10.3389/fcell.2021.695533

Identification of a Costimulatory Molecule Gene Signature to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 12
Author(s): Ling Aye, Xiaole Song, Jingyi Yang, Li Hu, Xicai Sun, Jiaju Zhou, Quan Liu, Hongmeng Yu, Dehui Wang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcell.2021.709498

The Dynamic Changes of Transcription Factors During the Development Processes of Human Biparental and Uniparental Embryos
Cited by: 3
Author(s): Chenxi Zhang, Conghui Li, Ling Yang, Lizhi Leng, Dragomirka Jovic, Jun Wang, Fang Fang, Guibo Li, Depeng Zhao, Xuemei Li, Lin Lin, Yonglun Luo, Lars Bolund, Jinrong Huang, Ge Lin, Fengping Xu
Software Mentions: 4
Published: almost 5 years ago

10.3389/fendo.2021.674616

Tumor Mutation Burden Predicts Relapse in Papillary Thyroid Carcinoma With Changes in Genes and Immune Microenvironment
Cited by: 7
Author(s): Mingming Guo, Zhe Chen, Yayi Li, Sijin Li, Fei Shen, Xiao‐Xiong Gan, Jianhua Feng, Wei Cai, Qingzhi Liu, Bo Xu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-015-1624-z

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens
Cited by: 132
Author(s): Abraham Morales‐Cruz, Katherine C. H. Amrine, Bárbara Blanco-Ulate, Daniel P. Lawrence, Renaud Travadon, Philippe E. Rolshausen, Kendra Baumgartner, Dario Cantu
Software Mentions: 4
Published: about 11 years ago

10.7554/eLife.47427

Default mode-visual network hypoconnectivity in an autism subtype with pronounced social visual engagement difficulties
Cited by: 42
Author(s): Michael Lombardo, Lisa T. Eyler, Adrienne Moore, Michael Datko, Cynthia Carter Barnes, Debra Cha, Eric Courchesne, Karen Pierce
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07902-w

Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae
Cited by: 16
Author(s): Jan Hendrik Nagel, Michael J. Wingfield, Bernard Slippers
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.26580

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Cited by: 56
Author(s): Feiqiao Brian Yu, Paul C. Blainey, Frederik Schulz, Tanja Woyke, Mark Horowitz, Stephen R. Quake
Software Mentions: 4
Published: about 9 years ago

10.3389/fgene.2021.664334

Disruption of Circadian Transcriptome in Lung by Acute Sleep Deprivation
Cited by: 6
Author(s): Yuntao Lu, Bing Liu, Junjie Ma, Shuo Yang, Ju Huang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12983-021-00391-3

Polymorphism of winter phenotype in Siberian hamster: consecutive litters do not differ in photoresponsiveness but prolonged acclimation to long photoperiod inhibits winter molt
Cited by: 4
Author(s): Anna S. Przybylska-Piech, Michał S. Wojciechowski, Małgorzata Jefimow
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.699385

Analysis of Immune–Stromal Score-Based Gene Signature and Molecular Subtypes in Osteosarcoma: Implications for Prognosis and Tumor Immune Microenvironment
Cited by: 3
Author(s): Dingzhao Zheng, Kai-Chun Yang, Xinjiang Chen, Yongwu Li, Yongchun Chen
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-43158-x

An HRM Assay to Differentiate Sheeppox Virus Vaccine Strains from Sheeppox Virus Field Isolates and other Capripoxvirus Species
Cited by: 19
Author(s): Tesfaye Rufael, Tirumala Bharani Kumar Settypalli, Francisco J. Berguido, Reingard Grabherr, Angelika Loitsch, Eeva Tuppurainen, Nick Nwankpa, K Tounkara, Hafsa Madani, Amel Omani, Mariame Diop, Giovanni Cattoli, Adama Diallo, Charles Euloge Lamien
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.629475

Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations
Cited by: 11
Author(s): Diana García-Cortés, Enrique Hernández‐Lemus, Jesús Espinal-Enríquez
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07558-6

The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)
Cited by: 5
Author(s): Huai‐Jun Xue, Yiwei Niu, Kari A. Segraves, Rui Nie, Ya Jing Hao, Li Li Zhang, Xin Cheng, Xuewen Zhang, Wen Zhu Li, Run Sheng Chen, Xing Yang
Software Mentions: 4
Published: over 5 years ago

