10.1038/s41598-020-66556-y

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations
Cited by: 9
Author(s): Ian M. Rose, Mallikarjun Bidarimath, Alex Webster, Andrew K. Godwin, Andrea Flesken‐Nikitin, Alexander Yu. Nikitin
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2021.649312

Characterising Post-mortem Bacterial Translocation Under Clinical Conditions Using 16S rRNA Gene Sequencing in Two Animal Models
Cited by: 2
Author(s): Lily Gates, Nigel Klein, Neil J. Sebire, Dagmar Alber
Software Mentions: 4
Published: about 5 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fnut.2021.640100

Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome
Cited by: 7
Author(s): Jason W. Arnold, Hunter D. Whittington, Sue F. Dagher, Jeffery Roach, M. Andrea Azcárate-Peril, José M. Bruno-Bárcena
Software Mentions: 4
Published: over 5 years ago

10.1093/database/bav047

GraP: platform for functional genomics analysis of Gossypium raimondii
Cited by: 12
Author(s): Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Software Mentions: 4
Published: over 11 years ago

10.3389/fcell.2021.709241

Characterization of Immune-Related Long Non-coding RNAs to Construct a Novel Signature and Predict the Prognosis and Immune Landscape of Soft Tissue Sarcoma
Cited by: 1
Author(s): Zhengjun Lin, Ke Pang, Hongli Liu, Xianghong Zhang, Jia Wan, Tao Zheng, Tang Liu, Weijun Peng
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0236347

Understanding the spatial dimension of natural language by measuring the spatial semantic similarity of words through a scalable geospatial context window
Cited by: 4
Author(s): Bozhi Wang, Teng Fei, Yuhao Kang, Meng Li, Qingyun Du, Meng Han, Ning Dong
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms9081737

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli
Cited by: 8
Author(s): Karla Vasco, Brian Nohomovich, Pallavi Singh, Cristina Venegas-Vargas, Rebekah E. Mosci, S. R. Rust, Paul C. Bartlett, Bo Norby, Daniel L. Grooms, Lixin Zhang, Shannon D. Manning
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-90653-1

Totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage
Cited by: 17
Author(s): Marino Maemura, Hiroaki Taketsuru, Yuki Nakajima, Ruiqi Shao, Ayaka Kakihara, Jumpei Nogami, Yasuyuki Ohkawa, Yu Ichi Tsukada
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.6989

Effects of maternal genotypic identity and genetic diversity of the red mangrove <i>Rhizophora mangle</i> on associated soil bacterial communities: A field‐based experiment
Cited by: 9
Author(s): Hayley Craig, John Paul Kennedy, Donna J. Devlin, Richard D. Bardgett, Jennifer K. Rowntree
Software Mentions: 4
Published: over 5 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: almost 7 years ago

10.15252/embj.2019103894

<scp>SCHENGEN</scp> receptor module drives localized <scp>ROS</scp> production and lignification in plant roots
Cited by: 67
Author(s): Satoshi Fujita, Damien De Bellis, Kai H. Edel, Philipp Köster, Tonni Grube Andersen, Emanuel Schmid‐Siegert, Valérie Dénervaud Tendon, Alexandre Pfister, Peter Marhavý, Robertas Ursache, Verónica G. Doblas, Marie Barberon, Jean Daraspe, Audrey Creff, Gwyneth Ingram, Jörg Kudla, Niko Geldner
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-16603-y

RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy
Cited by: 11
Author(s): Candice P. Chu, Jessica A. Hokamp, Rachel E. Cianciolo, Alan R. Dabney, Candice Brinkmeyer-Langford, George E. Lees, Mary B. Nabity
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pmed.1003336

Antibiotic prescribing for lower UTI in elderly patients in primary care and risk of bloodstream infection: A cohort study using electronic health records in England
Cited by: 16
Author(s): Laura Shallcross, Patrick Rockenschaub, Ruth Blackburn, Irwin Nazareth, Nick Freemantle, Andrew Hayward
Software Mentions: 4
Published: almost 6 years ago

