10.1128/mBio.01093-21

Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium
Cited by: 5
Author(s): Sushmita Sridhar, Sally Forrest, Derek Pickard, Claire Cormie, Emily A. Lees, Nicholas R. Thomson, Gordon Dougan, Stephen Baker
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0214372

Patterns of funerary variability, diet, and developmental stress in a Celtic population from NE Italy (3rd-1st c BC)
Cited by: 12
Author(s): Zita Laffranchi, Giuliana Cavalieri Manasse, Luciano Salzani, Marco Milella
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0064747

CD14 −159 C>T Gene Polymorphism with Increased Risk of Tuberculosis: Evidence from a Meta-Analysis
Cited by: 18
Author(s): Mohammed Y. Areeshi, Raju K. Mandal, Aditya K. Panda, Shekhar Chandra Bisht, Shafiul Haque
Software Mentions: 5
Published: about 13 years ago

10.1371/journal.pone.0171413

Large-scale bioactivity analysis of the small-molecule assayed proteome
Cited by: 4
Author(s): Tyler W. H. Backman, Daniel S. Evans, Thomas Girke
Software Mentions: 5
Published: over 9 years ago

10.1186/s12874-019-0875-9

Cross-cultural validation of the Functional Vision Questionnaire for Children and Young People (FVQ_CYP) with visual impairment in the Dutch population: challenges and opportunities
Cited by: 5
Author(s): Ellen B. M. Elsman, Valerija Tadić, Carel F.W. Peeters, Ger H. M. B. van Rens, Jugnoo S Rahi, Ruth M. A. van Nispen
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-018-1489-y

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells
Cited by: 25
Author(s): Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jérémy Denizot, Raquel Manzano García, Steven Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip T. Hawkins, Len R. Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick Varga‐Weisz
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0248485

16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya
Cited by: 21
Author(s): Edith M. Muwawa, Chinedu Christopher Obieze, Huxley Mae Makonde, Joyce Jefwa, James H. P. Kahindi, Damase Khasa
Software Mentions: 5
Published: over 5 years ago

10.1186/s13068-021-01975-1

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172
Cited by: 14
Author(s): Monika Tõlgo, Silvia Hüttner, Peter Rugbjerg, Nguyễn Thanh Thủy, Vu Nguyen Thanh, Johan Larsbrink, Lisbeth Olsson
Software Mentions: 5
Published: about 5 years ago

10.1186/s13024-020-00412-5

A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease
Cited by: 36
Author(s): Christoph Preuß, Ravi S. Pandey, Erin Piazza, Alexander D. Fine, Asli Uyar, Thanneer M. Perumal, Dylan Garceau, Kevin P. Kotredes, Huw Williams, Lara M. Mangravite, Bruce T. Lamb, Adrian L. Oblak, Gareth R. Howell, Michael Sasner, Benjamin A. Logsdon, Gregory W. Carter
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02386-z

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Cited by: 4
Author(s): Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Lior Pachter
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0032697

ArgR of Streptomyces coelicolor Is a Versatile Regulator
Cited by: 31
Author(s): Rosario Pérez‐Redondo, Antonio Rodríguez‐García, Alma Botas, Irene Santamarta, Juan F. Martı́n, Paloma Liras
Software Mentions: 5
Published: over 14 years ago

10.1371/journal.pone.0237601

Impact of calculated plasma volume status on all-cause and cardiovascular mortality: 4-year nationwide community-based prospective cohort study
Cited by: 14
Author(s): Yoichiro Otaki, Tetsu Watanabe, Tsuneo Konta, Masafumi Watanabe, Koichi Asahi, Kunihiro Yamagata, Shouichi Fujimoto, Kazuhiko Tsuruya, Ichiei Narita, Masato Kasahara, Yugo Shibagaki, Kunitoshi Iseki, Toshiki Moriyama, Masahide Kondo, Tsuyoshi Watanabe
Software Mentions: 5
Published: almost 6 years ago

10.1155/2021/6641838

Analysis of Molecular Mechanism of Erxian Decoction in Treating Osteoporosis Based on Formula Optimization Model
Cited by: 22
Author(s): Lang Yang, Liuyi Fan, Kexin Wang, Yu-peng Chen, Liuqin Liang, Xuemei Qin, Aiping Lü, Peng Cao, Bin Yu, Daogang Guan, Junxiang Peng
Software Mentions: 5
Published: about 5 years ago

