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 12 years ago

10.1155/2017/8347085

Identification of Transcriptional Modules and Key Genes in Chickens Infected with Salmonella enterica Serovar Pullorum Using Integrated Coexpression Analyses
Cited by: 7
Author(s): Baohong Liu, Jianping Cai
Software Mentions: 3
Published: almost 9 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 4 years ago

10.1038/s41598-021-84887-2

Slc1a3-2A-CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and effectors in the 129S4 genetic background
Cited by: 9
Author(s): Lech Kaczmarczyk, Nicole Reichenbach, Nelli Blank, Maria Jonson, Lars Dittrich, Gabor C. Petzold, Walker S. Jackson
Software Mentions: 3
Published: over 4 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: about 5 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 5 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: about 5 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 7 years ago

10.1155/2020/6725753

Comprehensive Characterization of Prognostic Long Noncoding RNAs in Osteosarcoma
Cited by: 4
Author(s): Hua Gao, Yuanyuan Guo, Miaomiao Zhang, Zuqiang Yi
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0224477

Are we ready for scaling up restoration actions? An insight from Mediterranean macroalgal canopies
Cited by: 21
Author(s): Laura Tamburello, Loredana Papa, Giuseppe Guarnieri, Laura Basconi, Serena Zampardi, Maria Beatrice Scipione, Antonio Terlizzi, Valerio Zupo, Simonetta Fraschetti
Software Mentions: 3
Published: about 6 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 5 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 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: almost 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: about 6 years ago

10.1038/s41598-019-50148-6

Gene co-expression network analysis reveals key potential gene modules in utero-vaginal junction associated with duration of fertility trait of breeder hens
Cited by: 1
Author(s): Lantao Gu, Ruoxi Jing, Yanzhang Gong, Mei Yu, Abdelmotaleb A. Elokil, Shijun Li
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-72477-7

Play fighting social networks do not predict injuries from later aggression
Cited by: 12
Author(s): Simon P. Turner, Jennifer E. Weller, Irene Camerlink, Gareth Arnott, Taegyu Choi, Andrea Doeschl‐Wilson, Marianne Farish, Simone Foister
Software Mentions: 3
Published: about 5 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 4 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 13 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 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 5 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: almost 5 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: about 8 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: almost 6 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: over 16 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 7 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 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 5 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 7 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 5 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 5 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 5 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 7 years ago

10.1016/j.jbc.2021.100285

Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice
Cited by: 4
Author(s): Katarína Lopušná, Paweł Nowialis, Jana Opavska, Ajay Abraham, Alberto Riva, Staci L. Haney, René Opavský
Software Mentions: 3
Published: almost 5 years ago

10.7150/jca.45553

The <i>miR-370</i>/UQCRC2 axis facilitates tumorigenesis by regulating epithelial-mesenchymal transition in Gastric Cancer
Cited by: 11
Author(s): Danwen Wang, Fei Su, Tao Zhang, Tiecheng Yang, Huaqiao Wang, Lei Yang, Fenfang Zhou, Feng Mao
Software Mentions: 3
Published: almost 6 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 4 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 8 years ago

10.1038/s41438-020-0287-3

Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera
Cited by: 39
Author(s): Zhaodong Hao, Siqin Liu, Lingfeng Hu, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0231771

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system
Cited by: 3
Author(s): Irina N. Shilova, Jonathan D. Magasin, Matthew M. Mills, Julie Robidart, Kendra A. Turk‐Kubo, Jonathan P. Zehr
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.97011

Peripheral tissues reprogram CD8+ T cells for pathogenicity during graft-versus-host disease
Cited by: 19
Author(s): Pedro M. Sousa, Séverine Cire, Thomas Conlan, Laura Jardine, Claire Tkacz, Ivana R. Ferrer, C Lomas, Sophie Ward, Heather C. West, Simone Dertschnig, Sven Blobner, Terry K. Means, Stephen Henderson, Daniel H. Kaplan, Matthew Collin, Vincent Plagnol, Clare Bennett, Ronjon Chakraverty
Software Mentions: 3
Published: over 7 years ago

10.1111/jcmm.13997

ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies
Cited by: 9
Author(s): Chenchen Feng, Chao Song, Ziyu Ning, Bo Ai, Qiuyu Wang, Yong Xu, Meng Li, Xuefeng Bai, Jian Zhao, Yuejuan Liu, Xuecang Li, Jian Zhang, Chunquan Li
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0257254

Knocking out TMEM38B in human foetal osteoblasts hFOB 1.19 by CRISPR/Cas9: A model for recessive OI type XIV
Cited by: 4
Author(s): Laura Leoni, Francesca Tonelli, Roberta Besio, Roberta Gioia, Francesco Moccia, Antonio Rossi, Antonella Forlino
Software Mentions: 3
Published: about 4 years ago