10.3390/ani11030865

Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts
Cited by: 7
Author(s): Lantian Su, Xinxin Liu, Guang-Yao Jin, Yue Ma, Haoxin Tan, Muhammed Abdul Khalid, Martin Romantschuk, Shan Yin, Nan Hui
Software Mentions: 4
Published: over 5 years ago

10.15252/embj.2019103932

<scp>RNF</scp> 43 truncations trap <scp>CK</scp> 1 to drive niche‐independent self‐renewal in cancer
Cited by: 24
Author(s): Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik G.H. Lindeboom, Jeroen M. Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E. Boonekamp, Kateřina Hanáková, David Potěšil, Zbyněk Zdráhal, Sylvia F. Boj, Jan Paul Medema, Vı́tězslav Bryja, Bon‐Kyoung Koo, Michiel Vermeulen, Madelon M. Maurice
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12915-019-0677-x

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes
Cited by: 19
Author(s): Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Nayuta Yakushiji-Kaminatsui, Asier Ullate-Agote, Denis Duboule
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-016-1428-4

An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Cited by: 45
Author(s): Roberto A. Barrero, Kathryn R. Napier, J. H. Cunnington, L. W. Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás Szabó, Simon Bulman, Adam Hunter, L. I. Ward, Mark Whattam, M. Bellgard
Software Mentions: 4
Published: over 9 years ago

10.3389/fimmu.2018.01626

Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence
Cited by: 23
Author(s): Alejandro M. Labella, Esther García-Rosado, Isabel Bandı́n, Carlos P. Dopazo, Dolores Castro, M. Carmen Alonso, Juan J. Borrego
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2020.00581

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato
Cited by: 16
Author(s): Johannes B Herpell, Florian Schindler, Mersad Bejtović, Lena Fragner, Bocar Diallo, Anke Bellaire, Susanne Kublik, Bärbel U. Foesel, Silvia Gschwendtner, Melina Kerou, Michael Schloter, Wolfram Weckwerth
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms7030072

Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina
Cited by: 3
Author(s): Martina Gonzalez Mateu, Cedric Evan Park, Cullen Patrick McAskill, Andrew H. Baldwin, Stephanie A. Yarwood
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0249540

Water sprinkling as a tool for heat abatement in farmed Iberian red deer: Effects on calf growth and behaviour
Cited by: 2
Author(s): F. Javier Pérez‐Barbería, I Arroyo-González, Andrés J. García, Martina Pérez Serrano, Laureano Gallego, Tomás Landete‐Castillejos
Software Mentions: 4
Published: over 5 years ago

10.3389/fmolb.2021.688298

Identification of a Prognostic Signature Associated With the Homeobox Gene Family for Bladder Cancer
Cited by: 9
Author(s): Bingqi Dong, Jiaming Liang, Li Ding, Wenping Song, Jinbo Song, Mingkai Zhu, Shufang Zhao, Yongkang Ma, Tiejun Yang
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms9040787

Gut Microbiota Dynamics, Growth Performance, and Gut Morphology in Broiler Chickens Fed Diets Varying in Energy Density with or without Bacitracin Methylene Disalicylate (BMD)
Cited by: 13
Author(s): Deborah Adewole, Fisayo Akinyemi
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.7500

Hatching date influences winter habitat occupancy: Examining seasonal interactions across the full annual cycle in a migratory songbird
Cited by: 4
Author(s): Michael E. Akresh, David I. King, Peter P. Marra
Software Mentions: 4
Published: about 5 years ago

10.1186/s12862-015-0416-z

A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea
Cited by: 21
Author(s): Carolina Granados Mendoza, Julia Naumann, Marie‐Stéphanie Samain, Paul Goetghebeur, Yannick De Smet, Stefan Wanke
Software Mentions: 4
Published: about 11 years ago