10.18632/aging.102399

DNA methylation profile is a quantitative measure of biological aging in children
Cited by: 23
Author(s): Xiaohui Wu, Weidan Chen, Fangqin Lin, Qingsheng Huang, Jiayong Zhong, Huan Gao, Yanyan Song, Huiying Liang
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pcbi.1003703

Inferring Clonal Composition from Multiple Sections of a Breast Cancer
Cited by: 104
Author(s): Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Joshua D. Smith, Deborah A. Nickerson, Chang Woo Song, Daniela Witten, C. Anthony Blau, William Stafford Noble
Software Mentions: 5
Published: about 12 years ago

10.3390/genes10030212

RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae
Cited by: 11
Author(s): Yury V. Malovichko, Kirill S. Antonets, Anna R. Maslova, Е. А. Андреева, Sergey G. Inge-Vechtomov, Anton A. Nizhnikov
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-31882-9

Investigating the genetic profile of dopaminergic neurons in the VTA in response to perinatal nicotine exposure using mRNA-miRNA analyses
Cited by: 14
Author(s): Renee F. Keller, Andrei Dragomir, Yonggang Fan, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: almost 8 years ago

10.1093/database/bau027

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences
Cited by: 11
Author(s): Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom
Software Mentions: 5
Published: over 12 years ago

10.1172/jci.insight.149257

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort
Cited by: 27
Author(s): Flavia Flaviani, Natasha L. Hezelgrave, Tokuwa Kanno, Erica M. Prosdocimi, Evonne Chin-Smith, Alexandra Ridout, Djuna K von Maydell, Vikash Mistry, William Wade, Andrew Shennan, Konstantina Dimitrakopoulou, Paul Seed, A. James Mason, Rachel Tribe
Software Mentions: 5
Published: almost 5 years ago

10.1038/s42003-021-01892-x

Transcriptomic analyses of the termite, Cryptotermes secundus, reveal a gene network underlying a long lifespan and high fecundity
Cited by: 15
Author(s): Silu Lin, Jana Werle, Judith Korb
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0242879

Validation of models using basic parameters to differentiate intestinal tuberculosis from Crohn’s disease: A multicenter study from Asia
Cited by: 9
Author(s): Julajak Limsrivilai, Choon Kin Lee, Piyapan Prueksapanich, Kamin Harinwan, Asawin Sudcharoen, Natcha Cheewasereechon, Satimai Aniwan, Pimsiri Sripongpan, Panu Wetwittayakhlang, Ananya Pongpaibul, Anapat Sanpavat, Nonthalee Pausawasdi, Phunchai Charatcharoenwitthaya, Peter Higgins, Siew C. Ng
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-10-391

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Cited by: 6
Author(s): Chunguang Liang, Alexander Schmid, María José López‐Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar
Software Mentions: 5
Published: over 16 years ago

10.1155/2021/8810849

Development of an Autophagy-Related Gene Prognostic Model and Nomogram for Estimating Renal Clear Cell Carcinoma Survival
Cited by: 7
Author(s): Ying Wang, Yinhui Yao, Jingyi Zhao, Chunhua Cai, Junhui Hu, Yan‐Wu Zhao
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.7052

Environment‐induced changes in reproductive strategies and their transgenerational effects in the three‐spined stickleback
Cited by: 3
Author(s): Náyade Álvarez‐Quintero, Alberto Velando, José C. Noguera, Sin‐Yeon Kim
Software Mentions: 5
Published: over 5 years ago

10.1186/s13007-019-0444-6

Combining self-organizing maps and biplot analysis to preselect maize phenotypic components based on UAV high-throughput phenotyping platform
Cited by: 6
Author(s): Huagen Liang, Guijun Yang, Huayang Dai, Hao Yang, Bo Xu, Heli Li, Long Huang, Zhenhai Li, Xiaodong Yang, Chunjiang Zhao
Software Mentions: 5
Published: about 7 years ago

