10.3389/fimmu.2021.716075

Transcriptome Analysis of Peripheral Blood Mononuclear Cells Reveals Distinct Immune Response in Asymptomatic and Re-Detectable Positive COVID-19 Patients
Cited by: 10
Author(s): Jiaqi Zhang, Dan Lin, Kui Li, Xiangming Ding, Lin Li, Yuntao Liu, Dongdong Liu, Jing Lin, Xiangyun Teng, Yizhe Li, Ming Liu, Jian Shen, Xiaodan Wang, He Dan, Yawei Shi, Dawei Wang, Jianhua Xu
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.10490

The ecomorphology of the shell of extant turtles and its applications for fossil turtles
Cited by: 7
Author(s): Laura Dziomber, Walter G. Joyce, Christian Foth
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01290

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes
Cited by: 23
Author(s): Christina Böck, Michaela M. Salcher, Manfred Jensen, Ram Vinay Pandey, Jens Boenigk
Software Mentions: 4
Published: about 8 years ago

10.1186/s13024-020-00394-4

Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice
Cited by: 40
Author(s): Nicholas F. Fitz, Cody M. Wolfe, Brittany E. Playso, Richard J. Biedrzycki, Yi Lü, Kyong Nyon Nam, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.5822

Meta-analysis of microarray datasets identify several chromosome segregation-related cancer/testis genes potentially contributing to anaplastic thyroid carcinoma
Cited by: 10
Author(s): Lan Mu, Yulu Qiu, Tong Jin, Zhou Yin, Zhiyuan Mao, Yongjie Zhang
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-020-6467-6

Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population
Cited by: 8
Author(s): Enoch Ng’oma, Patricka A. Williams-Simon, Aniqa Rahman, King Eg
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00439

Whole-Exome Sequencing Identifies Somatic Mutations Associated With Mortality in Metastatic Clear Cell Kidney Carcinoma
Cited by: 17
Author(s): Alejandro Mendoza-Álvarez, Beatriz Guillén‐Guío, Adrian Baez‐Ortega, Carolina Hernandez-Perez, Sita Lakhwani-Lakhwani, María-del-Carmen Maeso, José M. Lorenzo-Salazar, Manuel Morales, Carlos Flores
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-021-04110-x

Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis
Cited by: 0
Author(s): Xueyuan Cao, Stan Pounds
Software Mentions: 4
Published: over 5 years ago

10.1186/s13058-020-01295-6

Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration
Cited by: 24
Author(s): Thilde Terkelsen, Francesco Russo, Pavel Gromov, Vilde Drageset Haakensen, Søren Brunak, Irina Gromova, Anders Krogh, Elena Papaleo
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.8421

Glycerophosphodiester phosphodiesterase 1 (GDE1) acts as a potential tumor suppressor and is a novel therapeutic target for non-mucin-producing colon adenocarcinoma
Cited by: 2
Author(s): Shen Qiu, Chen Lü, Hua Yang, Ming-Xia Ge, Wangxiao Xia, Qing‐Peng Kong, Gong‐Hua Li, Yanhong Gu
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.01214

Weighted Gene Co-Expression Network Analysis Identifies Critical Genes in the Development of Heart Failure After Acute Myocardial Infarction
Cited by: 59
Author(s): Xiaowei Niu, Jingjing Zhang, Lanlan Zhang, Yufei Hou, Shuangshuang Pu, Ai-Ai Chu, Ming Bai, Zheng Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.00253

Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme
Cited by: 11
Author(s): Jian Yang, Long Wang, Zhou Xu, Liquan Wu, Baohui Liu, Junmin Wang, Daofeng Tian, Xiaoxing Xiong, Qianxue Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.680413

Identification of a Prognostic Signature for Ovarian Cancer Based on the Microenvironment Genes
Cited by: 9
Author(s): Xiao Huo, Hengzi Sun, Shuangwu Liu, Bing Liang, Huimin Bai, Shuzhen Wang, Shuhong Li
Software Mentions: 4
Published: over 5 years ago