10.3389/fcell.2020.00688

The Construction and Analysis of ceRNA Network and Patterns of Immune Infiltration in Colon Adenocarcinoma Metastasis
Cited by: 30
Author(s): Zhengyan Chang, Runzhi Huang, Wanting Fu, Jiehan Li, Guo Ji, Jinglei Huang, Weijun Shi, Huabin Yin, Weifeng Wang, Tong Meng, Zongqiang Huang, Qing Wei, Huanlong Qin
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-019-3115-8

GenGraph: a python module for the simple generation and manipulation of genome graphs
Cited by: 4
Author(s): Jon Ambler, Shandukani Mulaudzi, Nicola Mulder
Software Mentions: 4
Published: almost 7 years ago

10.3390/cells9081793

Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis
Cited by: 3
Author(s): Ho‐Su Lee, Maaike Vancamelbeke, Sare Verstockt, Tom Wilms, Bram Verstockt, João Sabino, Marc Ferrante, Séverine Vermeire, Isabelle Cleynen
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms8121954

The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota
Cited by: 8
Author(s): Emma Bergsten, Denis Mestivier, Iradj Sobhani
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms8101506

Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health
Cited by: 16
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Dhivya Priya Thenappan, Eveline Adam, Henry Müller, Gabriele Berg
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0233067

No evidence for a relationship between breed cooperativeness and inequity aversion in dogs
Cited by: 5
Author(s): Jim McGetrick, Désirée Brucks, Sarah Marshall-Pescini, Friederike Range
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41389-021-00311-4

Single-cell RNA sequencing reveals that targeting HSP90 suppresses PDAC progression by restraining mitochondrial bioenergetics
Cited by: 8
Author(s): Li-Peng Hu, Kaixia Zhou, Yan‐Miao Huo, Dejun Liu, Qing Li, Minwei Yang, Peng Huang, Chunjie Xu, Guang-Ang Tian, Lishuang Yao, Xueli Zhang, Yahui Wang, Jun Li, Zhigang Zhang, Shu-Heng Jiang, Xin Xing, Xu Wang, Weiting Qin, Qin Yang
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.27935

Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability
Cited by: 5
Author(s): Matthew Devall, Graham Casey
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0009450

High incidence of asymptomatic cases during an outbreak of Plasmodium malariae in a remote village of Malaysian Borneo
Cited by: 4
Author(s): Nurul Athirah Naserrudin, Emira Izzati Binti Abdul Aziz, Erdie Aljet, George Mangunji, Bumpei Tojo, Mohammad Saffree Jeffree, Richard Culleton, Kawsar Ahmed
Software Mentions: 4
Published: about 5 years ago

10.3389/fmolb.2021.679031

Identification and Validation of Immune-Related Gene Signature for Predicting Lymph Node Metastasis and Prognosis in Lung Adenocarcinoma
Cited by: 19
Author(s): Ru Jia, Zhilin Sui, Hongdian Zhang, Zhentao Yu
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-017-03390-9

Aberrant plasticity of peripheral sensory axons in a painful neuropathy
Cited by: 30
Author(s): Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Software Mentions: 4
Published: about 9 years ago

10.1093/bib/bbz170

Deep learning-based clustering approaches for bioinformatics
Cited by: 104
Author(s): Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz‐Schuhmann, Michael Cochez, Stefan Decker
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1004959

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis
Cited by: 16
Author(s): Amber J. Marty, Aimee Teo Broman, Robert Żarnowski, Teigan G. Dwyer, Laura M. Bond, Anissa Lounès-Hadj Sahraoui, Joël Fontaine, James M. Ntambi, Sündüz Keleş, Christina Kendziorski, Gregory M. Gauthier
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-015-2115-y