10.3390/genes12020227

Phenotypic Response to Light Versus Shade Associated with DNA Methylation Changes in Snapdragon Plants (Antirrhinum majus)
Cited by: 4
Author(s): Pierick Mouginot, Nelia Luviano Aparicio, Delphine Gourcilleau, Mathieu Latutrie, Sara Marin, Jean‐Louis Hemptinne, Christoph Grunau, Benoît Pujol
Software Mentions: 4
Published: over 5 years ago

10.1186/s12874-019-0680-5

A comparison of the polytomous Rasch analysis output of RUMM2030 and R (ltm/eRm/TAM/lordif)
Cited by: 26
Author(s): Michael C. Robinson, Andrew M. Johnson, David M. Walton, Joy C. MacDermid
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-6397-3

Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides
Cited by: 25
Author(s): Adam Pym, Kumar Saurabh Singh, A. Nordgren, T.G. Emyr Davies, Christoph Zimmer, Jan Eliáš, Russell Slater, Chris Bass
Software Mentions: 4
Published: over 6 years ago

10.3389/fpsyg.2018.02710

An Evaluation of Overall Goodness-of-Fit Tests for the Rasch Model
Cited by: 4
Author(s): Rudolf Debelak
Software Mentions: 4
Published: over 7 years ago

10.3390/genes12050702

Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests
Cited by: 3
Author(s): Simon Jansen, Ulrich Baulain, Christin Habig, Faisal Ramzan, Jens Schauer, Armin O. Schmitt, Armin M. Scholz, Ahmad Sharifi, Annett Weigend, Steffen Weigend
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.46418

Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes
Cited by: 20
Author(s): Lauren N. Booth, Travis J. Maures, Robin Yeo, Cindy Tantilert, Anne Brunet
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: about 8 years ago

10.3389/fimmu.2020.590618

A TP53-Associated Immune Prognostic Signature for the Prediction of Overall Survival and Therapeutic Responses in Muscle-Invasive Bladder Cancer
Cited by: 32
Author(s): Xiangkun Wu, Daojun Lv, Chao Cai, Zhijian Zhao, Ming Wang, Wenzhe Chen, Yongda Liu
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.684052

Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing
Cited by: 11
Author(s): Lia Walcher, Ann-Kathrin Kistenmacher, Charline Sommer, Sebastian Böhlen, Christina Ziemann, Susann Dehmel, Armin Braun, U. Sandy Tretbar, Stephan Klöß, Axel Schambach, Michael Morgan, Dennis Löffler, Christoph Kämpf, Conny Blumert, Kristin Reiche, Jana Beckmann, Ulla König, Bastian Standfest, Martin Thoma, Gustavo R. Makert, Sebastian Ulbert, Uta Kossatz-Böhlert, Ulrike Köhl, Anna Dünkel, Frank Stephan
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2021.679458

Comparative Proteomic Analysis Reveals Varying Impact on Immune Responses in Phorbol 12-Myristate-13-Acetate-Mediated THP-1 Monocyte-to-Macrophage Differentiation
Cited by: 21
Author(s): Sneha M. Pinto, Hera Kim, Yashwanth Subbannayya, Miriam S. Giambelluca, Korbinian Bösl, Liv Ryan, Animesh Sharma, Richard K. Kandasamy
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0058294

Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome
Cited by: 128
Author(s): Dapeng Bao, Ming Gong, Huajun Zheng, Mingjie Chen, Liang Zhang, Hong Wang, Jianping Jiang, Lin Wu, Yaping Zhu, Gang Zhu, Yan Zhou, Chuanhua Li, Shengyue Wang, Yan Zhao, Guoping Zhao, Qian Tan
Software Mentions: 4
Published: over 13 years ago

10.3389/fimmu.2020.594540

The Monocytes That Repopulate in Mice After Cyclophosphamide Treatment Acquire a Neutrophil Precursor Gene Signature and Immunosuppressive Activity
Cited by: 5
Author(s): Zhi Chun Ding, Nada S. Aboelella, Locke J. Bryan, Huidong Shi, Gang Zhou
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.630988