10.1002/brb3.660

Neural evidence for phonologically based language production deficits in older adults: An fMRI investigation of age-related differences in picture-word interference
Cited by: 19
Author(s): Avery A. Rizio, Karlee J. Moyer, Michèle T. Diaz
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2021.695699

Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone
Cited by: 3
Author(s): Shaozhen Liu, Qiong Yang, Yue Chen, Qing Liu, Weiwei Wang, Jing Song, Yao Zheng, Wenzhong Liu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-017-1571-6

Avoiding the pitfalls of gene set enrichment analysis with SetRank
Cited by: 87
Author(s): Cédric Simillion, Robin Liechti, Heidi E. L. Lischer, Vassilios Ioannidis, Rémy Bruggmann
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.102540

Screening, identification and validation of CCND1 and PECAM1/CD31 for predicting prognosis in renal cell carcinoma patients
Cited by: 23
Author(s): Jianfeng Yang, Shen-Nan Shi, Wenhao Xu, Yunhua Qiu, Jinzhou Zheng, Kyeong-Nam Yu, Xianrang Song, Feng Li, Yu Wang, Rui Wang, Yuanyuan Qu, Hai-Liang Zhang, Xiqiu Zhou
Software Mentions: 4
Published: over 6 years ago

10.3390/vaccines5040037

Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward
Cited by: 8
Author(s): David J. Lemler, Hayden Brochu, Fang Yang, Erin Harrell, Xinxia Peng
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-020-6613-1

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Cited by: 11
Author(s): Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qing Chu, Xiquan Zhang, Xuemei Lu
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.735103

Editorial: Computational Tools in Inferring Cancer Tissue-of-Origin and Molecular Classification Towards Personalized Cancer Therapy, Volume II
Cited by: 0
Author(s): Ling Kui, Wenzhe Mao, Aasim Majeed, Jian Chen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-017-1881-8

K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
Cited by: 14
Author(s): Chang Sik Kim, Martyn Winn, Vipin Sachdeva, Kirk E. Jordan
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2021.630215

Comparing Statistical Tests for Differential Network Analysis of Gene Modules
Cited by: 2
Author(s): Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris
Software Mentions: 4
Published: about 5 years ago

10.1038/s41380-020-0767-8

AP-1 controls the p11-dependent antidepressant response
Cited by: 25
Author(s): Revathy U. Chottekalapanda, Salina Kalik, Jodi Gresack, Alyssa Ayala, Melanie Gao, Wei Wang, Sarah J. Meller, Ammar Aly, Anne Schaefer, Paul Greengard
Software Mentions: 4
Published: about 6 years ago

10.3389/fendo.2021.705154

Weighted Gene Co-Expression Network Analysis Identifies ANGPTL4 as a Key Regulator in Diabetic Cardiomyopathy via FAK/SIRT3/ROS Pathway in Cardiomyocyte
Cited by: 8
Author(s): Lei Dai, Yang Xie, Wenjun Zhang, Xiaodan Zhong, Mengwen Wang, Hongchen Jiang, Zhen He, Xiaolei Liu, Hesong Zeng, Hongjie Wang
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.104134

The value of a metabolic reprogramming-related gene signature for pancreatic adenocarcinoma prognosis prediction
Cited by: 12
Author(s): Zhen Tan, Yubin Lei, Jin Xu, Si Shi, Jie Hua, Bo Zhang, Qingcai Meng, Jiang Liu, Yiyin Zhang, Miaoyan Wei, Xianjun Yu, Chen Liang
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20156108

Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers
Cited by: 72
Author(s): Tiziano Pramparo, Michael Lombardo, Kathleen Campbell, Cynthia Carter Barnes, Steven Marinero, Stephanie Solso, Julia Young, Maisi Mayo, Anders M. Dale, Clelia Ahrens‐Barbeau, Sarah Murray, Linda Lopez, Nathan E. Lewis, Karen Pierce, Eric Courchesne
Software Mentions: 4
Published: over 10 years ago

10.1042/BSR20203812

An autophagy-related prognostic signature associated with immune microenvironment features of uveal melanoma
Cited by: 8
Author(s): Zhuotao Zheng, Lingyue Zhang, Zewei Tu, Yan Deng, Xingtian Yin
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 9 years ago

