10.1371/journal.pgen.1006294

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts
Cited by: 44
Author(s): Maléne E. Lindholm, Stefania Giacomello, Beata Werne Solnestam, Håkan Fischer, Mikael Huss, Sanela Kjellqvist, Carl Johan Sundberg
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pcbi.1000920

Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers
Cited by: 48
Author(s): Joseph E. Lucas, Hsiu‐Ni Kung, Jen‐Tsan Chi
Software Mentions: 3
Published: about 16 years ago

10.1186/s40164-020-00164-4

Frequent upregulation of G9a promotes RelB-dependent proliferation and survival in multiple myeloma
Cited by: 8
Author(s): Xi Yun Zhang, Deepa Rajagopalan, Tae-Hoon Chung, Lissa Hooi, Tan Boon Toh, Johann Shane Tian, Masturah Bte Mohd Abdul Rashid, Noor Rashidha Bte Meera Sahib, Meijia Gu, Jackwee Lim, Wilson Wang, Wee Joo Chng, Sudhakar Jha, Edward Kai‐Hua Chow
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pmed.1003100

Metabolic risk factors and incident advanced liver disease in non-alcoholic fatty liver disease (NAFLD): A systematic review and meta-analysis of population-based observational studies
Cited by: 177
Author(s): Helen Jarvis, Dawn Craig, Robert Barker, Gemma Spiers, Daniel Stow, Quentin M. Anstee, Barbara Hanratty
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0249593

Identifying geographically differentiated features of Ethopian Nile tilapia (Oreochromis niloticus) morphology with machine learning
Cited by: 3
Author(s): Wilfried Wöber, Manuel Curto, Papius Dias Tibihika, Paul Meulenbroek, Esayas Alemayehu, Lars Mehnen, Harald Meimberg, Peter Sykacek
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1005335

Representing high throughput expression profiles via perturbation barcodes reveals compound targets
Cited by: 22
Author(s): Tracey Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-11-257

Detecting microRNA activity from gene expression data
Cited by: 33
Author(s): Stephen F. Madden, Susan Carpenter, Ian B. Jeffery, Harry Björkbacka, Katherine A. Fitzgerald, Luke A. J. O’Neill, Desmond G. Higgins
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2105-15-162

A multivariate approach to the integration of multi-omics datasets
Cited by: 214
Author(s): Chen Meng, Bernhard Küster, Aedín C. Culhane, Amin Moghaddas Gholami
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pcbi.1007308

Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
Cited by: 14
Author(s): Joel A. Paulson, Marc Martin-Casas, Ali Mesbah
Software Mentions: 3
Published: about 7 years ago

10.1016/j.dib.2017.10.014

Waste management CDM projects barriers NVivo 10® qualitative dataset
Cited by: 5
Author(s): André Luiz Bufoni, Aracéli Cristina de Sousa Ferreira, Luciano Basto Oliveira
Software Mentions: 3
Published: almost 9 years ago

10.3390/nu11020418

Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids
Cited by: 40
Author(s): Nijiati Abulizi, Candice Quin, Kirsty Brown, Yee Kwan Chan, S K Gill, Deanna L. Gibson
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2015.00383

Pathway Analysis: State of the Art
Cited by: 170
Author(s): Miguel Angel García-Campos, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pbio.3001364

The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation
Cited by: 14
Author(s): Cecilia B. Levandowski, Taylor Jones, Margaret Gruca, Sivapriya Ramamoorthy, Robin D. Dowell, Dylan J. Taatjes
Software Mentions: 3
Published: about 5 years ago

10.1016/j.dib.2021.106730

Gaze tracking dataset for comparison of smooth and saccadic eye tracking
Cited by: 2
Author(s): Adam Pantanowitz, Kimoon Kim, Chelsey Chewins, David M. Rubin
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/8836243

Altered Genes and Biological Functions in Response to Severe Burns
Cited by: 2
Author(s): Xinheng Liu, Yong-Xian Rong, Deng-Shing Huang, Zheng Liang, Xiao-Lin Yi, Fengyao Wu, Dandan Zhu, Steven Mo, Wenhai Nong, Hong-Mian Li
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-14-95

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
Cited by: 34
Author(s): Jinkui Cheng, Zhiai Xu, Guomin Ren, Zhihua Liu
Software Mentions: 3
Published: over 13 years ago