Transcriptomic Profiling of Fibropapillomatosis in Green Sea Turtles (Chelonia mydas) From South Texas
Cited by: 9
Author(s): Nicholas B. Blackburn, Ana C Leandro, Nina Nahvi, Mariana A. Devlin, Marcelo Leandro, Ignacio Martinez Escobedo, Juan M. Peralta, Jeff George, Brian A. Stacy, Thomas W. deMaar, John Blangero, Megan Keniry, Joanne E. Curran
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-79320-z

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)
Cited by: 32
Author(s): Katie Murphy, Joseph Edwards, Katherine Louie, Benjamin P. Bowen, Venkatesan Sundaresan, Trent Northen, Philipp Zerbe
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.691142

Dynamic Network Biomarker of Pre-Exhausted CD8+ T Cells Contributed to T Cell Exhaustion in Colorectal Cancer
Cited by: 16
Author(s): Jiaqi Hu, Chongyin Han, Jiayuan Zhong, Huisheng Liu, Rui Li, Wei Luo, Pei Chen, Fei Ling
Software Mentions: 4
Published: almost 5 years ago

10.12688/f1000research.26429.2

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
Cited by: 2
Author(s): Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Manjool Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.666163

Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients
Cited by: 22
Author(s): Stéphanie Bibert, Nicolas Guex, João Lourenço, Thomas Brahier, Matthaios Papadimitriou-Olivgeris, Lauro Damonti, Oriol Manuel, Robin Liechti, Lou Götz, Jonathan Tschopp, Mathieu Quinodoz, Péter Vollenweider, Jean‐Luc Pagani, Mauro Oddo, Olivier Hügli, Frédéric Lamoth, Véronique Erard, Cathy Voide, Mauro Delorenzi, Nathalie Rufer, Fabio Candotti, Carlo Rivolta, Noémie Boillat‐Blanco, Pierre‐Yves Bochud
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: about 5 years ago

10.1007/s12079-020-00575-2

Spermatozoa induce transcriptomic alterations in bovine oviductal epithelial cells prior to initial contact
Cited by: 7
Author(s): Qurat Ul Ain Reshi, Janeli Viil, James Ord, Freddy Lättekivi, Kasun Godakumara, Mohammad Mehedi Hasan, Monika Nõmm, Kersti Jääger, Agne Velthut-Meikas, Ülle Jaakma, Andres Salumets, Alireza Fazeli
Software Mentions: 4
Published: almost 6 years ago

10.1111/1462-2920.15554

Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi
Cited by: 7
Author(s): Baojun Wu, Murray P. Cox
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2020.615976

Identification of Core Genes and Screening of Potential Targets in Glioblastoma Multiforme by Integrated Bioinformatic Analysis
Cited by: 12
Author(s): Jian Yang, Qian Yang
Software Mentions: 4
Published: over 5 years ago

10.3390/jcm10132797

Predictors for Perioperative Blood Transfusion in Patients Undergoing Open Cystectomy and Urinary Diversion and Development of a Nomogram: An Observational Cohort Study
Cited by: 4
Author(s): Dominique Engel, Christian M. Beilstein, Pascal Jerney, Marc A. Furrer, Fiona C. Burkhard, Lukas M. Löffel, Patrick Y. Wuethrich
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2019.00712

Prognostic lncRNAs, miRNAs, and mRNAs Form a Competing Endogenous RNA Network in Colon Cancer
Cited by: 33
Author(s): Qianrong Huang, Xin-Bin Pan
Software Mentions: 4
Published: almost 7 years ago

10.3389/fonc.2020.628608

Upregulation of Long Non-Coding RNA GCC2-AS1 Facilitates Malignant Phenotypes and Correlated With Unfavorable Prognosis for Lung Adenocarcinoma
Cited by: 6
Author(s): Fengqiang Yu, Mingqiang Liang, Weidong Wu, Yu Huang, Juanjuan Zheng, Bin Zheng, Chun Chen
Software Mentions: 4
Published: over 5 years ago

10.1007/s00360-020-01322-0

Phenotypic flexibility in heat production and heat loss in response to thermal and hydric acclimation in the zebra finch, a small arid-zone passerine
Cited by: 10
Author(s): Michał S. Wojciechowski, Anna Kowalczewska, Roger Colominas‐Ciuró, Małgorzata Jefimow
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2021.714267