10.1186/s12935-020-01632-x

Targeting Lymphotoxin Beta and Paired Box 5: a potential therapeutic strategy for soft tissue sarcoma metastasis
Cited by: 0
Author(s): Runzhi Huang, Zhiwei Zeng, Penghui Yan, Huabin Yin, Xiaolong Zhu, Peng Hu, Juanwei Zhuang, Jiaju Li, Siqi Li, Dianwen Song, Tong Meng, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13024-021-00462-3

A proteomic network approach resolves stage-specific molecular phenotypes in chronic traumatic encephalopathy
Cited by: 4
Author(s): Laura Gutierrez-Quiceno, Eric B. Dammer, Ashlyn G. Johnson, James Webster, Rhythm Shah, Duc M. Duong, Luming Yin, Nicholas T. Seyfried, Victor E. Alvarez, Thor D. Stein, Ann C. McKee, Chadwick M. Hales
Software Mentions: 4
Published: about 5 years ago

10.1186/s13024-018-0254-8

Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimer’s disease
Cited by: 227
Author(s): Srikant Rangaraju, Eric B. Dammer, Syed Ali Raza, Priyadharshini Rathakrishnan, Hailian Xiao, Tianwen Gao, Duc M. Duong, Michael W. Pennington, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.46981

Transcriptional landscape of myogenesis from human pluripotent stem cells reveals a key role of TWIST1 in maintenance of skeletal muscle progenitors
Cited by: 27
Author(s): In Young Choi, Hotae Lim, Hyeon Jin Cho, Yohan Oh, Bin Kuan Chou, Hao Bai, Linzhao Cheng, Yong Jun Kim, Sang‐Hwan Hyun, Hyesoo Kim, Joo Heon Shin, Gabsang Lee
Software Mentions: 4
Published: over 6 years ago

10.1186/1868-7083-4-20

Genome-scale case-control analysis of CD4+ T-cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease
Cited by: 41
Author(s): Justine A. Ellis, Jane Munro, Raul A Chavez, Lavinia Gordon, Jihoon E. Joo, Jonathan Akikusa, Roger C. Allen, Anne‐Louise Ponsonby, Jeffrey M Craig, Richard Saffery
Software Mentions: 4
Published: almost 14 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-020-06909-z

Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle
Cited by: 23
Author(s): Ze Yan, Hanyu Huang, Ellen Freebern, D. R. dos Santos, Dongmei Dai, Jingfang Si, Chengbin Ma, Jie Cao, Gang Guo, George E. Liu, Li Ma, Lingzhao Fang, Yi Zhang
Software Mentions: 4
Published: about 6 years ago

10.3389/fcell.2020.558961

Identification of Prognostic Model and Biomarkers for Cancer Stem Cell Characteristics in Glioblastoma by Network Analysis of Multi-Omics Data and Stemness Indices
Cited by: 27
Author(s): Jianyang Du, Xiuwei Yan, Shan Mi, Yuan Li, Hang Ji, Kezuo Hou, Shuai Ma, Yixu Ba, Peng Zhou, Lei Chen, Rui Xie, Shaoshan Hu
Software Mentions: 4
Published: almost 6 years ago

10.3389/fcell.2021.710558

Construction and Validation of a Novel Immunosignature for Overall Survival in Uveal Melanoma
Cited by: 3
Author(s): Chufeng Gu, Xiaohong Gu, Yujie Wang, Zhixian Yao, Chuandi Zhou
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2021.661296

Combined Analysis of Volatile Terpenoid Metabolism and Transcriptome Reveals Transcription Factors Related to Terpene Synthase in Two Cultivars of Dendrobium officinale Flowers
Cited by: 20
Author(s): Ninghong Li, Yan Dong, Min Lv, Qian Li, Xinwei Sun, Liu Lin, Yongping Cai, Honghong Fan
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2019.07.091

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes
Cited by: 204
Author(s): Myles Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John, David S. Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michèle Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 4
Published: about 7 years ago