10.1186/s12967-021-02845-y

Identification of an immune classification for cervical cancer and integrative analysis of multiomics data
Cited by: 7
Author(s): Xintong Lyu, Guang Li, Qiao Qiao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12967-020-02691-4

Model based on five tumour immune microenvironment-related genes for predicting hepatocellular carcinoma immunotherapy outcomes
Cited by: 24
Author(s): Xinyu Gu, Jun Guan, Jia Xu, Qiuxian Zheng, Chao Chen, Qin Yang, ChunHong Huang, Wang Gang, Haibo Zhou, Zhi Chen, Haihong Zhu
Software Mentions: 3
Published: almost 6 years ago

10.3390/plants10040798

Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron
Cited by: 2
Author(s): Reunreudee Kaewcheenchai, Phanchita Vejchasarn, Kousuke Hanada, Kazumasa Shirai, Chatchawan Jantasuriyarat, Piyada Juntawong
Software Mentions: 3
Published: over 5 years ago

10.1155/2019/8265958

Competing Endogenous RNA and Coexpression Network Analysis for Identification of Potential Biomarkers and Therapeutics in association with Metastasis Risk and Progression of Prostate Cancer
Cited by: 9
Author(s): Xu Pang, Ying Zhao, Jinhua Wang, Wan Li, Qian Xiang, Zhuo Zhang, Shi-Liang Wu, Ailin Liu, Guanhua Du, Yimin Chen
Software Mentions: 3
Published: about 7 years ago

10.3389/fcvm.2021.713983

Pan-Cancer Analysis of Atrial-Fibrillation-Related Innate Immunity Gene ANXA4
Cited by: 6
Author(s): Tao Yan, Shijie Zhu, Yu Shi, Changming Xie, Miao Zhu, Yangyang Zhang, Chunsheng Wang, Changfa Guo
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.17011

Association between PSCA gene polymorphisms and the risk of cancer: an updated meta-analysis and trial sequential analysis
Cited by: 6
Author(s): Zhiqiang Qin, Jingyuan Tang, Xiao Li, Yu Yan, Chuanjie Zhang, Peng Han, Ran Li, Xin Jiang, Chengying Yang, Wei Wang, Min Tang, Wei Zhang
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-020-03921-8

MiBiOmics: an interactive web application for multi-omics data exploration and integration
Cited by: 39
Author(s): Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
Software Mentions: 3
Published: almost 6 years ago

10.1155/2021/9971353

P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma
Cited by: 5
Author(s): Xiangfeng Jin, Haiqing Zhou, Jianfang Song, Hong Cui, Yiren Luo, Haiping Jiang
Software Mentions: 3
Published: over 5 years ago

10.1111/pbi.13132

Genome sequencing and <scp>CRISPR</scp>/Cas9 gene editing of an early flowering Mini‐Citrus (<i>Fortunella hindsii</i>)
Cited by: 76
Author(s): Chenqiao Zhu, Xiongjie Zheng, Yue Huang, Junli Ye, Peng Chen, Chenglei Zhang, Fei Zhao, Zongzhou Xie, Siqi Zhang, Nan Wang, Hang Li, Lun Wang, Xiaomei Tang, Lijun Chai, Qiang Xu, Xiuxin Deng
Software Mentions: 3
Published: over 7 years ago

10.1016/j.csbj.2020.04.011

Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke
Cited by: 21
Author(s): Bjoern Titz, Justyna Szostak, Alain Sewer, Blaine Phillips, Catherine Nury, Thomas Schneider, Sophie Dijon, Oksana Lavrynenko, Ashraf Elamin, Emmanuel Guedj, Ee Tsin Wong, Stefan Lebrun, Grégory Vuillaume, Athanasios Kondylis, Sylvain Gubian, Stéphane Cano, Patrice Leroy, Brian Keppler, Nikolai V. Ivanov, Patrick Vanscheeuwijck, Florian Martin, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12883-020-01709-0

The prevalence of Restless Legs Syndrome/Willis-ekbom disease (RLS/WED) in the third trimester of pregnancy: a systematic review
Cited by: 18
Author(s): Niloofar Darvishi, Alireza Daneshkhah, Behnam Khaledi-Paveh, Asad Vaisi-Raygani, Masoud Mohammadi, Nader Salari, Fateme Darvishi, Alireza Abdi, Rostam Jalali
Software Mentions: 3
Published: over 6 years ago