M6A Classification Combined With Tumor Microenvironment Immune Characteristics Analysis of Bladder Cancer
Cited by: 12
Author(s): Huili Zhu, Xiaocan Jia, Yuping Wang, Zhijuan Song, Nana Wang, Yongli Yang, Xiaoguang Shi
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2020.00707

Construction and Validation of an Autophagy-Related Prognostic Risk Signature for Survival Predicting in Clear Cell Renal Cell Carcinoma Patients
Cited by: 12
Author(s): Huiying Yang, Mengjiao Han, Hua Li
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.624752

Down-Regulation of Long Non-Coding RNA TINCR Induces Cell Dedifferentiation and Predicts Progression in Oral Squamous Cell Carcinoma
Cited by: 6
Author(s): Zerui Zhuang, Jing Huang, Weiwang Wang, Cheng Wang, Pei Yu, Jing Hu, Haichao Liu, Hanqi Yin, Jinsong Hou, Xiqiang Liu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009697

Listeria monocytogenes infection rewires host metabolism with regulatory input from type I interferons
Cited by: 3
Author(s): Duygu Demiröz, Ekaterini Platanitis, Marsha Bryant, Philipp Fischer, Michaela Prchal-Murphy, Alexander Lercher, Caroline Lassnig, Manuela Baccarini, Mathias Müller, Andréas Bergthaler, Veronika Sexl, Marlies Dolezal, Thomas Decker
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2020.567931

A Ten-N6-Methyladenosine (m6A)-Modified Gene Signature Based on a Risk Score System Predicts Patient Prognosis in Rectum Adenocarcinoma
Cited by: 10
Author(s): Wei Huang, Gen Li, Zihang Wang, Lin Zhou, Xin Yin, Tianshu Yang, Pei Wang, Xu Teng, Yajuan Feng, Hefen Yu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12888-021-03154-w

Attention-deficit/hyperactivity disorder with developmental coordination disorder: 24-year follow-up of a population-based sample
Cited by: 8
Author(s): Valdemar Landgren, Elisabeth Fernell, Christopher Gillberg, Magnus Landgren, Mats Johnson
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.00615

Long Non-coding RNA LINC02195 as a Regulator of MHC I Molecules and Favorable Prognostic Marker for Head and Neck Squamous Cell Carcinoma
Cited by: 29
Author(s): Hao Li, Hong‐Gang Xiong, Yao Xiao, Qi‐Chao Yang, Shao‐Chen Yang, Hongchao Tang, Wenfeng Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.590861

Clinical and Biological Significances of a Ferroptosis-Related Gene Signature in Glioma
Cited by: 89
Author(s): Shenghua Zhuo, Zhimin Chen, Yibei Yang, Jinben Zhang, Jianming Tang, Kun Yang
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2019.01269

An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients
Cited by: 27
Author(s): Yuhang Liu, Bingxin Liu, Guoying Jin, Jia Zhang, Xue Wang, Yuyang Feng, Zehua Bian, Bojian Fei, Yuan Yin, Zhaohui Huang
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2020.00681

Identification of Hub Genes Associated With Development of Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 50
Author(s): Chia‐Ying Li, Jia-Hua Cai, Jeffrey J. P. Tsai, Charles C.N. Wang
Software Mentions: 4
Published: about 6 years ago

10.1128/mBio.02302-20

Identification of Zinc-Dependent Mechanisms Used by Group B <i>Streptococcus</i> To Overcome Calprotectin-Mediated Stress
Cited by: 27
Author(s): Lindsey R. Burcham, Yoann Le Breton, Jana N. Radin, Brady L. Spencer, Liwen Deng, Aurélia Hiron, Monica Ransom, Jéssica da C. Mendonça, Ashton T. Belew, Najib M. El-Sayed, Kevin S. McIver, Thomas E. Kehl-Fie, Kelly S. Doran
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.597877