10.1155/2020/5974350

A Prognostic Model Based on Six Metabolism-Related Genes in Colorectal Cancer
Cited by: 14
Author(s): Yuanlin Sun, Yang Zhang, Yuchen Guo, Zihao Yang, You Xu
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/4612158

<i>CCNB2</i>, <i>TOP2A</i>, and <i>ASPM</i> Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis
Cited by: 9
Author(s): Yuping Zeng, He He, Yu Zhang, Xia Wang, Yang Lin-de, Zhenmei An
Software Mentions: 4
Published: about 6 years ago

10.1038/onc.2016.242

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network
Cited by: 16
Author(s): Yan Zhou, Oliver Frings, Rui M. Branca, Jorrit Boekel, Carlos le Sage, Erik Fredlund, Reuven Agami, Lukas M. Orre
Software Mentions: 4
Published: about 10 years ago

10.1016/j.celrep.2017.08.010

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
Cited by: 92
Author(s): Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalvès, Clara Alsinet, Martín Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michaël Schubert, Stacey Price, James C. Wright, Lu Yu, Meizhu Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrão, Alvis Brāzma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Sáez-Rodríguez, Ultan McDermott, Jyoti S. Choudhary
Software Mentions: 4
Published: about 9 years ago

10.3390/cells8121566

Stromal Cell Signature Associated with Response to Neoadjuvant Chemotherapy in Locally Advanced Breast Cancer
Cited by: 20
Author(s): Maria Lúcia Hirata Katayama, René Aloísio da Costa Vieira, Victor Piana de Andrade, Rosimeire Aparecida Roela, Luciana Lima, Lígia Maria Kerr, Adriano Polpo de Campos, Carlos Alberto Pereira, Pedro Adolpho de Menezes Pacheco Serio, Giselly Encinas, Simone Maistro, Matheus de Almeida Leite Petroni, Maria Mitzi Brentani, Maria Aparecida Azevedo Koike Folgueira
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.203030

Downregulation of USP18 reduces tumor-infiltrating activated dendritic cells in extranodal diffuse large B cell lymphoma patients
Cited by: 5
Author(s): Chong Zhao, Runzhi Huang, Zhiwei Zeng, Siqi Yang, Wei Lü, Jiali Liu, Yanyu Wei, Hong Guo, Yanjie Zhang, Penghui Yan, Zongqiang Huang, Jun Shi
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00070-17

Abiotic Stresses Shift Belowground <i>Populus</i> -Associated Bacteria Toward a Core Stress Microbiome
Cited by: 75
Author(s): Collin M. Timm, Kelsey Carter, Alyssa A. Carrell, Se‐Ran Jun, Sara Jawdy, Jessica M. Vélez, Lee E. Gunter, Zamin K. Yang, Intawat Nookaew, Nancy L. Engle, Tse-Yuan S. Lu, Christopher W. Schadt, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Dale A. Pelletier, David J. Weston
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-08796-z

Surface PD-L1, E-cadherin, CD24, and VEGFR2 as markers of epithelial cancer stem cells associated with rapid tumorigenesis
Cited by: 42
Author(s): Goodwin G. Jinesh, Ganiraju C. Manyam, Chinedu O. Mmeje, Keith A. Baggerly, Ashish M. Kamat
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41421-021-00271-4

Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response
Cited by: 90
Author(s): Yu Wang, Yongfeng Liang, Haiyan Xu, Xiao Zhang, Tiebo Mao, Jiujie Cui, Jiyong Yao, Yongchao Wang, Feng Jiao, Xiuying Xiao, Jiong Hu, Qing Xia, Xiaofei Zhang, Xujun Wang, Yongwei Sun, Deliang Fu, Lei Shen, Ximing Xu, Jing Xue, Liwei Wang
Software Mentions: 4
Published: about 5 years ago

10.1007/s00018-017-2695-6

Downregulation of p53 drives autophagy during human trophoblast differentiation
Cited by: 23
Author(s): Martin Gauster, Sabine Maninger, Monika Siwetz, Alexander Deutsch, Amin El‐Heliebi, Dagmar Kolb-Lenz, Ursula Hiden, Gernot Desoyé, Florian Herse, Andreas Prokesch
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-015-1816-6