10.1186/s41065-021-00183-z

RTP4 is a novel prognosis-related hub gene in cutaneous melanoma
Cited by: 7
Author(s): Yiqi Li, Jue Qi, Jiankang Yang
Software Mentions: 3
Published: over 4 years ago

10.1136/gutjnl-2019-320430

Western-type diet influences mortality from necrotising pancreatitis and demonstrates a central role for butyrate
Cited by: 57
Author(s): Fons F van den Berg, Demi van Dalen, Sanjiv Hyoju, Hjalmar C. van Santvoort, Marc G. Besselink, W. Joost Wiersinga, Olga Zaborina, Marja A. Boermeester, John C. Alverdy
Software Mentions: 3
Published: about 5 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 7 years ago

10.1371/journal.pone.0022295

Randomizing Genome-Scale Metabolic Networks
Cited by: 16
Author(s): Areejit Samal, O. C. Martin
Software Mentions: 3
Published: over 14 years ago

10.1186/s41065-019-0096-6

Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico
Cited by: 45
Author(s): Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang, Yongjie Zhang, Yichao Zhu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0138204

A Systematic Review and Meta-Analysis of the Efficacy of Anti-Toxoplasma gondii Medicines in Humans
Cited by: 90
Author(s): Haixia Wei, Shanshan Wei, David S. Lindsay, Hong‐Juan Peng
Software Mentions: 3
Published: about 10 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 4 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: almost 11 years ago

10.1186/gm130

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes
Cited by: 228
Author(s): Iain J. Gallagher, Camilla Schéele, Pernille Keller, Annemette Nielsen, Judit Reményi, Christian P. Fischer, Karim Roder, John Babraj, Claes Wahlestedt, György Hutvágner, Bente Klarlund Pedersen, James A. Timmons
Software Mentions: 3
Published: almost 16 years ago

10.1093/gigascience/giz138

Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
Cited by: 64
Author(s): Gareth Linsmith, Stéphane Rombauts, Sara Montanari, Cecilia Deng, Jean‐Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles‐Eric Durel, Riccardo Velasco, David B. Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco
Software Mentions: 3
Published: almost 6 years ago

10.3390/ht8010004

A Selective Review of Multi-Level Omics Data Integration Using Variable Selection
Cited by: 127
Author(s): Cen Wu, Fei Zhou, Jie Ren, Xiaoxi Li, Yu Jiang, Shuangge Ma
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0067922

Roles for Treg Expansion and HMGB1 Signaling through the TLR1-2-6 Axis in Determining the Magnitude of the Antigen-Specific Immune Response to MVA85A
Cited by: 26
Author(s): Magali Matsumiya, Elena Stylianou, Kristin Griffiths, Zoe Lang, Joel N. Meyer, Stephanie A. Harris, Rosalind Rowland, Angela M. Minassian, Ansar A. Pathan, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: over 12 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 10 years ago

10.1186/s13059-016-1005-1

Ligation-free ribosome profiling of cell type-specific translation in the brain
Cited by: 47
Author(s): Nicholas Hornstein, Daniela Torres, Sohani Das Sharma, Guomei Tang, Peter Canoll, Peter A. Sims
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0094031

Disruption of the Homogentisate Solanesyltransferase Gene Results in Albino and Dwarf Phenotypes and Root, Trichome and Stomata Defects in Arabidopsis thaliana
Cited by: 12
Author(s): Yuehui Chao, Junmei Kang, Tiejun Zhang, Qingchuan Yang, Margaret Y. Gruber, Yan Sun
Software Mentions: 3
Published: over 11 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 6 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: about 17 years ago

10.1186/s13059-017-1194-2

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort
Cited by: 222
Author(s): Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J. Kangas, Pasi Soininen, Zeneng Wang, Mika Ala‐Korpela, Stanley L. Hazen, Markku Laakso, Aldons J. Lusis
Software Mentions: 3
Published: over 8 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 6 years ago

10.1371/journal.pone.0137829

Indirect Energy Flows in Niche Model Food Webs: Effects of Size and Connectance
Cited by: 4
Author(s): Jane Shevtsov, Rosalyn Rael
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0164353

Induced Human Decidual NK-Like Cells Improve Utero-Placental Perfusion in Mice
Cited by: 20
Author(s): Ricardo de Carvalho Cavalli, Ana Sofia Cerdeira, Elizabeth Pernicone, Henri Augusto Korkes, Suzanne D. Burke, Augustine Rajakumar, Ravi Thadhani, Drucilla J. Roberts, Manoj Bhasin, S. Ananth Karumanchi, Hernan D. Kopcow
Software Mentions: 3
Published: about 9 years ago