Identification of a Glycolysis-Related LncRNA Signature to Predict Survival in Diffuse Glioma Patients
Cited by: 11
Author(s): Yangyang Wang, Wenqiang Zhou, Shunchang Ma, Xiudong Guan, Dainan Zhang, Jiayi Peng, Xi Wang, Linhao Yuan, Peiliang Li, Beibei Mao, Kang Peng, Deling Li, Chuanbao Zhang, Wang Jia
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.51143.1

periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
Cited by: 5
Author(s): Jacques Serizay, Julie Ahringer
Software Mentions: 4
Published: over 5 years ago

10.1016/j.gpb.2019.05.005

Genome-wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer
Cited by: 8
Author(s): Shuang‐Ling Wu, Xiaoyi Zhang, Mengqi Chang, Changcai Huang, Jun Qian, Qing Li, Fang Yuan, Lihong Sun, Xinmiao Yu, Xinmiao Cui, Jiaxin Jiang, Meng-Yao Cui, Ye Liu, Hengchao Wu, Liang Zeng, Xiaoyue Wang, Yamei Niu, Wei‐Min Tong, Feng Jin
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0243595

Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes
Cited by: 2
Author(s): Natsuki Tokutomi, Kenta Nakai, Sumio Sugano
Software Mentions: 4
Published: almost 5 years ago

10.1093/gigascience/giaa109

A map of tumor–host interactions in glioma at single-cell resolution
Cited by: 31
Author(s): Francesca Pia Caruso, Luciano Garofano, Fulvio D’Angelo, Kai Yu, Fuchou Tang, Jinzhou Yuan, Jing Zhang, Luigi Cerulo, Stefano Maria Pagnotta, Davide Bedognetti, Peter A. Sims, Mario L. Suvà, Xiao‐Dong Su, Anna Lasorella, Antonio Iavarone, Michele Ceccarelli
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.dib.2020.106704

Datasets and analyses of molecular dynamics simulations of covalent binary and ternary complexes of MHC class I-related molecule/T-cell receptor (MR1/TCR) agonists to understand complex formation and conditions of fluorescent labelling
Cited by: 0
Author(s): Anke Steinmetz, Thomas Yvorra, Pascal Retailleau, Olivier Lantz, Frédéric Schmidt
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-016-1145-3

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
Cited by: 539
Author(s): Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Bâa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamás Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara López-Gomollón, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel D. Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock van Oosterhout, David Swarbreck, Saskia A. Hogenhout
Software Mentions: 4
Published: over 9 years ago

10.7150/jca.44436

DNA methylation profiling to predict overall survival risk in gastric cancer: development and validation of a nomogram to optimize clinical management
Cited by: 7
Author(s): Xianxiong Ma, Hengyu Chen, Guobin Wang, Lei Li, Kaixiong Tao
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.49262

Pathologic evolution-related Gene Analysis based on both single-cell and bulk transcriptomics in Colorectal Cancer
Cited by: 3
Author(s): Jiali Li, Zhao-Yi Zeng, Jiarui Chen, Xingyu Liu, Xueping Jiang, Wenjie Sun, Yuan Luo, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.48664

MMP9 and IGFBP1 Regulate Tumor Immune and Drive Tumor Progression in Clear Cell Renal Cell Carcinoma
Cited by: 13
Author(s): Tianbo Xu, Su Gao, Jingchong Liu, Yu Huang, Ke Chen, Xiaoping Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fbioe.2020.602937

Evaluation of Hydrogen Peroxide Fumigation and Heat Treatment for Standard Emergency Arthropod Inactivation in BSL-3 Insectaries
Cited by: 1
Author(s): Irina Häcker, R. Koller, Gerrit Eichner, Martin Jakob, Eleni Liapi, Johanna Rühl, Tanja Rehling, Marc F. Schetelig
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.52105

Identification of the hub genes and prognostic indicators of gastric cancer and correlation of indicators with tumor-infiltrating immune cell levels
Cited by: 4
Author(s): Yun Ji, Lu Gao, Can Zhang, Xu Sun, Liping Dai, Zhenyu Ji, Jianying Zhang, Zhida Zhang, Weimin Cao, Yang Zhao, Liguo Zhang
Software Mentions: 4
Published: over 5 years ago