10.1016/j.isci.2021.102686

PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα
Cited by: 14
Author(s): Evelyn Ramberger, Valeria Sapozhnikova, Elisabeth Kowenz‐Leutz, Karin Zimmermann, Nathalie Nicot, Petr V. Nazarov, Daniel Pérez-Hernández, Ulf Reimer, Philipp Mertins, Gunnar Dittmar, Achim Leutz
Software Mentions: 3
Published: over 5 years ago

10.1186/s13018-021-02329-1

Machine learning analysis of gene expression profile reveals a novel diagnostic signature for osteoporosis
Cited by: 5
Author(s): Xinlei Chen, Guangping Liu, Shuxiang Wang, Haiyang Zhang, Peng Xue
Software Mentions: 3
Published: over 5 years ago

10.2196/jmir.5391

Toward a Mixed-Methods Research Approach to Content Analysis in The Digital Age: The Combined Content-Analysis Model and its Applications to Health Care Twitter Feeds
Cited by: 56
Author(s): Eradah O Hamad, Marie Y. Savundranayagam, Jeffrey D. Holmes, Elizabeth Anne Kinsella, Andrew M. Johnson
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms221810117

LncRNA-CR11538 Decoys Dif/Dorsal to Reduce Antimicrobial Peptide Products for Restoring Drosophila Toll Immunity Homeostasis
Cited by: 9
Author(s): Hongjian Zhou, Shengjie Li, Shanshan Wu, Jin Park, Fei Ma
Software Mentions: 3
Published: about 5 years ago

10.1186/s12974-020-01898-y

Meta-analysis of mouse transcriptomic studies supports a context-dependent astrocyte reaction in acute CNS injury versus neurodegeneration
Cited by: 54
Author(s): Sudeshna Das, Zhaozhi Li, Ayush Noori, Bradley T. Hyman, Alberto Serrano-Pozo
Software Mentions: 3
Published: about 6 years ago

10.3390/ph14040351

Absence of Association between Methylene Blue Reduced Susceptibility and Polymorphisms in 12 Genes Involved in Antimalarial Drug Resistance in African Plasmodium falciparum
Cited by: 2
Author(s): Mathieu Gendrot, Océane Delandre, M Robert, Francis Tsombeng Foguim, B. Nicolas, Rémy Amalvict, Isabelle Fonta, Joël Mosnier, Marylin Madamet, Bruno Pradines
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22158249

Transcriptome-Based WGCNA Analysis Reveals Regulated Metabolite Fluxes between Floral Color and Scent in Narcissus tazetta Flower
Cited by: 20
Author(s): Jingwen Yang, Yujun Ren, Deyu Zhang, Xuewei Chen, Jiazhi Huang, Yun Xu, Cristina Belén Aucapiña Criollo, Yu Zhang, Ying Miao
Software Mentions: 3
Published: about 5 years ago

10.1016/j.csbj.2021.05.055

Genetic mapping of developmental trajectories for complex traits and diseases
Cited by: 1
Author(s): Eldad D. Shulman, Ran Elkon
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.8456

Key genes and co-expression modules involved in asthma pathogenesis
Cited by: 12
Author(s): Yuyi Huang, Hui Liu, Li Zuo, Ailin Tao
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22031167

Glutamine Uptake via SNAT6 and Caveolin Regulates Glutamine–Glutamate Cycle
Cited by: 14
Author(s): Nikhil R. Gandasi, Vasiliki Arapi, Michel‐Edwar Mickael, Prajakta A. Belekar, Louise Granlund, Lakshmi Kothegala, Robert Fredriksson, Sonchita Bagchi
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-10-405

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients
Cited by: 151
Author(s): Christiaan G J Saris, Steve Horvath, Paul W.J. van Vught, Michael A. van Es, Hylke M. Blauw, Tova Fuller, Peter Langfelder, Joseph DeYoung, John H. J. Wokke, Jan H. Veldink, Leonard H van den Berg, Roel A. Ophoff
Software Mentions: 3
Published: about 17 years ago

10.1038/s42003-021-01946-0

Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod
Cited by: 14
Author(s): Petra H. Lenz, Vittoria Roncalli, Matthew Cieslak, Ann M. Tarrant, Ann M. Castelfranco, Daniel K. Hartline
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms20236033

TCGA-TCIA Impact on Radiogenomics Cancer Research: A Systematic Review
Cited by: 33
Author(s): Mario Zanfardino, Katia Pane, Peppino Mirabelli, Marco Salvatore, Monica Franzese
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.4384