10.1186/s12903-021-01587-z

A four-hypoxia-genes-based prognostic signature for oral squamous cell carcinoma
Cited by: 10
Author(s): Chenguang Zhao, Yingrui Zhou, Hongwei Ma, Jinhui Wang, Hongxu Guo, Hao Líu
Software Mentions: 5
Published: about 5 years ago

10.1007/s10522-019-09818-1

Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength
Cited by: 7
Author(s): Mette Soerensen, Weilong Li, Birgit Debrabant, Marianne Nygaard, Jonas Mengel‐From, Morten Frost, Kaare Christensen, Lene Christiansen, Qihua Tan
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0214878

Statistical models discriminating between complex samples measured with microfluidic receptor-cell arrays
Cited by: 2
Author(s): Ron Wehrens, Margriet Roelse, Maurice Henquet, Marco van Lenthe, P.W. Goedhart, M.A. Jongsma
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2021.622683

Bioinformatics Analysis Identifies Molecular Markers Regulating Development and Progression of Endometriosis and Potential Therapeutic Drugs
Cited by: 7
Author(s): Ying Peng, Cheng Peng, Fang Zheng, Gang Chen
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-020-6495-2

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features
Cited by: 8
Author(s): Yang Li, Menggen Dalai, Rongguo Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
Software Mentions: 5
Published: over 6 years ago

10.1155/2020/3909416

Recognition of Immune Microenvironment Landscape and Immune-Related Prognostic Genes in Breast Cancer
Cited by: 7
Author(s): Huiling Wang, Sylvaine You, Meng Fang, Qian Fang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-021-07724-w

Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken
Cited by: 4
Author(s): Heidi A. Van Every, Carl J. Schmidt
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.62857

TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex
Cited by: 23
Author(s): Nicole Merritt, Keith Garcia, Dushyandi Rajendran, Zhen‐Yuan Lin, Xiaomeng Zhang, Katrina A. Mitchell, Nicholas Borcherding, Colleen Fullenkamp, Michael S. Chimenti, Anne‐Claude Gingras, Kieran F. Harvey, Munir R. Tanas
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-97619-3

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)
Cited by: 13
Author(s): Kleopatra Leontidou, Despoina Vokou, Anna Sandionigi, Antonia Bruno, Maria Lazarina, Johannes De Groeve, Mingai Li, Claudio Varotto, Matteo Girardi, Andrea Galimberti, Alessandro Cristofori
Software Mentions: 5
Published: almost 5 years ago

10.1172/JCI91363

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes
Cited by: 70
Author(s): Bon Ham Yip, Violetta Steeples, Emmanouela Repapi, Richard N. Armstrong, Miriam Llorian, S. Roy, Jacqueline Shaw, Hamid Dolatshad, Stephen Taylor, Amit Verma, Matthias Bartenstein, Paresh Vyas, Nicholas C. P. Cross, Luca Malcovati, Mario Cazzola, Eva Hellström‐Lindberg, Seishi Ogawa, Christopher W.J. Smith, Andrea Pellagatti, Jacqueline Boultwood
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0203625

Mean platelet volume and lymphocyte-to-monocyte ratio are associated with shorter progression-free survival in EGFR-mutant lung adenocarcinoma treated by EGFR tyrosine kinase inhibitor
Cited by: 28
Author(s): Kousuke Watanabe, Atsushi Yasumoto, Yosuke Amano, Hidenori Kage, Yasushi Goto, Yutaka Yatomi, Daiya Takai, Takahide Nagase
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13195-021-00862-z

Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer’s disease by meta-analysis and adaptive boosting ensemble learning
Cited by: 26
Author(s): Sze Chung Yuen, Xueya Liang, Hongmei Zhu, Yongliang Jia, Siu-wai Leung
Software Mentions: 5
Published: about 5 years ago

10.1002/ctm2.498

An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single‐base resolution methylome and hydroxymethylome
Cited by: 6
Author(s): Yingxin Han, Liyan Ji, Yanfang Guan, Mengya Ma, Pansong Li, Yinge Xue, Yinxin Zhang, Wanqiu Huang, Yuhua Gong, Li Jiang, Xipeng Wang, Hong Xie, Boping Zhou, Jiayin Wang, Junwen Wang, Jinghua Han, Yuliang Deng, Xin Yi, Fei Gao, Jian Huang
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pbio.3001166