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars
Cited by: 36
Author(s): Ryan Ghan, Steven C. Van Sluyter, Uri Hochberg, Asfaw Degu, Daniel Hopper, Richard L. Tillet, Karen Schlauch, Paul A. Haynes, Aaron Fait, Grant R. Cramer
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-017-02391-y

Whole blood transcriptome analysis reveals potential competition in metabolic pathways between negative energy balance and response to inflammatory challenge
Cited by: 13
Author(s): Juliette Bouvier-Muller, Charlotte Allain, Guillaume Tabouret, Francis Enjalbert, David Portes, Céline Noirot, Rachel Rupp, Gilles Foucras
Software Mentions: 4
Published: about 9 years ago

10.3389/fmolb.2021.653805

High Expression Levels of CDK1 and CDC20 in Patients With Lung Squamous Cell Carcinoma are Associated With Worse Prognosis
Cited by: 3
Author(s): Huan Deng, Hang Qin, Deyan Shen, Hangjie Ying, Yibi Zhang, Qinying Xu, Ming Chen
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-017-01943-6

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1
Cited by: 16
Author(s): Tim-Michael Decker, Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum, Caroline C. Friedel, Dirk Eick
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0121558

Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data
Cited by: 36
Author(s): Minerva Singh, Damian Evans, Boun Suy Tan, Chan Samean Nin
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0169648

The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: over 9 years ago

10.1038/s41422-019-0251-7

Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors
Cited by: 39
Author(s): Rong Guo, Fang Hu, Qitong Weng, Chen Lv, Hongling Wu, Lijuan Liu, Zongcheng Li, Yang Zeng, Zhijie Bai, Mengyun Zhang, Yuting Liu, Xiaofei Liu, Chengxiang Xia, Tongjie Wang, Pingwei Zhou, Kaitao Wang, Yong Dong, Yuxuan Luo, Xiangzhong Zhang, Yuxian Guan, Geng Yang, Juan Du, Yangqiu Li, Yu Lan, Jiekai Chen, Bing Liu, Jinyong Wang
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.7313

Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma
Cited by: 37
Author(s): Tingting Guo, Hongwen Ma, Yuting Zhou
Software Mentions: 4
Published: about 7 years ago

10.3390/cancers13051007

A Lung Organotypic Coculture Reveals a Role for TFEB-Lysosomal Axis in the Survival of Disseminated Dormant Cancer Cells
Cited by: 5
Author(s): Manuela Zangrossi, Probir Chakravarty, Patrizia Romani, Sirio Dupont, Steven Hooper, Erik Sahai, Marco Montagner
Software Mentions: 4
Published: over 5 years ago

10.1002/ajh.25994

The prognostic value of additional copies of <scp>1q21</scp> in multiple myeloma depends on the primary genetic event
Cited by: 20
Author(s): Maurus Locher, Michael Steurer, Emina Jukic, Markus A. Keller, Friedrich Fresser, Carmen Ruepp, Ewald Wöll, Irmgard Verdorfer, Günther Gastl, Wolfgang Willenbacher, Roman Weger, David Nachbaur, Dominik Wolf, Eberhard Gunsilius, Johannes Zschocke, Normann Steiner
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.4535

Reference gene selection for qRT-PCR assays in<i>Stellera chamaejasme</i>subjected to abiotic stresses and hormone treatments based on transcriptome datasets
Cited by: 18
Author(s): Xin Liu, Hongwei Guan, Min Jae Song, Yànpíng Fù, Xiao Han, Lei Meng, Jingyu Ren, Bin Guo, Wei He, Yahui Wei
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-00267-9

Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis
Cited by: 12
Author(s): Anthony R. Soltis, Shmulik Motola, Santiago Vérnia, Christopher Ng, Norman J. Kennedy, Simona Dalin, Bryan J. Matthews, Roger J. Davis, Ernest Fraenkel
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-015-1689-8

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Cited by: 15
Author(s): Lars Eijssen, Varshna Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjić
Software Mentions: 4
Published: about 11 years ago