Phylogenetic surveys on the newt genus <i>Tylototriton sensu lato</i> (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts
Cited by: 15
Author(s): Bin Wang, Kanto Nishikawa, Masafumi Matsui, Truong Q. Nguyen, Feng Xie, Cheng Li, Janak Raj Khatiwada, Baowei Zhang, Gong Dajie, Yunming Mo, Gang Wei, Xiaohong Chen, Youhui Shen, Daode Yang, Rongchuan Xiong, Jianping Jiang
Software Mentions: 3
Published: over 8 years ago

10.1002/ctm2.138

Cell cycle progression score as a predictive biomarker for overall survival in patients with adrenocortical carcinoma
Cited by: 0
Author(s): Jing Sun, Run Shi, Felix Beuschlein, C. Belka, Minglun Li
Software Mentions: 3
Published: over 6 years ago

10.3390/biology9090260

Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2
Cited by: 7
Author(s): Hibah Shaath, Nehad M. Alajez
Software Mentions: 3
Published: about 6 years ago

10.1038/s41398-021-01421-8

Transcriptomics identifies STAT3 as a key regulator of hippocampal gene expression and anhedonia during withdrawal from chronic alcohol exposure
Cited by: 13
Author(s): Wei-Yang Chen, Changwei Hu, Kana Hamada, Eleonora Gatta, Ying Chen, Huaibo Zhang, Jenny Drnevich, Harish R. Krishnan, Mark Maienschein‐Cline, Dennis R. Grayson, Subhash C. Pandey, Amy W. Lasek
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.00454-19

Metabolic Model of the <i>Phytophthora infestans</i> -Tomato Interaction Reveals Metabolic Switches during Host Colonization
Cited by: 19
Author(s): Sander Y.A. Rodenburg, Michael Seidl, Howard S. Judelson, A. L. Vu, F. Govers, Dick de Ridder
Software Mentions: 3
Published: about 7 years ago

10.1038/s41398-020-0772-3

Gene expression changes associated with trajectories of psychopathology in a longitudinal cohort of children and adolescents
Cited by: 3
Author(s): Vanessa Kiyomi Ota, Marcos Santoro, Letícia Spíndola, Pedro Mário Pan, Andressa Simabucuro, Gabriela Xavier, Tamiris Vieira-Fonseca, Évelin Aline Zanardo, Felipe R. C. dos Santos, Julia Schäfer, Leslie Domenici Kulikowski, Pedro A. F. Galante, Paula Fontes Asprino, Elisa Brietzke, Rodrigo Grassi‐Oliveira, Luís Augusto Rohde, Eurı́pedes Constantino Miguel, Ary Gadelha, Jair J. Mari, Rodrigo Affonseca Bressan, Giovanni Abrahão Salum, Sintia Belangero
Software Mentions: 3
Published: over 6 years ago

10.1098/rsbl.2018.0064

Non-uniform evolutionary response of gecko eye size to changes in diel activity patterns
Cited by: 12
Author(s): Lars Schmitz, Timothy E. Higham
Software Mentions: 3
Published: over 8 years ago

10.1038/s41398-017-0054-x

Cerebral organoids reveal early cortical maldevelopment in schizophrenia—computational anatomy and genomics, role of FGFR1
Cited by: 123
Author(s): Ewa K. Stachowiak, Courtney A. Benson, Sridhar T. Narla, Alexander Dimitri, L. E. Bayona Chuye, Siddhartha Dhiman, K. Harikrishnan, Seerat Elahi, David A. Freedman, Kristen J. Brennand, Pinaki Sarder, Michal K. Stachowiak
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.11319

Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study
Cited by: 6
Author(s): Jiang Lin, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 3
Published: over 5 years ago

10.3390/cells10061271

Nucleoporin TPR Affects C2C12 Myogenic Differentiation via Regulation of Myh4 Expression
Cited by: 3
Author(s): Jana Uhlířová, Lenka Šebestová, Karel Fišer, Tomáš Sieger, Jindřiška Fišerová, Pavel Hozák
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.4174

Is there a link between aging and microbiome diversity in exceptional mammalian longevity?
Cited by: 26
Author(s): Graham M. Hughes, John Leech, Sébastien J. Puechmaille, Jose V. Lopez, Emma C. Teeling
Software Mentions: 3
Published: almost 9 years ago