Neural stem cells traffic functional mitochondria via extracellular vesicles
Cited by: 79
Author(s): Luca Peruzzotti-Jametti, Joshua D. Bernstock, Cory M. Willis, Giulia Manferrari, Rebecca Rogall, Erika Fernández-Vizarra, James C Williamson, Alice Braga, Aletta van den Bosch, Tommaso Leonardi, Grzegorz Krzak, Ágnes Kittel, Cristiane Benincá, Nunzio Vicario, Sisareuth Tan, Carlos Bastos, Iacopo Bicci, Nunzio Iraci, JA Smith, Ben Peacock, Karin H. Müller, Paul J. Lehner, Edit I. Buzás, Nuno Faria, Massimo Zeviani, Christian Frezza, Alain Brisson, Nicholas J Matheson, Carlo Viscomi, Stefano Pluchino
Software Mentions: 5
Published: over 5 years ago

10.1098/rsos.191883

No evidence for neonicotinoid preferences in the bumblebee <i>Bombus impatiens</i>
Cited by: 17
Author(s): Felicity Muth, Rebekah L. Gaxiola, Anne S. Leonard
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.ppat.1009256

A murine model of Lyme disease demonstrates that Borrelia burgdorferi colonizes the dura mater and induces inflammation in the central nervous system
Cited by: 23
Author(s): Timothy Casselli, Ali Divan, Emilie E. Vomhof-DeKrey, Yvonne Tourand, Heidi L. Pecoraro, Catherine A. Brissette
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pntd.0005223

MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil
Cited by: 55
Author(s): Kennio Ferreira‐Paim, Leonardo Andrade-Silva, Fernanda Machado Fonseca, Thatiana Bragine Ferreira, Delio José Mora, Juliana Andrade-Silva, Aziza Khan, Aiken Dao, Eduardo C. Reis, Margarete Teresa Gottardo de Almeida, André Luiz Maltos, R. Virmondes, Luciana Trilles, Volker Rickerts, Ariya Chindamporn, Jane E. Sykes, Massimo Cogliati, Kirsten Nielsen, Teun Boekhout, Matthew C. Fisher, June Kwon‐Chung, David M. Engelthaler, Márcia dos Santos Lazéra, Wieland Meyer, Mário León Silva-Vergara
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-019-5561-0

In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant
Cited by: 42
Author(s): Alessandro Silvestri, Valentina Fiorilli, Laura Miozzi, G. P. Accotto, Massimo Turina, Luisa Lanfranco
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-019-51379-3

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium
Cited by: 9
Author(s): Les Kallestad, Seth Blackshaw, Ahmad M. Khalil, Krzysztof Palczewski
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-6-253

ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
Cited by: 23
Author(s): Tomas Ohlson, Arne Elofsson
Software Mentions: 5
Published: over 20 years ago

10.3389/fvets.2020.580400

Spatial and Simultaneous Seroprevalence of Anti-Leptospira Antibodies in Owners and Their Domiciled Dogs in a Major City of Southern Brazil
Cited by: 9
Author(s): Aline do Nascimento Benitez, Thaís Cabral Monica, Ana Carolina Miura, Micheline Sahyun Romanelli, Lucienne Garcia Pretto‐Giordano, Roberta Lemos Freire, Regina Mitsuka‐Breganó, Camila Marinelli Martins, Alexander Welker Biondo, Isabela Machado Serrano, Thiago Henrique Carneiro Rios Lopes, Renato Barbosa Reis, Jancarlo Ferreira Gomes, Federico Costa, Elsio A. Wunder, Albert I. Ko, Italmar Teodorico Navarro
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-016-3288-8

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Cited by: 24
Author(s): Giovanna Ambrosini, René Dreos, Sunil Kumar, Philipp Bücher
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2105-14-169

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data
Cited by: 21
Author(s): Yanchun Bao, Veronica Vinciotti, Ernst Wit, Peter A C ‘t Hoen
Software Mentions: 5
Published: about 13 years ago