Uncovering co-expression gene network modules regulating fruit acidity in diverse apples
Cited by: 54
Author(s): Yang Bai, Laura Dougherty, Lailiang Cheng, Gan-Yuan Zhong, Kenong Xu
Software Mentions: 4
Published: about 11 years ago

10.1155/2020/3641231

Immune-Related Four-lncRNA Signature for Patients with Cervical Cancer
Cited by: 19
Author(s): Jianfeng Zheng, Benben Cao, Xia Zhang, Zhenbin Niu, Jinyi Tong
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: about 9 years ago

10.1111/cpr.12861

RNA processing genes characterize RNA splicing and further stratify colorectal cancer
Cited by: 4
Author(s): Xiaofan Lu, Yu Jie Zhou, Jialin Meng, Liyun Jiang, Jun Gao, Changhong Yu, Hangyu Yan, Yang Wang, Bing Zhang, Xiaobo Li, Fangrong Yan
Software Mentions: 4
Published: about 6 years ago

10.3390/cells10071821

Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma
Cited by: 8
Author(s): Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Florian Weiß, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar M. Chromik, M. Bahra, Fritz Klein, Christian Pilarsky, Robert Grützmann, Markus M. Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle
Software Mentions: 4
Published: about 5 years ago

10.1002/cbf.3491

Identification and functional analysis of long non‐coding RNAs in the synovial membrane of osteoarthritis patients
Cited by: 7
Author(s): Xiaolong Shui, Qipeng Xie, Shaomin Chen, Chengwei Zhou, Jianzhong Kong, Yi Wang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-04300-9

Altered miRNA expression network in locus coeruleus of depressed suicide subjects
Cited by: 59
Author(s): Bhaskar Roy, Qingzhong Wang, M. Palkóvits, Gábor Faludi, Yogesh K. Dwivedi
Software Mentions: 4
Published: about 9 years ago

10.1093/bioinformatics/btz275

NGSEP3: accurate variant calling across species and sequencing protocols
Cited by: 44
Author(s): Daniel Tello, Juanita Gil, Cristian D Loaiza, John J. Riascos, Nicolás Cardozo, Jorge Duitama
Software Mentions: 4
Published: over 7 years ago

10.1186/s12931-020-01368-2

IRF4 and STAT3 activities are associated with the imbalanced differentiation of T-cells in responses to inhalable particulate matters
Cited by: 2
Author(s): Jinzhun Wu, Dongyu Ge, Taoling Zhong, Zuojia Chen, Ying Zhou, Lingyun Hou, Xinhua Lin, Jiaxu Hong, Kuai Liu, Hui Qi, Chaoying Wang, Yulin Zhou, Cheng Li, Chuan Wu, Shi Wu, Zuguo Liu, Qiyuan Li
Software Mentions: 4
Published: about 6 years ago

10.1038/srep09027

Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma
Cited by: 28
Author(s): Ali Rihani, Alan Van Goethem, Maté Ongenaert, Sara De Brouwer, Pieter-Jan Volders, Saurabh Agarwal, Katleen De Preter, Pieter Mestdagh, Jason M. Shohet, Franki Speleman, Jo Vandesompele, Tom Van Maerken
Software Mentions: 4
Published: over 11 years ago

10.1007/s00248-017-1108-6

Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent
Cited by: 44
Author(s): Thiago R. Schlemper, Johannes A. van Veen, Eiko E. Kuramae
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12931-016-0496-3

Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples
Cited by: 5
Author(s): Andre Koper, Leo Zeef, Leena Dennis Joseph, Keith M. Kerr, John R. Gosney, Mark A. Lindsay, Richard Booton
Software Mentions: 4
Published: over 9 years ago

10.1038/srep12615

Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
Cited by: 27
Author(s): Antonio Fabio Di Narzo, Alexey Kozlenkov, Yongchao Ge, Bin Zhang, Leo Sanelli, Zacnicte May, Yanqing Li, Karim Fouad, Christopher P. Cardozo, Eugene V. Koonin, David J. Bennett, Stella Dracheva
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0122339

