67436

Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenesis
Cited by: 48
Author(s): Arantxa Cebrián-Silla, Marcos Assis Nascimento, Stephanie Redmond, Benjamin Mansky, David Wu, Kirsten Obernier, Ricardo Romero Rodriguez, Susana González-Granero, José Manuel García‐Verdugo, Daniel A. Lim, Arturo Álvarez-Buylla
Software Mentions: 4
Published: about 3 years ago

10.1186/s12918-017-0440-2

Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size
Cited by: 14
Author(s): Wenbin Guo, Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Ping Lin, Robbie Waugh, John W. Brown, Runxuan Zhang
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.00729-19

Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
Cited by: 7
Author(s): Ryan McClure, Ashwini Sunkavalli, Phillip M. Balzano, Paola Massi, Christine Cho, William M. Nauseef, Michael A. Apicella, Caroline A. Genco
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-17143-1

Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
Cited by: 16
Author(s): Jigar Desai, Ryan C. Sartor, Lovely Mae F Lawas, S. V. Krishna Jagadish, Colleen J. Doherty
Software Mentions: 4
Published: almost 7 years ago

10.15252/embj.2019104159

Deciphering the regulatory landscape of fetal and adult γδ T‐cell development at single‐cell resolution
Cited by: 38
Author(s): Sagar, Maria Pokrovskii, Josip Stefan Herman, Shruti Naik, Elisabeth Sock, Patrice Zeis, Ute Lausch, Michael Wegner, Yakup Tanriver, Dan R. Littman, Dominic Grün
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-018-2217-z

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
Cited by: 175
Author(s): Shuonan Chen, Jessica C. Mar
Software Mentions: 4
Published: over 6 years ago

10.3390/biomedicines9010034

Shared Blood Transcriptomic Signatures between Alzheimer’s Disease and Diabetes Mellitus
Cited by: 14
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12936-021-03848-2

MALBoost: a web-based application for gene regulatory network analysis in Plasmodium falciparum
Cited by: 0
Author(s): Roelof van Wyk, Riëtte van Biljon, Lyn-Marié Birkholtz
Software Mentions: 4
Published: about 3 years ago

10.1093/bib/bbw139

Gene co-expression analysis for functional classification and gene–disease predictions
Cited by: 511
Author(s): Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Software Mentions: 3
Published: over 7 years ago

10.1093/bfgp/elx046

Mapping gene regulatory networks from single-cell omics data
Cited by: 165
Author(s): Mark Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.617282

Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms
Cited by: 19
Author(s): Yoonjee Kang, Denis Thieffry, Laura Cantini
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj-cs.363

MKL-GRNI: A parallel multiple kernel learning approach for supervised inference of large-scale gene regulatory networks
Cited by: 4
Author(s): Nisar Ahmad Wani, Khalid Raza
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2018.01770

Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets
Cited by: 45
Author(s): Keiichi Mochida, Satoru Koda, Komaki Inoue, Ryuei Nishii
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12918-017-0419-z

Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization
Cited by: 14
Author(s): Saskia Trescher, Jannes Münchmeyer, Ulf Leser
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.3001025

Single-cell transcriptome landscape of ovarian cells during primordial follicle assembly in mice
Cited by: 55
Author(s): Jun-Jie Wang, Wei Ge, Qiu-Yue Zhai, Jing-Cai Liu, Xiaowen Sun, Wen-Xiang Liu, Lan Li, Chuzhao Lei, Paul W. Dyce, Massimo De Felici, Wei Shen
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2021.687652

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling
Cited by: 4
Author(s): Renee Dale, S. Oswald, Amogh Prabhav Jalihal, Mary-Francis LaPorte, Daniel McKay Fletcher, Allen Hubbard, Shin-Han Shiu, Andrew D. L. Nelson, Alexander Bucksch
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1007241

Unified feature association networks through integration of transcriptomic and proteomic data
Cited by: 6
Author(s): Ryan McClure, Jason P. Wendler, Joshua N. Adkins, Jesica Swanstrom, Ralph S. Baric, Brooke L. Deatherage Kaiser, Kristie Oxford, Katrina M. Waters, Jason McDermott
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.00535