10.1371/journal.pone.0241861

Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections
Cited by: 5
Author(s): Raquel Morais de Paiva Daibert, Carlos Alberto Oliveira de Biagi, Felipe de Oliveira Vieira, Marcos Vinícius Gualberto Barbosa da Silva, Eugênio D. Hottz, Mariana Brandi Mendonça Pinheiro, Daniele Ribeiro de Lima Reis Faza, Hyago Passe Pereira, Marta Fonseca Martins, Humberto M. Brandão, M. A. Machado, Wanessa A. Carvalho
Software Mentions: 5
Published: over 5 years ago

10.1186/s12862-021-01753-5

Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals
Cited by: 4
Author(s): Simin Chai, Ran Tian, Juanjuan Bi, Shixia Xu, Wenhua Ren
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-021-00876-0

In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers
Cited by: 9
Author(s): Menglong Chen, Hui Shi, Shixue Gou, Xiaomin Wang, Lei Li, Jin Qiu, Han Wu, Huili Zhang, Yaqin Li, Liang Wang, Huan Li, Jixian Lin, Wenjing Guo, Zhiwu Jiang, Xiaoyu Yang, Anding Xu, Yunping Zhu, Cheng Zhang, Liangxue Lai, Xiaoping Li
Software Mentions: 5
Published: about 5 years ago

10.3389/fvets.2020.601640

Factors Associated With Lameness in Tie Stall Housed Dairy Cows in South Germany
Cited by: 11
Author(s): Andreas W. Oehm, Katharina Charlotte Jensen, Annegret Tautenhahn, Kerstin-Elisabeth Mueller, Michele I. Feist, Roswitha Merle
Software Mentions: 5
Published: over 5 years ago

10.3389/fpsyg.2018.02168

Effect of Long-Term Music Training on Emotion Perception From Drumming Improvisation
Cited by: 6
Author(s): Martina Di Mauro, Enrico Toffalini, Massimo Grassi, Karin Petrini
Software Mentions: 5
Published: over 7 years ago

10.1002/jcsm.12741

Meta‐analysis of genome‐wide DNA methylation and integrative omics of age in human skeletal muscle
Cited by: 29
Author(s): Sarah Voisin, Jacques Michaux, Shanie Landen, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Sofiya Gancheva, Meriem Ouni, Markus Jähnert, Kevin J. Ashton, Vernon G. Coffey, Jamie-Lee M Thompson, Thomas Doering, Anne Gabory, Claudine Junien, Robert Caïazzo, Hélène Verkindt, Violetta Raverdy, François Pattou, Philippe Froguel, Jeffrey M. Craig, Sara Blocquiaux, Martine Thomis, Adam P. Sharples, Annette Schürmann, Michael Roden, Steve Horvath, Nir Eynon
Software Mentions: 5
Published: about 5 years ago

10.1084/jem.20191257

Combined deletion of <i>Bap1</i>, <i>Nf2</i>, and <i>Cdkn2ab</i> causes rapid onset of malignant mesothelioma in mice
Cited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.00266

Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models
Cited by: 7
Author(s): Nabil Hanna, Sébastien Kicka, Gianpaolo Chiriano, Christopher F. Harrison, Hajer Ouertatani Sakouhi, Valentin Trofimov, Agata Kranjc, Jahn Nitschke, Marco Pagni, Pierre Cosson, Hubert Hilbi, Léonardo Scapozza, Thierry Soldati
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-017-17623-4

Genomic diversity and macroecology of the crop wild relatives of domesticated pea
Cited by: 57
Author(s): Petr Smýkal, Iveta Hradilová, Oldřich Trněný, Jan Brus, Abhishek Rathore, Michael Bariotakis, Roma Rani Das, Debjyoti Bhattacharyya, Christopher M. Richards, Clarice J. Coyne, Stergios Pirintsos
Software Mentions: 5
Published: over 8 years ago

10.1098/rspb.2019.0738

Transient local adaptation and source–sink dynamics in experimental populations experiencing spatially heterogeneous environments
Cited by: 14
Author(s): Karen Bisschop, Frederik Mortier, Rampal S. Etienne, Dries Bonte
Software Mentions: 5
Published: about 7 years ago

10.1186/s12263-021-00692-6

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis
Cited by: 7
Author(s): Kaitlin Day, Aimee L. Dordevic, Helen Truby, Melissa C. Southey, Susan L. Coort, Chiara Murgia
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-020-07313-3