10.1002/jcb.29128

NCF2, MYO1F, S1PR4, and FCN1 as potential noninvasive diagnostic biomarkers in patients with obstructive coronary artery: A weighted gene co‐expression network analysis
Cited by: 24
Author(s): Xiangang Mo, Wei Liu, Yunan Yang, Saber Imani, Shan Lu, Guorong Dan, Xuqiang Nie, Jun Yan, Rong Zhan, Xiaohui Li, Youcai Deng, Bingbo Chen, Yuchen Cai
Software Mentions: 4
Published: about 7 years ago

10.1111/jcmm.14585

Differential coexpression networks in bronchiolitis and emphysema phenotypes reveal heterogeneous mechanisms of chronic obstructive pulmonary disease
Cited by: 11
Author(s): Jiangyue Qin, Ting Yang, Ni Zeng, Chun Wan, Lijuan Gao, Xiaoou Li, Lei Chen, Yongchun Shen, Fuqiang Wen
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12866-018-1154-3

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera
Cited by: 108
Author(s): Rachael Lappan, Kara Imbrogno, Chisha Sikazwe, Denise Anderson, D. Mok, Harvey Coates, Shyan Vijayasekaran, Paul Bumbak, Christopher C Blyth, Sarra E. Jamieson, Christopher Peacock
Software Mentions: 4
Published: over 8 years ago

10.1111/jcmm.14830

Identification of immune‐enhanced molecular subtype associated with BRCA1 mutations, immune checkpoints and clinical outcome in ovarian carcinoma
Cited by: 23
Author(s): Mingjun Zheng, Yuexin Hu, Rui Gou, Ouxuan Liu, Xin Nie, Xiao Li, Qing Liu, Yingying Hao, Juanjuan Liu, Bei Lin
Software Mentions: 4
Published: over 6 years ago

10.1111/jcmm.15370

Genome‐Wide Analysis of circular RNAs and validation of hsa_circ_0006719 as a potential novel diagnostic biomarker in congenital scoliosis patients
Cited by: 1
Author(s): Gang Liu, Jianxiong Shen, Chong Chen, Yang Jiao, Zheng Li, Haining Tan, Youxi Lin, Tianhua Rong
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0178217

Automated prediction of emphysema visual score using homology-based quantification of low-attenuation lung region
Cited by: 8
Author(s): Motohiro Nishio, Kazuaki Nakane, Takeshi Kubo, Masahiro Yakami, Yutaka Emoto, Masaki Nishio, Kaori Togashi
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-021-02333-y

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean
Cited by: 28
Author(s): Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu, Li D
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-020-01356-8

Machine learning enables improved runtime and precision for bio-loggers on seabirds
Cited by: 20
Author(s): Joseph Korpela, Hirokazu Suzuki, S. Matsumoto, Yuichi Mizutani, Masaki Samejima, Taira Maekawa, Junichi Nakai, Ken Yoda
Software Mentions: 4
Published: almost 6 years ago

10.1111/jcmm.15505

Asiaticoside might attenuate bleomycin‐induced pulmonary fibrosis by activating cAMP and Rap1 signalling pathway assisted by A2AR
Cited by: 18
Author(s): Jing Luo, Ting Zhang, Ce Zhu, Junwei Sun, Wenjing Zhu, Wenxiu Ai, Xiaoying Huang, Xiaobing Wang
Software Mentions: 4
Published: about 6 years ago

10.1111/jcmm.16221

Expression and prognostic characteristics of m ⁵ C regulators in low‐grade glioma
Cited by: 11
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.16393

TTN/OBSCN ‘Double‐Hit’ predicts favourable prognosis, ‘immune‐hot’ subtype and potentially better immunotherapeutic efficacy in colorectal cancer
Cited by: 33
Author(s): Xinwei Han, Libo Wang, Chunguang Guo, Long Liu, Dechao Jiao, Zhenqiang Sun, Kunpeng Wu, Yanan Zhao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0115842

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
Cited by: 14
Author(s): Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo J. Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad
Software Mentions: 4
Published: over 11 years ago

10.1111/jcmm.16831

Bioinformatics analysis of the prognostic value of NEK8 and its effects on immune cell infiltration in glioma
Cited by: 7
Author(s): Meng Xiao, Chuang Du, Chuanbo Zhang, Xinzhong Zhang, Shaomin Li, Dainan Zhang, Wang Jia
Software Mentions: 4
Published: almost 5 years ago