10.1039/c7tx00047b

Systems toxicology meta-analysis of in vitro assessment studies: biological impact of a candidate modified-risk tobacco product aerosol compared with cigarette smoke on human organotypic cultures of the aerodigestive tract
Cited by: 22
Author(s): Anita Iskandar, Bjoern Titz, Alain Sewer, Patrice Leroy, Thomas Schneider, Filippo Zanetti, Carole Mathis, Ashraf Elamin, Stefan Frentzel, Walter K. Schlage, Florian Martin, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12989-019-0309-1

Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation
Cited by: 25
Author(s): Marit Ilves, Pia Anneli Sofia Kinaret, Joseph Ndika, Piia Karisola, Veer Singh Marwah, Vittorio Fortino, Yuri Fedutik, Manuel Correia, Nicky Ehrlich, Katrin Loeschner, Alexandros Besinis, Joanne Vassallo, Richard D. Handy, Henrik Wolff, Kai Savolainen, Dario Greco, Harri Alenius
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1675-1

Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs
Cited by: 36
Author(s): Carlos Villacorta-Martín, Francisco Gonzalez, Jorn de Haan, Kitty Huijben, Paul Passarinho, Maya Lugassi-Ben Hamo, Michèle Zaccai
Software Mentions: 3
Published: about 11 years ago

10.12669/pjms.343.14644

Whole Genome Sequencing instead of Whole Exome Sequencing is required to identify the Genetic Causes of Polycystic Ovary Syndrome in Pakistani families
Cited by: 6
Author(s): Muhammad Tariq Masood Khan, Rubina Nazli, Jawad Ahmed, Sulman Basit
Software Mentions: 3
Published: over 8 years ago

10.1111/cpr.12879

LncRNAs are regulated by chromatin states and affect the skeletal muscle cell differentiation
Cited by: 8
Author(s): Xiaolong Qi, Mingyang Hu, Yue Xiang, Daoyuan Wang, Yongming Xu, Ye Hou, Huanhuan Zhou, Yu Luan, Zhangxu Wang, Weiya Zhang, Xinyun Li, Zhao Song, Yi‐Fang Zhao
Software Mentions: 3
Published: about 6 years ago

10.1186/s12957-018-1381-y

Identification of key gene modules for human osteosarcoma by co-expression analysis
Cited by: 19
Author(s): Jing Zhang, Qing Lan, Jiasheng Lin
Software Mentions: 3
Published: over 8 years ago

10.1038/celldisc.2016.41

NANOG reprograms prostate cancer cells to castration resistance via dynamically repressing and engaging the AR/FOXA1 signaling axis
Cited by: 40
Author(s): Collene Jeter, Bigang Liu, Yue Lu, Hsueh-Ping Chao, Dingxiao Zhang, Xin Liu, Xin Chen, Qiuhui Li, Kiera Rycaj, Tammy Calhoun-Davis, Li Yan, Qiang Hu, Jianmin Wang, Jianjun Shen, Song Liu, Dean G. Tang
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-017-1301-4

Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis
Cited by: 60
Author(s): Jacki Heraud-Farlow, Alistair M. Chalk, Sandra Linder, Qin Li, Scott Taylor, Joshua M. White, Lokman Pang, Brian Liddicoat, Ankita Gupte, Carl R. Walkley
Software Mentions: 3
Published: about 9 years ago

10.1016/j.bioflm.2021.100051

Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle
Cited by: 7
Author(s): Brian J. Eddie, Anthony P. Malanoski, Elizabeth L. Onderko, Daniel A. Phillips, Sarah M. Glaven
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41419-019-1835-3

The transcriptional landscape of lncRNAs reveals the oncogenic function of LINC00511 in ER-negative breast cancer
Cited by: 44
Author(s): Jian Zhang, Shiyao Sui, Hao Wu, Jinfeng Zhang, Xingda Zhang, Shouping Xu, Da Pang
Software Mentions: 3
Published: about 7 years ago

10.1186/s12985-014-0236-6

Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCs
Cited by: 4
Author(s): Jing Qin Wu, Monica Miranda Saksena, Vincent Soriano, Eugenia Vispo, Nitin K. Saksena
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-021-84080-5

Persistent COUP-TFII expression underlies the myopathy and impaired muscle regeneration observed in resistance to thyroid hormone-alpha
Cited by: 1
Author(s): Paola Aguiari, Yanyun Liu, Astgik Petrosyan, Sheue-yann Cheng, Gregory A. Brent, Laura Perin, Anna Milanesi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-96635-7