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
Cited by: 7
Author(s): Longsheng Xing, Yu X, Xi Qiao, Cong Huang, Qiang Wu, Yang Ni, Jiao Guo, Wan‐Xue Liu, Wei Fan, Fang‐Hao Wan, Wanqiang Qian
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.15716

The Arabidopsis thaliana mobilome and its impact at the species level
Cited by: 242
Author(s): Leandro Quadrana, Amanda Bortolini Silveira, George F. Mayhew, Chantal LeBlanc, Robert A. Martienssen, Jeffrey A. Jeddeloh, Vincent Colot
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: over 13 years ago

10.3389/frai.2021.668035

Linking Linguistic and Geographic Distance in Four Semantic Domains: Computational Geo-Analyses of Internal and External Factors in a Dialect Continuum
Cited by: 1
Author(s): John L. A. Huisman, Karlien Franco, R.W.N.M. van Hout
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-87779-7

Identification of genes associated with altered gene expression and m6A profiles during hypoxia using tensor decomposition based unsupervised feature extraction
Cited by: 10
Author(s): Sanjiban Sekhar Roy, Y-h. Taguchi
Software Mentions: 5
Published: about 5 years ago

10.1098/rspb.2020.2577

Multidimensional plasticity in the Glanville fritillary butterfly: larval performance is temperature, host and family specific
Cited by: 25
Author(s): Nadja Verspagen, Suvi Ikonen, Marjo Saastamoinen, Erik van Bergen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-30157-7

Multi-marker metabarcoding approach to study mesozooplankton at basin scale
Cited by: 72
Author(s): Sérgio Stefanni, D Stanković, Diego Borme, Alessandra de Olazabal, Tea Juretić, Alberto Pallavicini, Valentina Tirelli
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pcbi.1008012

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
Cited by: 24
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 5
Published: almost 6 years ago

10.3390/e22111198

FASTENER Feature Selection for Inference from Earth Observation Data
Cited by: 2
Author(s): Filip Koprivec, Klemen Kenda, Beno Šircelj
Software Mentions: 5
Published: over 5 years ago

10.1155/2021/8895723

Identification and Construction of a Long Noncoding RNA Prognostic Risk Model for Stomach Adenocarcinoma Patients
Cited by: 14
Author(s): Zhiqiang Zha, Peiling Zhang, Dailing Li, Guolong Liu, Lin Lü
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-019-2645-4

reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction
Cited by: 5
Author(s): Risa Karakida Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-021-02414-y

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
Cited by: 38
Author(s): Melania Barile, Iván Imaz-Rosshandler, Isabella Inzani, Shila Ghazanfar, Jennifer Nichols, John C. Marioni, Carolina Guibentif, Berthold Göttgens
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0254159

Non-territorial GPS-tagged golden eagles Aquila chrysaetos at two Scottish wind farms: Avoidance influenced by preferred habitat distribution, wind speed and blade motion status
Cited by: 6
Author(s): Alan H. Fielding, David J. Anderson, Stuart Benn, R.A. Dennis, Matthew Geary, Ewan Weston, D. Philip Whitfield
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-018-31795-7

Macrofungal species distributions depend on habitat partitioning of topography, light, and vegetation in a temperate mountain forest
Cited by: 29
Author(s): Yun Chen, Zuoqiang Yuan, Bi Shi, Xueying Wang, Ye Yongzhong, Jens‐Christian Svenning
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0256268

Investigation of population-based mental health staffing and efficiency-based mental health productivity using an information-theoretic approach
Cited by: 5
Author(s): Matthew Tyler Boden, Clifford A. Smith, Jodie A. Trafton
Software Mentions: 5
Published: almost 5 years ago

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: over 6 years ago

10.1172/jci.insight.148435

A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients
Cited by: 70
Author(s): Samantha M. Morrissey, Anne E Geller, Xiaoling Hu, David Tieri, Chuan‐Fan Ding, Christopher K Klaes, Elizabeth A. Cooke, Matthew R Woeste, Zachary C Martin, Oscar Chen, Sarah A. Bush, Huang‐Ge Zhang, Rodrigo Cavallazzi, Sean P. Clifford, James Chen, Smita Ghare, Shirish Barve, Lu Cai, Maiying Kong, Eric C. Rouchka, Kenneth R. McLeish, Silvia M. Uriarte, Corey T. Watson, Jiapeng Huang, Jun Yan
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0201630