Inferring Interaction Networks From Multi-Omics Data
Cited by: 95
Author(s): Johann S. Hawe, Fabian J. Theis, Matthias Heinig
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-07003-0

Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity
Cited by: 28
Author(s): Maria Lytrivi, Kassem Ghaddar, Miguel Lopes, Victoria Rosengren, Anthony Piron, Xiaoyan Yi, Henrik J. Johansson, Janne Lehtiö, Mariana Igoillo-Esteve, Daniel Andrade Da Cunha, Lorella Marselli, Piero Marchetti, Henrik Ortsäter, Décio L. Eizirik, Miriam Cnop
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-021-07940-4

Gene co-expression network analysis in zebrafish reveals chemical class specific modules
Cited by: 6
Author(s): Prarthana Shankar, Ryan McClure, Katrina M. Waters, Robyn L Tanguay
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1004103

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks
Cited by: 23
Author(s): Saheed Imam, Daniel R. Noguera, Timothy J. Donohue
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pcbi.1008379

Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples
Cited by: 12
Author(s): Xiaoqiang Sun, Ji Zhang, Qing Nie
Software Mentions: 3
Published: over 3 years ago

10.1186/s12918-018-0637-z

Systems biology analysis reveals new insights into invasive lung cancer
Cited by: 2
Author(s): Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang
Software Mentions: 3
Published: almost 6 years ago

10.1534/g3.120.401477

Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana
Cited by: 5
Author(s): Margi Hartanto, Ronny V.L. Joosen, L. Basten Snoek, Leo A.J. Willems, Mark G. Sterken, Dick de Ridder, Henk W. M. Hilhorst, Wilco Ligterink, Harm Nijveen
Software Mentions: 3
Published: almost 4 years ago

10.1093/jmcb/mjy089

Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum
Cited by: 34
Author(s): Jian Peng, Ai-Li Sheng, Qi Xiao, Libing Shen, Xiang-Chun Ju, Min Zhang, Siting He, Chao Wu, Zhen-Ge Luo
Software Mentions: 3
Published: over 5 years ago

10.1111/acel.13428

Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction
Cited by: 13
Author(s): Tomobumi Mishina, Namine Tabata, Tetsutaro Hayashi, Mika Yoshimura, Mana Umeda, Midori Mori, Yayoi Ikawa, Hiroshi Hamada, Itoshi Nikaido, Tomoya S. Kitajima
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1005703

Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
Cited by: 32
Author(s): Lingfei Wang, Tom Michoel
Software Mentions: 3
Published: about 7 years ago

10.1038/s12276-020-00528-0

Single-cell network biology for resolving cellular heterogeneity in human diseases
Cited by: 66
Author(s): Junha Cha, Insuk Lee
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-019-2695-7

VIGLA-M: visual gene expression data analytics
Cited by: 8
Author(s): Ismael Navas‐Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybiński, Rocío Lavado, Miguel‐Ángel Berciano‐Guerrero, José F. Aldana‐Montes
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-019-3042-8

BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus
Cited by: 5
Author(s): Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus, Isobel Claire Gormley
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-15-336

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection
Cited by: 34
Author(s): Zhi Ping Liu, Hulin Wu, Jian Zhu, Hongyu Miao
Software Mentions: 2
Published: about 10 years ago

10.1186/s12859-016-0913-0

Netter: re-ranking gene network inference predictions using structural network properties
Cited by: 8
Author(s): Joeri Ruyssinck, Piet Demeester, Tom Dhaene, Yvan Saeys
Software Mentions: 2
Published: over 8 years ago

10.1186/s12885-015-1884-7

Network analysis of an in vitro model of androgen-resistance in prostate cancer
Cited by: 2
Author(s): Sujitra Detchokul, Aparna Elangovan, Edmund J. Crampin, Melissa J. Davis, Albert G Frauman
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-020-07079-8

Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data
Cited by: 1
Author(s): Ming Shi, Sheng Tan, Xueping Xie, Ao Li, Wulin Yang, Tao Zhu, Hongqiang Wang
Software Mentions: 2
Published: almost 4 years ago

Projects: bioconductor: GENIE3

Papers Mentioning GENIE3 172