The Active Tamoxifen Metabolite Endoxifen (4OHNDtam) Strongly Down-Regulates Cytokeratin 6 (CK6) in MCF-7 Breast Cancer Cells
Cited by: 4
Author(s): Thomas Helland, Jennifer Gjerde, Simon N. Dankel, Ingvild S. Fenne, Linn Skartveit, Andreas Drangevåg, Olivera Bozickovic, Marianne Hauglid Flågeng, Håvard Søiland, Gunnar Mellgren, Ernst A. Lien
Software Mentions: 4
Published: over 11 years ago

10.1155/2013/187509

Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data
Cited by: 8
Author(s): Ai-Di Zhang, Shao‐Xing Dai, Jing‐Fei Huang
Software Mentions: 4
Published: over 13 years ago

10.1002/reg2.48

Genome‐wide analysis reveals conserved transcriptional responses downstream of resting potential change in<i>Xenopus</i>embryos, axolotl regeneration, and human mesenchymal cell differentiation
Cited by: 51
Author(s): Vaibhav P. Pai, Christopher J. Martyniuk, Karen Echeverri, Sarah Sundelacruz, David L. Kaplan, Michael Levin
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.ppat.1009789

Pulmonary mesenchymal stem cells are engaged in distinct steps of host response to respiratory syncytial virus infection
Cited by: 5
Author(s): Melanie Brügger, Thomas Démoulins, G. Tuba Barut, Béatrice Zumkehr, Blandina I. Oliveira Esteves, Kemal Mehinagic, Quentin Haas, Aline Schögler, Marie‐Anne Rameix‐Welti, Jean François Eléouët, Ueli Moehrlen, Thomas Marti, Ralph A. Schmid, Artur Summerfield, Horst Posthaus, Nicolas Ruggli, Sean Hall, Marco P. Alves
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-021-07989-1

Global identification of long non-coding RNAs involved in the induction of spinach flowering
Cited by: 11
Author(s): Fatemeh Ghorbani, Reza Abolghasemi, Maryam Haghighi, Nematollah Etemadi, Shui Wang, Marzieh Karimi, Aboozar Soorni
Software Mentions: 4
Published: almost 5 years ago

10.1155/2016/4241293

Differential Regulatory Analysis Based on Coexpression Network in Cancer Research
Cited by: 12
Author(s): Junyi Li, Yixue Li, Yuanyuan Li
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2020.00574

Decoding Gene Networks Modules That Explain the Recovery of Hymenoglossum cruentum Cav. After Extreme Desiccation
Cited by: 6
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, Patrício Manque, Luisa Bascuñán‐Godoy, León A. Bravo
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2021.630243

Identification of Key Gene Networks Associated With Cell Wall Components Leading to Flesh Firmness in Watermelon
Cited by: 11
Author(s): Muhammad Anees, Lei Gao, Muhammad Umer, Pingli Yuan, Huiling Zhu, Xingrong Lu, Nan He, Chengsheng Gong, Mohamed Omar Kaseb, Shengjie Zhao, Wenge Liu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12862-019-1420-5

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore
Cited by: 6
Author(s): Rita Gomes Rocha, Vanessa Magalhães, José V. López‐Bao, W. van der Loo, Luís Llaneza, Francisco Álvares, Pedro J. Esteves, Raquel Godinho
Software Mentions: 4
Published: over 7 years ago

10.1186/s12918-018-0542-5

Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica
Cited by: 51
Author(s): Pramod Kumar Mishra, Na-Rae Lee, Meiyappan Lakshmanan, Minsuk Kim, Byung‐Gee Kim, Dong-Yup Lee
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2019.01098

Identification of Candidate Adaxial–Abaxial-Related Genes Regulating Petal Expansion During Flower Opening in Rosa chinensis “Old Blush”
Cited by: 10
Author(s): Yu Han, Yong Xue, Jiayao Yu, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: over 6 years ago