BioNet: A Python interface to NEURON for modeling large-scale networks
Cited by: 49
Author(s): Sergey L. Gratiy, Yazan N. Billeh, Kael Dai, Catalin Mitelut, David Feng, Nathan W. Gouwens, Nicholas Cain, Christof Koch, Costas A. Anastassiou, Anton Arkhipov
Software Mentions: 5
Published: almost 8 years ago

10.3390/biology10090907

Dissecting Bread Wheat Heterosis through the Integration of Agronomic and Physiological Traits
Cited by: 6
Author(s): Kevin Gimenez, Pierre Blanc, O. Argillier, Jean-Baptiste Pierre, Jacques Le Gouis, Etienne Paux
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-79014-6

Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
Cited by: 15
Author(s): Rosa Alba Sola Martínez, José M. Pastor, Gema Lozano Terol, Julia Gallego‐Jara, Luis García‐Marcos, Manuel Cánovas Díaz, Teresa De Diego
Software Mentions: 5
Published: over 5 years ago

10.1242/dmm.040147

Dynamic MAPK signaling activity underlies a transition from growth arrest to proliferation in <i>Drosophila scribble</i> mutant tumors
Cited by: 17
Author(s): Tiantian Ji, Lina Zhang, Mingxi Deng, Shan Huang, Jiguang Wang, Tri Pham, Andrew A. Smith, Varun Sridhar, Clemens Cabernard, Yan Yan
Software Mentions: 5
Published: over 7 years ago

10.1186/s40594-017-0080-5

The test of basic Mechanics Conceptual Understanding (bMCU): using Rasch analysis to develop and evaluate an efficient multiple choice test on Newton’s mechanics
Cited by: 14
Author(s): Sarah Hofer, Ralph Schumacher, Herbert J. Rubin
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0163711

hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine
Cited by: 7
Author(s): Steffen Falgreen, Anders Ellern Bilgrau, Rasmus Froberg Brøndum, Lasse Hjort Jakobsen, Jonas Have, Kasper Lindblad Nielsen, Tarec Christoffer El‐Galaly, Julie Støve Bødker, Alexander Schmitz, Ken H. Young, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 5
Published: almost 10 years ago

10.15252/embj.2020105479

Repression of Irs2 by let‐7 mi <scp>RNA</scp> s is essential for homeostasis of the telencephalic neuroepithelium
Cited by: 9
Author(s): Virgínia Fernández, Maria Ángeles Martínez-Martinez, Anna Prieto-Colomina, Adrián Cárdenas, Rafael Soler, Martina Dori, Ugo Tomasello, Yuki Nomura, José P. López‐Atalaya, Federico Calegari, Vı́ctor Borrell
Software Mentions: 5
Published: almost 6 years ago

10.1093/bioinformatics/btv634

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
Cited by: 54
Author(s): Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2021.707713

Identification of Candidate Blood mRNA Biomarkers in Intracerebral Hemorrhage Using Integrated Microarray and Weighted Gene Co-expression Network Analysis
Cited by: 3
Author(s): Feng Jin, Lei Li, Yuehan Hao, Ling Tang, Yuye Wang, Zhiyi He
Software Mentions: 5
Published: almost 5 years ago

10.15252/emmm.202012461

Combination therapies induce cancer cell death through the integrated stress response and disturbed pyrimidine metabolism
Cited by: 12
Author(s): Goetz Hartleben, Kenji Schorpp, Yongseok Kwon, Barbara Betz, Foivos-Filippos Tsokanos, Zahra Dantes, A Schäfer, Ina Rothenaigner, José Manuel Monroy Kuhn, Pauline Morigny, Lisa Mehr, Sean Lin, Susanne Seitz, Janina Tokarz, Anna Artati, Jerzy Adamsky, Oliver Plettenburg, Dominik Lutter, Martin Irmler, Johannes Beckers, Maximilian Reichert, Kamyar Hadian, Anja Zeigerer, Stephan Herzig, Mauricio Berriel Díaz
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008790