10.3390/jcm10132973

Meteorin Is a Novel Therapeutic Target for Wet Age-Related Macular Degeneration
Cited by: 4
Author(s): Kimberley Delaunay, Alexandre Sellam, Virginie Dinet, Alexandre Moulin, Min Zhao, Emmanuelle Gélizé, Jérémie Canonica, Marie‐Christine Naud, Patricia Crisanti-Lassiaz, Francine Behar‐Cohen
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/4581954

Comprehensive Analysis of Differentially Expressed miRNAs and mRNAs Reveals That miR-181a-5p Plays a Key Role in Diabetic Dermal Fibroblasts
Cited by: 4
Author(s): Peng Liu, Yi Zhu, Qin Li, Biao Cheng
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.gpb.2019.01.006

Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis
Cited by: 3
Author(s): Jun Wang, Xiaowen Chen, Funan He, Xian‐Rong Song, Shu Huang, Wucheng Yue, Yipei Chen, Zhixi Su
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2407-13-58

Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients
Cited by: 79
Author(s): Liesbeth Hameetman, Suzan Commandeur, Jan Nico Bouwes Bavinck, Hermina C. Wisgerhof, Frank R. de Gruijl, Rein Willemze, Leon H.F. Mullenders, Cornelis P. Tensen, Harry Vrieling
Software Mentions: 4
Published: over 13 years ago

10.3390/genes12081282

A Novel Missense Mutation in TNNI3K Causes Recessively Inherited Cardiac Conduction Disease in a Consanguineous Pakistani Family
Cited by: 5
Author(s): Shafaq Ramzan, Stephanie Tennstedt, Muhammad Tariq, Sheraz Khan, Hafiza Noor Ul Ayan, Aamir Ali, Matthias Munz, Holger Thiele, Asad Aslam Korejo, Abdul Razzaq Mughal, Syed Zahid Jamal, Peter Nürnberg, Shahid Mahmood Baig, Jeanette Erdmann, Ilyas Ahmad
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-98806-y

Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis
Cited by: 36
Author(s): Zhongyi Wang, Adrian Keogh, Annick Waldt, Rachel Cuttat, Marilisa Neri, Shuchai Zhu, Sven Schuierer, Alexandra Ruchti, Christophe Crochemore, Judith Knehr, Julie Bastien, Iwona Ksiazek, Daniel Sánchez-Taltavull, Hui Ge, Jing Wu, Guglielmo Roma, Stephen B. Helliwell, Deborah Stroka, Florian Nigsch
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13073-020-00791-w

Best practices for variant calling in clinical sequencing
Cited by: 136
Author(s): Daniel C. Koboldt
Software Mentions: 4
Published: almost 6 years ago

10.1093/gigascience/gix109

Genome sequence of the small brown planthopper, Laodelphax striatellus
Cited by: 90
Author(s): Jiachen Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yan-Yuan Bao, Wan Zhao, Wei Wang, Hong Liang, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Luo Li, Jianping Yu, Le Kang, Feng Cui
Software Mentions: 4
Published: over 8 years ago

10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Cited by: 49
Author(s): Yu Xing, Yang Liu, Qing Zhang, Xinghua Nie, Yamin Sun, Zhiyong Zhang, Huchen Li, Kefeng Fang, Guangpeng Wang, Hongwen Huang, Ton Bisseling, Qingqin Cao, Ling Qin
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-93878-2

Benchmarking germline CNV calling tools from exome sequencing data
Cited by: 27
Author(s): Veronika Gordeeva, Е. И. Шарова, Konstantin Babalyan, Rinat Sultanov, Vadim M. Govorun, Georgij Arapidi
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-94292-4

Prevalence of cancer susceptibility variants in patients with multiple Lynch syndrome related cancers
Cited by: 7
Author(s): Yoon Young Choi, Su‐Jin Shin, Jae Eun Lee, Lisa Madlensky, Seung Tae Lee, Ji Soo Park, Jeong-Hyeon Jo, Hyun Ki Kim, Daniela Nachmanson, Xiaojun Xu, Sung Hoon Noh, Jae‐Ho Cheong, Olivier Harismendy
Software Mentions: 4
Published: about 5 years ago