10.1186/s12935-019-0950-7

A six-gene prognostic model predicts overall survival in bladder cancer patients
Cited by: 37
Author(s): Liwei Wang, Jiazhong Shi, Yaqin Huang, Sha Li, Jingqi Zhang, Hua Ding, Jin Yang, Zhiwen Chen
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13195-021-00892-7

Leukotriene receptor antagonist use and cognitive decline in normal cognition, mild cognitive impairment, and Alzheimer’s dementia
Cited by: 10
Author(s): Lisa Y. Xiong, Michael Ouk, Che‐Yuan Wu, Jennifer S. Rabin, Krista L. Lanctôt, Nathan Herrmann, Sandra E. Black, Jodi D. Edwards, Walter Swardfager
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcimb.2017.00317

Global Epidemiology of Dengue Outbreaks in 1990–2015: A Systematic Review and Meta-Analysis
Cited by: 220
Author(s): Congcong Guo, Zixing Zhou, Zihao Wen, Yumei Liu, Chengli Zeng, Di Xiao, Minglin Ou, Yuge Han, Shiqi Huang, Dandan Liu, Xiaohong Ye, Xiaoqian Zou, Jing Wu, Huanyu Wang, Eddy Y. Zeng, Chunxia Jing, Guang Yang
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2021.658927

Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?
Cited by: 14
Author(s): Carolina Calero Preciado, Joby Boxall, Víctor Soria‐Carrasco, Santiago Martínez, Isabel Douterelo
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0236548

Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe
Cited by: 16
Author(s): Davide Delpiano, Thorsten Uthmeier
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2020.01658

Circulating Tumor Cells Expressing the Prostate Specific Membrane Antigen (PSMA) Indicate Worse Outcome in Primary, Non-Metastatic Triple-Negative Breast Cancer
Cited by: 14
Author(s): Sabine Kasimir‐Bauer, Corinna Keup, Oliver Hoffmann, Siegfried Hauch, Rainer Kimmig, Ann‐Kathrin Bittner
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.9307

Succession of bacterial communities on carrion is independent of vertebrate scavengers
Cited by: 8
Author(s): Cody R. Dangerfield, Ethan Frehner, Evan R. Buechley, Çağan H. Şekercioğlu, William J. Brazelton
Software Mentions: 4
Published: about 6 years ago

10.1186/s13195-018-0394-7

Alzheimer’s disease master regulators analysis: search for potential molecular targets and drug repositioning candidates
Cited by: 62
Author(s): Daiani Machado de Vargas, Marco Antônio De Bastiani, Eduardo R. Zimmer, Fábio Klamt
Software Mentions: 4
Published: about 8 years ago

10.7150/jca.51321

AURKA and FAM83A are prognostic biomarkers and correlated with Tumor-infiltrating Lymphocytes in smoking related Lung Adenocarcinoma
Cited by: 7
Author(s): Mengyu Zhang, Huo Chen, Yingxiao Jiang, Jianyu Liu, Yi-Can Yang, Yunhong Yin, Yi-Qing Qu
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph16040632

Association Between the Activity Space Exposure to Parks in Childhood and Adolescence and Cognitive Aging in Later Life
Cited by: 19
Author(s): Mark Cherrie, Niamh Shortt, Catharine Ward Thompson, Ian J. Deary, Jamie Pearce
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0218899

Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2020.615481

Microbial Flow Within an Air-Phyllosphere-Soil Continuum
Cited by: 19
Author(s): Shu‐Yi‐Dan Zhou, Hu Li, Madeline Giles, Roy Neilson, Xiao‐Ru Yang, Jian‐Qiang Su
Software Mentions: 4
Published: over 5 years ago

10.1007/s00432-021-03557-y

Are there sex differences among colorectal cancer patients in treatment and survival? A Swiss cohort study
Cited by: 1
Author(s): Manuela Limam, Katarina L. Matthes, Giulia Pestoni, Eleftheria Michalopoulou, Leonhard Held, Silvia Dehler, Dimitri Korol, Sabine Rohrmann
Software Mentions: 4
Published: over 5 years ago