Exclusive breastfeeding can attenuate body-mass-index increase among genetically susceptible children: A longitudinal study from the ALSPAC cohort
Cited by: 11
Author(s): Yan Yan Wu, Stephen J. Lye, Cindy‐Lee Dennis, Laurent Briollais
Software Mentions: 5
Published: about 6 years ago

10.1186/s12967-020-02503-9

Genomic landscape of the immune microenvironments of brain metastases in breast cancer
Cited by: 11
Author(s): Wei-Cheng Lu, Hui Xie, Ce Yuan, Jinjiang Li, Zhaoyang Li, Andrew Wu
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12916-020-01806-4

ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis
Cited by: 7
Author(s): Sara Charmsaz, Ben Doherty, Sinéad Cocchiglia, Damir Varešlija, Attilio Marino, Nicola Cosgrove, Ricardo Marques, Nolan Priedigkeit, Siobhan Purcell, Fiona T. Bane, Jarlath Bolger, Christopher Byrne, Philip J. O’Halloran, Francesca Brett, Katherine M. Sheehan, Kieran Brennan, Ann M. Hopkins, Stephen Keelan, Petra Jagušt, Stephen F. Madden, Chiara Martinelli, Matteo Battaglini, Steffi Oesterreich, Adrian V. Lee, Gianni Ciofani, Arnold D. Hill, Leonie S. Young
Software Mentions: 5
Published: over 5 years ago

10.3389/fneur.2021.633390

Development of a Prognostic Five-Gene Signature for Diffuse Lower-Grade Glioma Patients
Cited by: 3
Author(s): Qiang Zhang, Wenhao Liu, Shunbin Luo, Fuchen Xie, Xiaojun Liu, Ren-ai Xu, Lixi Chen, Zhi-Lin Su
Software Mentions: 5
Published: about 5 years ago

10.1093/beheco/aru156

Biparental incubation-scheduling: no experimental evidence for major energetic constraints
Cited by: 31
Author(s): Martin Bulla, Will Cresswell, Anne L. Rutten, Mihai Vâlcu, Bart Kempenaers
Software Mentions: 5
Published: almost 12 years ago

10.1073/pnas.1822046116

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-018-25748-3

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9
Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: about 8 years ago

10.3389/fnhum.2021.632702

Trajectories of Mother-Infant Communication: An Experiential Measure of the Impacts of Early Life Adversity
Cited by: 8
Author(s): Lauren Granata, Alissa Valentine, Jason L. Hirsch, Prabarna Ganguly, Heather C. Brenhouse
Software Mentions: 5
Published: over 5 years ago

10.1186/s40249-018-0506-4

Integrating ecological approaches to interrupt schistosomiasis transmission: opportunities and challenges
Cited by: 10
Author(s): Song Liang, Eniola Michael Abe, Xiao‐Nong Zhou
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pbio.1000335

The Sexually Antagonistic Genes of Drosophila melanogaster
Cited by: 294
Author(s): Paolo Innocenti, Edward H. Morrow
Software Mentions: 5
Published: over 16 years ago

10.1038/s41598-020-77318-1

Improving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data
Cited by: 9
Author(s): Quang-Huy Nguyen, Duc-Hau Le
Software Mentions: 5
Published: over 5 years ago

10.3390/genes12060824

Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data
Cited by: 4
Author(s): Sunghyun Cho, Prabuddha Manjula, Minjun Kim, Eunjin Cho, Dooho Lee, Seung Hwan Lee, Jun Heon Lee, Dongwon Seo
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pntd.0009587

Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus
Cited by: 9
Author(s): Ivana Sierra, José Manuel Latorre-Estivalis, Lucila Traverso, Paula Valeria Gonzalez, Ariel A Aptekmann, Alejandro D. Nadra, Héctor Mario Masuh, Sheila Ons
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-021-02460-6

Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability
Cited by: 23
Author(s): Xin Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D. Buckley, Gisela Orozco, Oliver Distler, Andrew P. Morris, Paul Martin, Stephen Eyre, Caroline Ospelt
Software Mentions: 5
Published: almost 5 years ago