Multi-layered proteogenomic analysis unravels cancer metastasis directed by MMP-2 and focal adhesion kinase signaling
Cited by: 11
Author(s): Yumi Kwon, Seongjun Park, Binh Thanh Nguyen, Mi Jeong Kim, Sejin Oh, Hwanho Lee, Narae Park, Hyun‐Seok Kim, Min‐Jung Kang, Byung Soh Min, Jinwon Lee, Eun Gyeong Yang, Cheolju Lee
Software Mentions: 3
Published: about 5 years ago

10.3762/bjnano.6.252

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials
Cited by: 49
Author(s): Andrew Williams, Sabina Halappanavar
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-020-76474-8

Gut microbiota and metabolic health among overweight and obese individuals
Cited by: 60
Author(s): Mi‐Hyun Kim, Kyung Eun Yun, Jimin Kim, Eunkyo Park, Yoosoo Chang, Seungho Ryu, Hyung Lae Kim, Han Na Kim
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers12061642

The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B
Cited by: 13
Author(s): Jaideep Chakladar, Lauren Wong, Selena Z. Kuo, Wei Tse Li, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 3
Published: over 6 years ago

10.15252/msb.20188462

Enzyme promiscuity shapes adaptation to novel growth substrates
Cited by: 47
Author(s): Gabriela I. Guzmán, Troy E. Sandberg, Ryan A. LaCroix, Ákos Nyerges, Henrietta Papp, Markus de Raad, Zachary A. King, Ying Hefner, Trent Northen, Richard A. Notebaart, Csaba Pál, Bernhard Palsson, Balázs Papp, Adam M. Feist
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-9-561

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
Cited by: 250
Author(s): Wen Chi Chang, Tzong-Yi Lee, Hsien Da Huang, His Yuan Huang, Rong Pan
Software Mentions: 3
Published: almost 18 years ago

10.1038/s41598-020-76139-6

Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability
Cited by: 16
Author(s): Geoffrey Finch, Sonya Nandyal, Carlie Perretta, Benjamin Davies, Andrew J. Rosendale, Christopher J. Holmes, J. D. Gantz, Drew E. Spacht, Samuel T. Bailey, Marc E. Rothenberg, Kennan Oyen, Elise M. Didion, Souvik Chakraborty, Richard Lee, David L. Denlinger, Stephen F. Matter, Geoffrey M. Attardo, Matthew T. Weirauch, Joshua B. Benoit
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-73847-x

Differentiating Staphylococcus infection-associated glomerulonephritis and primary IgA nephropathy: a mass spectrometry-based exploratory study
Cited by: 9
Author(s): Anjali A. Satoskar, John P. Shapiro, Mikayla Jones, Cherri Bott, Samir Parikh, Sergey V. Brodsky, Lianbo Yu, Haikady N. Nagaraja, Daniel W. Wilkey, Michael L. Merchant, Jon B. Klein, Tibor Nádasdy, Brad H. Rovin
Software Mentions: 3
Published: about 6 years ago

10.1186/s12917-019-1815-y

A spatial assessment of Nipah virus transmission in Thailand pig farms using multi-criteria decision analysis
Cited by: 7
Author(s): Weerapong Thanapongtharm, Mathilde Paul, Anuwat Wiratsudakul, Vilaiporn Wongphruksasoong, Wantanee Kalpravidh, Kachen Wongsathapornchai, Sudarat Damrongwatanapokin, Daniel Schar, Marius Gilbert
Software Mentions: 3
Published: over 7 years ago

10.3390/cancers11121967

Pannexin1 Is Associated with Enhanced Epithelial-To-Mesenchymal Transition in Human Patient Breast Cancer Tissues and in Breast Cancer Cell Lines
Cited by: 25
Author(s): Nour Jalaleddine, Layal El-Hajjar, Hassan Dakik, Abdullah Shaito, Jessica Saliba, Rémi Safi, Kazem Zibara, Marwan El-Sabban
Software Mentions: 3
Published: almost 7 years ago

10.1186/1476-4598-9-74

Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive hepatocellular carcinoma
Cited by: 69
Author(s): Mai Tsuchiya, Joel S. Parker, Hiroshi Kono, Masanori Matsuda, Hideki Fujii, Ivan Rusyn
Software Mentions: 3
Published: over 16 years ago