10.3390/genes12020257

Differential Expression of a Panel of Ten CNTN1-Associated Genes during Prostate Cancer Progression and the Predictive Properties of the Panel towards Prostate Cancer Relapse
Cited by: 2
Author(s): Yan Gu, Mathilda Jing Chow, Anil Kapoor, Xiaozeng Lin, Wenjuan Mei, Damu Tang
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0157426

An Integrative Transcriptomic Analysis for Identifying Novel Target Genes Corresponding to Severity Spectrum in Spinal Muscular Atrophy
Cited by: 6
Author(s): Chunrong Yang, Chien‐Lin Chen, Wei-Chun Chou, Ho-Chen Lin, Yuh Jyh Jong, Li-Kai Tsai, Chun‐Yu Chuang
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0245501

Balancing time use for children’s fitness and adiposity: Evidence to inform 24-hour guidelines for sleep, sedentary time and physical activity
Cited by: 16
Author(s): Dorothea Dumuid, Melissa Wake, David Burgner, Mark S. Tremblay, Anthony D. Okely, Ben Edwards, Terence Dwyer, Tim Olds
Software Mentions: 3
Published: almost 5 years ago

10.3390/genes12050753

Weighted Gene Co-Expression Network Analysis Reveals Hub Genes Contributing to Fuzz Development in Gossypium arboreum
Cited by: 6
Author(s): Feng Xu, Liyan Shang, Hongyan Cheng, Dongyun Zuo, Youping Zhang, Qiaolian Wang, Limin Lv, Guoli Song
Software Mentions: 3
Published: over 4 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 8 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 10 years ago

10.3390/genes8100269

The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome
Cited by: 27
Author(s): Ludivine Renaud, Willian A. da Silveira, E. Starr Hazard, Jonathan Simpson, Silvia Falcinelli, Dongjun Chung, Oliana Carnevali, Gary Hardiman
Software Mentions: 3
Published: about 8 years ago

10.3390/genes10020074

Macrophages from Susceptible and Resistant Chicken Lines have Different Transcriptomes following Marek’s Disease Virus Infection
Cited by: 17
Author(s): Pankaj Chakraborty, Richard Kuo, Lonneke Vervelde, Bernadette M. Dutia, Pete Kaiser, Jacqueline Smith
Software Mentions: 3
Published: almost 7 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: about 17 years ago

10.1371/journal.pone.0229334

Age-related modulations of alpha and gamma brain activities underlying anticipation and distraction
Cited by: 20
Author(s): Hesham A. ElShafei, Lesly Fornoni, Rémy Masson, Olivier Bertrand, Aurélie Bidet-Caulet
Software Mentions: 3
Published: over 5 years ago

10.3390/genes10070536

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut
Cited by: 16
Author(s): Xiaobo Zhao, Li‐Ming Gan, Yan Cheng, Chunjuan Li, Quanxi Sun, Juan Wang, Cuiling Yuan, Hao Zhang, Shiguang Shan, Jian Ning Liu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0179065

Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
Cited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: over 8 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: about 6 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 9 years ago

10.3389/fpls.2021.662091

Calcium Positively Mediates Blue Light-Induced Anthocyanin Accumulation in Hypocotyl of Soybean Sprouts
Cited by: 3
Author(s): Gang Hu, Xiaomeng Yue, Jinxue Song, Guipei Xing, Jun Chen, Haixia Wang, Nana Su, Jin Cui
Software Mentions: 3
Published: over 4 years ago

10.3389/fpsyt.2020.00354

A Novel LINS1 Truncating Mutation in Autosomal Recessive Nonsyndromic Intellectual Disability
Cited by: 2
Author(s): Babylakshmi Muthusamy, Anikha Bellad, Pramada Prasad, Aravind K. Bandari, G. Bhuvanalakshmi, R. M. Kiragasur, Satish Chandra Girimaji, Akhilesh Pandey
Software Mentions: 3
Published: over 5 years ago

10.3389/fpsyg.2014.00477

Toward a dynamical theory of body movement in musical performance
Cited by: 33
Author(s): Alexander P. Demos, Roger Chaffin, Vivek Kant
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0212513

Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway
Cited by: 262
Author(s): Yu Kato, Kimiyo Tabata, Takayuki Kimura, Ayako Yachie‐Kinoshita, Yoichi Ozawa, Kazuhiko Yamada, Junichi Ito, Sho Tachino, Yusaku Hori, Masahiro Matsuki, Yoshikazu Matsuoka, Samik Ghosh, Hiroaki Kitano, Ken’ichi Nomoto, Junji Matsui, Yasuhiro Funahashi
Software Mentions: 3
Published: almost 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: almost 6 years ago