10.3390/life11050367

Activation of Blood Vessel Development in Endometrial Stromal Cells In Vitro Cocultured with Human Peri-Implantation Embryos Revealed by Single-Cell RNA-Seq
Cited by: 4
Author(s): Bo Lv, Xiaoyu Xu, Xunyi Zhang, Lingbin Qi, He We, Lu Wang, Xian Chen, Luying Peng, Jinfeng Xue, Yao Ji, Zhigang Xue
Software Mentions: 4
Published: over 5 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: over 5 years ago

10.1186/1752-0509-6-65

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases
Cited by: 49
Author(s): Yu Liu, Mehmet Koyutürk, Jill S. Barnholtz‐Sloan, Mark R. Chance
Software Mentions: 4
Published: about 14 years ago

10.1186/s40478-021-01232-4

Metabolic and transcriptomic profiles of glioblastoma invasion revealed by comparisons between patients and corresponding orthotopic xenografts in mice
Cited by: 5
Author(s): Cristina Cudalbu, Pierre Bady, Marta Lai, Lijing Xin, Olga Gusyatiner, Marie‐France Hamou, Mario Lepore, Jean‐Philippe Brouland, Roy Thomas Daniel, Andreas F. Hottinger, Monika E. Hegi
Software Mentions: 4
Published: about 5 years ago

10.3390/jcm10112259

Learning from Embryogenesis—A Comparative Expression Analysis in Melanoblast Differentiation and Tumorigenesis Reveals miRNAs Driving Melanoma Development
Cited by: 4
Author(s): Lisa Linck-Paulus, Lisa Lämmerhirt, Daniel Völler, Katharina Meyer, Julia C. Engelmann, Rainer Spang, Norbert Eichner, Gunter Meister, Silke Kuphal, Anja‐Katrin Bosserhoff
Software Mentions: 4
Published: about 5 years ago

10.1016/j.crtox.2021.07.003

Reproducibility and robustness of high-throughput S1500+ transcriptomics on primary rat hepatocytes for chemical-induced hepatotoxicity assessment
Cited by: 3
Author(s): Fan Lee, Imran Shah, Yun Ting Soong, Jiangwa Xing, Inn Chuan Ng, Farah Tasnim, Hanry Yu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0056228

canEvolve: A Web Portal for Integrative Oncogenomics
Cited by: 39
Author(s): Mehmet K. Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Li Cheng, Parantu K. Shah
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-021-89364-4

Diversification of the Balloon bushcrickets (Orthoptera, Hexacentrinae, Aerotegmina) in the East African mountains
Cited by: 3
Author(s): Beata Grzywacz, Elżbieta Warchałowska‐Śliwa, Maciej Kociński, Klaus‐Gerhard Heller, Claudia Hemp
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0032453

Astrocyte-Specific Expression Patterns Associated with the PDGF-Induced Glioma Microenvironment
Cited by: 66
Author(s): Amanda Katz, Nduka Amankulor, Kenneth L. Pitter, Karim Y. Helmy, Massimo Squatrito, Eric C. Holland
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0252647

Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica
Cited by: 2
Author(s): Nicholas S. Kron, Lynne A. Fieber
Software Mentions: 4
Published: about 5 years ago

10.1186/s12711-021-00656-9

Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content
Cited by: 7
Author(s): Hao Kang, Di Zhao, Hai Xiang, Jing Li, Guiping Zhao, Hua Li
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-86504-8

Identification and external validation of a prognostic signature associated with DNA repair genes in gastric cancer
Cited by: 5
Author(s): Shimin Chen, Wenbo Liu, Haojun Yu
Software Mentions: 4
Published: over 5 years ago

10.3390/genes10110944

Dissecting the Regulatory Network of Leaf Premature Senescence in Maize (Zea mays L.) Using Transcriptome Analysis of ZmELS5 Mutant
Cited by: 12
Author(s): Mao Chai, Zhanyong Guo, Xia Shi, Yingbo Li, Jian Tang, Zhan‐Hui Zhang
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-019-0286-5