10.3390/cancers13102452

Efficacy and Safety of Durvalumab Combined with Daratumumab in Daratumumab-Refractory Multiple Myeloma Patients
Cited by: 9
Author(s): Kristine A. Frerichs, Christie P.M. Verkleij, Meletios Α. Dimopoulos, Jhon A. Marin Soto, Sonja Zweegman, Mary Young, Kathryn J. Newhall, Tuna Mutis, Niels W.C.J. van de Donk
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-51627-6

Multi-tissue network analysis for drug prioritization in knee osteoarthritis
Cited by: 11
Author(s): Michael Neidlin, Smaragda Dimitrakopoulou, Leonidas G. Alexopoulos
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-74877-1

Low E2F2 activity is associated with high genomic instability and PARPi resistance
Cited by: 4
Author(s): Jonathan Rennhack, Eran R. Andrechek
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-82169-5

Transcriptome-wide Mendelian randomization study prioritising novel tissue-dependent genes for glioma susceptibility
Cited by: 6
Author(s): Jamie Robinson, Richard M. Martin, Spiridon Tsavachidis, Amy Howell, Caroline L Relton, Georgina Armstrong, Melissa L. Bondy, Jie Zheng, Kathreena M. Kurian
Software Mentions: 3
Published: over 5 years ago

10.1074/mcp.RA120.002345

Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy
Cited by: 20
Author(s): van Westering Tle., Henrik J. Johansson, Britt Hanson, Anna M.L. Coenen-Stass, Yulia Lomonosova, Jun Tanihata, Norio Matsuki, Toshifumi Yokota, Shin’ichi Takeda, Janne Lehtiö, Matthew J. Wood, Samir El Andaloussi, Yosuke Aoki, Thomas C. Roberts
Software Mentions: 3
Published: almost 6 years ago

10.1074/mcp.RA119.001737

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease
Cited by: 19
Author(s): Hazal Haytural, Georgios Mermelekas, Ceren Emre, Saket Milind Nigam, Steven L. Carroll, Bengt Winblad, Nenad Bogdanović, Gaël Barthet, Ann‐Charlotte Granholm, Lukas M. Orre, Lars O. Tjernberg, Susanne Frykman
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12918-015-0155-1

Spatially-resolved metabolic cooperativity within dense bacterial colonies
Cited by: 69
Author(s): John A. Cole, Lars Köhler, Jamila Hedhli, Zaida Luthey‐Schulten
Software Mentions: 3
Published: over 11 years ago

10.3390/cancers10080273

Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer
Cited by: 26
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Sahib Zada, Jin Seok Hwang, Trang Minh Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 3
Published: about 8 years ago

10.1186/1752-0509-2-95

Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Cited by: 152
Author(s): Angela P. Presson, Eric M. Sobel, Jeanette C. Papp, Charlyn Suarez, Toni Whistler, Mangalathu S. Rajeevan, Suzanne D. Vernon, Steve Horvath
Software Mentions: 3
Published: almost 18 years ago

10.1111/1755-0998.12674

Graphics for relatedness research
Cited by: 6
Author(s): Iván Galván-Femenía, Jan Graffelman, Carles Barceló-i-Vidal
Software Mentions: 3
Published: over 9 years ago

10.1186/s10020-019-0116-z

Inhibition of phosphatidylinositol 3-kinase by PX-866 suppresses temozolomide-induced autophagy and promotes apoptosis in glioblastoma cells
Cited by: 24
Author(s): Bryan Harder, Sen Peng, Chris Sereduk, Andrej M. Sodoma, Gaspar J. Kitange, Joseph C. Loftus, Jann N. Sarkaria, Nhan L. Tran
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12918-016-0336-6

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
Cited by: 51
Author(s): Jason McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Liu, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-019-43587-8

Predicting the decision making chemicals used for bacterial growth
Cited by: 14
Author(s): Kazuha Ashino, Kenta Sugano, Toshiyuki Amagasa, Bei‐Wen Ying
Software Mentions: 3
Published: over 7 years ago

10.3390/molecules25040904

Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis
Cited by: 26
Author(s): Arnold Amusengeri, Rolland Bantar Tata, Özlem Tastan Bishop
Software Mentions: 3
Published: over 6 years ago

10.1111/jcmm.15193

To construct a ceRNA regulatory network as prognostic biomarkers for bladder cancer
Cited by: 45
Author(s): Jiazhi Jiang, Yaqiong Bi, Xiaoping Li, Donghu Yu, Xin Yan, Jie Yao, Tongzu Liu, Li Sheng
Software Mentions: 3
Published: over 6 years ago