10.3389/fpls.2017.01545

De novo Assembly of the Camellia nitidissima Transcriptome Reveals Key Genes of Flower Pigment Biosynthesis
Cited by: 41
Author(s): Xingyi Zhou, Jiyuan Li, Yong‐Guan Zhu, Ni Sui, Jinling Chen, Xiaojuan Feng, Yunfeng Zhang, Shuangquan Li, Hongxiang Zhu, Wen Yu
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0219486

Caenorhabditis elegans hub genes that respond to amyloid beta are homologs of genes involved in human Alzheimer’s disease
Cited by: 14
Author(s): Rasoul Godini, Roger Pocock, Hossein Fallahi
Software Mentions: 3
Published: over 6 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 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: over 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 6 years ago

10.1371/journal.pone.0087804

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach
Cited by: 33
Author(s): Nag Chetan, Karanth K. Praveen, Gururaja Kotambylu Vasudeva
Software Mentions: 3
Published: almost 12 years ago

10.3389/fphys.2015.00413

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine
Cited by: 96
Author(s): Cheng Cheng Zhang, Qiang Hua
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0192606

Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring
Cited by: 86
Author(s): Madeline Rose Keleher, Syeda Nuzhat Fatima Zaidi, Shyam Shah, MaryAnn Oakley, Cassondra Pavlatos, Samir El Idrissi, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0074256

Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms
Cited by: 90
Author(s): Federico Martinelli, Russell L. Reagan, Sandra L. Uratsu, My L. Phu, Ute Albrecht, Wenwei Zhao, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 3
Published: about 12 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 10 years ago

10.3389/fpls.2019.00145

Global Responses of Resistant and Susceptible Sorghum (Sorghum bicolor) to Sugarcane Aphid (Melanaphis sacchari)
Cited by: 39
Author(s): Hannah M. Tetreault, Sajjan Grover, Erin D. Scully, Tammy Gries, Nathan A. Palmer, Gautam Sarath, Joe Louis, Scott E. Sattler
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphar.2021.645862

Catenin Alpha-2 Mutation Changes the Immune Microenvironment in Lung Adenocarcinoma Patients Receiving Immune Checkpoint Inhibitors
Cited by: 6
Author(s): Wen Yang, Anqi Lin, Wei Zhu, Ting Wei, Peng Luo, Linlang Guo, Jian Zhang
Software Mentions: 3
Published: over 4 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 13 years ago

10.3389/fphys.2020.00735

An Overview of the Role of Calcium/Calmodulin-Dependent Protein Kinase in Cardiorenal Syndrome
Cited by: 29
Author(s): Carolina Victória Cruz Junho, Wellington Caio‐Silva, Mayra Trentin-Sonoda, Marcela Sorelli Carneiro‐Ramos
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0070429

Identification and Validation of a Multigene Predictor of Recurrence in Primary Laryngeal Cancer
Cited by: 39
Author(s): Elena Fountzilas, Vassiliki Kotoula, Nikolaos Angouridakis, Ilias Karasmanis, Ralph M. Wirtz, Anastasia G Eleftheraki, Elke Veltrup, Konstantinos Markou, Angelos Nikolaou, Dimitrios Pectasides, George Fountzilas
Software Mentions: 3
Published: over 12 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: over 7 years ago

10.1172/jci.insight.145928

Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells
Cited by: 29
Author(s): Wouter A van der Heijden, Lisa Van de Wijer, Farid Keramati, Wim Trypsteen, Sofie Rutsaert, Rob ter Horst, Martin Jaeger, Hans J. P. M. Koenen, Hendrik G. Stunnenberg, Irma Joosten, Paul E. Verweij, Jan van Lunzen, Charles A. Dinarello, Linos Vandekerckhove, Mihai G. Netea, A.J.A.M. van der Ven, Quirijn de Mast
Software Mentions: 3
Published: over 4 years ago

10.3389/fphys.2021.621830

Identification of the Crucial Gene in Overflow Arteriovenous Fistula by Bioinformatics Analysis
Cited by: 3
Author(s): Zhengde Zhao, Qining Fu, Liangzhu Hu, Yangdong Liu
Software Mentions: 3
Published: over 4 years ago

10.3390/genes11070760

Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response
Cited by: 90
Author(s): Radhakrishnan Vishnubalaji, Hibah Shaath, Nehad M. Alajez
Software Mentions: 3
Published: over 5 years ago