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity
Cited by: 20
Author(s): Pierre Khoueiry, Aoife Ward Gahlawat, Massimo Petretich, Anne-Marie Michon, Daniel F. Simola, Enid Y.N. Lam, Eileen E. M. Furlong, Vladimı́r Beneš, Mark A. Dawson, Rab K. Prinjha, Gerard Drewes, Paola Grandi
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms22116101

Loss of Nnt Increases Expression of Oxidative Phosphorylation Complexes in C57BL/6J Hearts
Cited by: 4
Author(s): Jack Williams, Charlotte Hall, Eirini Meimaridou, Louise A. Metherell
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-74391-4

Analysis of gene expression from systemic lupus erythematosus synovium reveals myeloid cell-driven pathogenesis of lupus arthritis
Cited by: 9
Author(s): Erika L. Hubbard, Michelle D. Catalina, Sarah Heuer, Prathyusha Bachali, Robert Robl, Nicholas S. Geraci, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0036161

Effect of Age on Variability in the Production of Text-Based Global Inferences
Cited by: 9
Author(s): Lynne J. Williams, Joseph Dunlop, Hervé Abdi
Software Mentions: 4
Published: over 14 years ago

10.1038/s41598-020-64623-y

Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome
Cited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21062079

Whole-Genome Uterine Artery Transcriptome Profiling and Alternative Splicing Analysis in Rat Pregnancy
Cited by: 4
Author(s): Kathirvel Gopalakrishnan, Sathish Kumar
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.13814

The bromodomain inhibitor OTX015 (MK-8628) exerts anti-tumor activity in triple-negative breast cancer models as single agent and in combination with everolimus
Cited by: 74
Author(s): Ramiro Vàzquez, María E. Riveiro, Lucile Astorgues‐Xerri, Elodie Odore, Keyvan Rezai, Eugenio Erba, Nicolò Panini, Andrea Rinaldi, Ivo Kwee, Luca Beltrame, Mohamed Békradda, Esteban Cvitkovic, Francesco Bertoni, Roberta Frapolli, Maurizio D’Incalci
Software Mentions: 4
Published: over 9 years ago

10.1186/s13073-019-0638-6

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
Cited by: 628
Author(s): Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncová, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke E. Ijsselsteijn, Thomas P. Brouwer, Douglas B. Johnson, Yaomin Xu, Yu Wang, Melinda E. Sanders, Mónica Valéria Estrada, Paula I. Ericsson-Gonzalez, Pornpimol Charoentong, Justin M. Balko, Noel F.C.C. de Miranda, Zlatko Trajanoski
Software Mentions: 4
Published: about 7 years ago

10.1002/ctm2.364

Clinical and functional significance of a novel ferroptosis‐related prognosis signature in lung adenocarcinoma
Cited by: 9
Author(s): Ziqi Wang, Jie Diao, Xingru Zhao, Zhiwei Xu, Xiaoju Zhang
Software Mentions: 4
Published: over 5 years ago

10.1007/s10339-021-01012-x

Landmarks in wayfinding: a review of the existing literature
Cited by: 33
Author(s): Demet Yeşiltepe, Ruth Dalton, Ayşe Özbil Torun
Software Mentions: 4
Published: over 5 years ago

10.1186/s13073-018-0551-4

Genetic variants associated with Alzheimer’s disease confer different cerebral cortex cell-type population structure
Cited by: 42
Author(s): Zeran Li, Jorge L. Del-Águila, Umber Dube, John Budde, Rita Martinez, Kathleen Black, Qingli Xiao, Nigel J. Cairns, Joseph D. Dougherty, Lee J, John C. Morris, Randall J. Bateman, Celeste M. Karch, Carlos Cruchaga, Oscar Harari
Software Mentions: 4
Published: about 8 years ago

10.1186/s13073-016-0355-3

Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease
Cited by: 191
Author(s): Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen J. Brennand, Gabriele C. DeLuca, John F. Crary, Patrizia Casaccia, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Alison M. Goate, Pavel Katsel, Eric E. Schadt, Vahram Haroutunian, Bin Zhang
Software Mentions: 4
Published: almost 10 years ago