10.7150/jca.51591

Increased Expression of <i>KNSTRN</i> in Lung Adenocarcinoma Predicts Poor Prognosis: A Bioinformatics Analysis Based on TCGA Data
Cited by: 11
Author(s): Pengbo Deng, Rongrong Zhou, Jinghui Zhang, Liming Cao
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0037108

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation
Cited by: 10
Author(s): Jamie Bates, Julia Salzman, Damon May, Patty B. Garcia, Gregory J. Hogan, Martin W. McIntosh, Mark S. Schlissel, Pat Brown
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0203275

Genetic diversity and biogeography of T. officinale inferred from multi locus sequence typing approach
Cited by: 3
Author(s): Mahdi Jafari, Waheed Akram, Yanju Pang, Aqeel Ahmad, Shakeel Ahmed, Nasim Ahmad Yasin, Tehmina Anjum, Basharat Ali, Xiangdong Hu, Xiaohua Li, Shuang-Lin Dong, Qian Cai, Matteo Ciprian, Monika Bielec, Sheng Hu, Fatemeh Sefidkon, Xuebo Hu
Software Mentions: 3
Published: about 8 years ago

10.7150/jca.52170

Five-gene signature associating with Gleason score serve as novel biomarkers for identifying early recurring events and contributing to early diagnosis for Prostate Adenocarcinoma
Cited by: 10
Author(s): Lingyu Zhang, Li Yu, Xuchu Wang, Ying Ping, Danhua Wang, Ying Cao, Yibei Dai, Weiwei Liu, Zhihua Tao
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2020.01210

Identification of Energy Metabolism Genes for the Prediction of Survival in Hepatocellular Carcinoma
Cited by: 29
Author(s): Qinjunjie Chen, Fengwei Li, Yuzhen Gao, Gaoran Xu, Leilei Liang, Jing Xu
Software Mentions: 3
Published: about 6 years ago

10.3390/cells9071643

The E2F Pathway Score as a Predictive Biomarker of Response to Neoadjuvant Therapy in ER+/HER2− Breast Cancer
Cited by: 75
Author(s): Masanori Oshi, Hideo Takahashi, Yoshihisa Tokumaru, Li Yan, Omar M. Rashid, Masayuki Nagahashi, Ryusei Matsuyama, Itaru Endo, Kazuaki Takabe
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2407-12-426

Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients
Cited by: 5
Author(s): Siv Kjølsrud Bøhn, Kjell Magne Russnes, Amrit Kaur Sakhi, Magne Thoresen, Matthew T. G. Holden, Jan Øivind Moskaug, Mari Myhrstad, Ole Kristoffer Olstad, Sigbjørn Smeland, Rune Blomhoff
Software Mentions: 3
Published: about 14 years ago

10.1186/s13000-014-0210-z

Unveiling transcription factor regulation and differential co-expression genes in Duchenne muscular dystrophy
Cited by: 7
Author(s): Lijun Tian, Junhua Cao, Xingqiang Deng, Chuanling Zhang, Tong Qian, Xianxiang Song, Baoshan Huang
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0217105

Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes
Cited by: 21
Author(s): Hiroki Nakamura, Kiyonaga Fujii, Vipul Gupta, Hiroko Hata, Hirotaka Koizumu, Masahiro Hoshikawa, Saeko Naruki, Yuka Miyata, Ikuya Takahashi, Tomoki Miyazawa, Hiroki Sakai, Kouhei Tsumoto, Masayuki Takagi, Hisashi Saji, Toshihide Nishimura
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0177819

Network architecture associated with the highly specialized hindlimb of frogs
Cited by: 17
Author(s): Daniel Andrés Dos Santos, Jéssica Fratani, María Laura Ponssa, Virginia Abdala
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0208400

Using a coupled dynamic factor – random forest analysis (DFRFA) to reveal drivers of spatiotemporal heterogeneity in the semi-arid regions of southern Africa
Cited by: 4
Author(s): Jane Southworth, Erin Bunting, Likai Zhu, Sadie J. Ryan, Hannah Victoria Herrero, Peter R. Waylen, Rafael Muñoz‐Carpena, Miguel Ángel Campo‐Bescós, D. A. Kaplan
Software Mentions: 3
Published: almost 8 years ago