10.1111/1759-7714.13998

Prognostic value of ferroptosis‐related genes in patients with lung adenocarcinoma
Cited by: 10
Author(s): Guangsheng Zhu, Huang Hua, Songlin Xu, Ruifeng Shi, Zhouyong Gao, Xi Liu, Shuai Zhu, Ning Zhou, Lingling Zu, Ramon Andrade De Mello, Jun Chen, Song Xu
Software Mentions: 4
Published: about 5 years ago

10.1093/gigascience/giz136

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Cited by: 20
Author(s): Joeri S. Strijk, Damien Daniel Hinsinger, Fengping Zhang, Kaihua Cao
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-58942-3

Amplicon sequencing analysis of arbuscular mycorrhizal fungal communities colonizing maize roots in different cover cropping and tillage systems
Cited by: 25
Author(s): Masao Higo, Yuya Tatewaki, Karen Iida, Kana Yokota, Katsunori Isobe
Software Mentions: 4
Published: over 6 years ago

10.3906/biy-2005-115

Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks
Cited by: 8
Author(s): Hamza Umut Karakurt, Pınar Pir
Software Mentions: 4
Published: about 6 years ago

10.1093/gigascience/giab037

The genome of the venomous snail <i>Lautoconus ventricosus</i> sheds light on the origin of conotoxin diversity
Cited by: 21
Author(s): José Ramón Pardos-Blas, Iker Irisarri, Samuel Abalde, Carlos M.L. Afonso, Manuel Jiménez‐Tenorio, Rafael Zardoya
Software Mentions: 4
Published: over 5 years ago

10.1186/s13046-019-1254-4

Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma
Cited by: 74
Author(s): Hong‐Gang Xiong, Hao Li, Yao Xiao, Qi‐Chao Yang, Leilei Yang, Lei Chen, Lin‐Lin Bu, Wenfeng Zhang, Jiali Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: about 7 years ago

10.1084/jem.20201290

Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation
Cited by: 16
Author(s): Marcel S Woo, Friederike Ufer, Nicola Rothammer, Giovanni Di Liberto, Lars Binkle, Undine Haferkamp, Jana K. Sonner, Jan Broder Engler, Sönke Hornig, Simone Bauer, Ingrid Wagner, Kristóf Égervári, Jacob Raber, Robert M. Duvoisin, Ole Pleß, Doron Merkler, Manuel A. Friese
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

10.7150/ijms.42151

Profiles of Immune Infiltration in Bladder Cancer and its Clinical Significance: an Integrative Genomic Analysis
Cited by: 16
Author(s): Zonglong Wu, Ke-Cheng Zhu, Qinggang Liu, Yaxiao Liu, Lipeng Chen, Jianfeng Cui, Hongda Guo, Nan Zhou, Yao Zhu, Yan Li, Benkang Shi
Software Mentions: 4
Published: over 6 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 5 years ago

10.4049/jimmunol.1901358

TNF-α Regulates Human Plasmacytoid Dendritic Cells by Suppressing IFN-α Production and Enhancing T Cell Activation
Cited by: 29
Author(s): Antonios Psarras, Agne Antanaviciute, Adewonuola Alase, Ian Carr, Miriam Wittmann, Paul Emery, George C. Tsokos, Edward M Vital
Software Mentions: 4
Published: over 5 years ago

10.1038/s41388-019-1005-1

Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines
Cited by: 12
Author(s): Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shan Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41388-020-01429-2

Androgen receptor signaling regulates the transcriptome of prostate cancer cells by modulating global alternative splicing
Cited by: 21
Author(s): Kalpit Shah, Teresa Gagliano, L. H. Garland, Timothy O’Hanlon, Daria Bortolotti, Valentina Gentili, Roberta Rizzo, Georgios Giamas, Michael Dean
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13018-021-02552-w

Study on the potential active components and molecular mechanism of Xiao Huoluo Pills in the treatment of cartilage degeneration of knee osteoarthritis based on bioinformatics analysis and molecular docking technology
Cited by: 13
Author(s): Weijian Chen, Tianye Lin, Qi He, Peng Yang, Gangyu Zhang, Fayi Huang, Zihao Wang, Hao Peng, Baolin Li, Liqing Du, Haibin Wang
Software Mentions: 4
Published: about 5 years ago