10.1186/s12915-020-00860-x

Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models
Cited by: 15
Author(s): Charlène Roussel, Kim De Paepe, Wessam Galia, Jana De Bodt, Sandrine Chalancon, Françoise Leriche, Nathalie Ballet, Sylvain Denis, Monique Alric, Tom Van de Wiele, Stéphanie Blanquet‐Diot
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-89607-4

Viral load, not food availability or temperature, predicts colony longevity in an invasive eusocial wasp with plastic life history
Cited by: 7
Author(s): Kevin J. Loope, Erin E. Wilson Rankin
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers13010072

Prognostic Impact of Pedicle Clamping during Liver Resection for Colorectal Metastases
Cited by: 1
Author(s): Tobias S. Schiergens, Moritz Drefs, M Dörsch, Florian Kühn, Markus Albertsmeier, Hanno Nieß, Markus Bo Schoenberg, Matthias Aßenmacher, Helmut Küchenhoff, Wolfgang E. Thasler, Markus Guba, Martin K. Angele, Markus Rentsch, Jens Werner, Joachim Andrassy
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ajhg.2015.11.018

Autosomal-Dominant Corneal Endothelial Dystrophies CHED1 and PPCD1 Are Allelic Disorders Caused by Non-coding Mutations in the Promoter of OVOL2
Cited by: 65
Author(s): Alice E. Davidson, Petra Lišková, Cerys J. Evans, Ľubica Ďuďáková, Lenka Nosková, Nikolas Pontikos, Hana Hartmannová, Kateřina Hodaňová, Viktor Stránecký, Zbyněk Kozmík, Hannah J. Levis, Nwamaka Juliana Idigo, Noriaki Sasai, Geoffrey J. Maher, James Bellingham, Neyme Veli, Neil D. Ebenezer, Michael E. Cheetham, Julie T. Daniels, Caroline Thaung, Kateřina Jirsová, Vincent Plagnol, Martin Filipec, Stanislav Kmoch, Stephen Tuft, Alison J. Hardcastle
Software Mentions: 4
Published: over 10 years ago

10.3390/cells9020387

Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types
Cited by: 7
Author(s): Marianna Penzo, Rosanna Clima, Davide Treré, Lorenzo Montanaro
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-020-0837-0

Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells
Cited by: 39
Author(s): Jackson A. Hoffman, Brian N. Papas, Kevin W. Trotter, Trevor Archer
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-019-2703-y

FitTetra 2.0 – improved genotype calling for tetraploids with multiple population and parental data support
Cited by: 32
Author(s): Konrad Zych, Gerrit Gort, Chris Maliepaard, Ritsert C. Jansen, Roeland E. Voorrips
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2020.00829

Evolutionary History of the Marchantia polymorpha Complex
Cited by: 9
Author(s): Anna Malin Linde, Weerachon Sawangproh, Nils Cronberg, Péter Szövényi, Ulf Lagercrantz
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pntd.0008703

Complex relationships between Aedes vectors, socio-economics and dengue transmission—Lessons learned from a case-control study in northeastern Thailand
Cited by: 16
Author(s): Bénédicte Fustec, Thipruethai Phanitchat, Mohammad Injamul Hoq, Sirinart Aromseree, Chamsai Pientong, Kesorn Thaewnongiew, Tipaya Ekalaksananan, Michael J. Bangs, Vincent Corbel, Alexander Nast, Hans J. Overgaard
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0214282

DNA methylation among firefighters
Cited by: 13
Author(s): Jin Zhou, Timothy G. Jenkins, Alesia M. Jung, Kyoung Sook Jeong, Jing Zhai, Elizabeth T. Jacobs, Stephanie Griffin, Devi Dearmon-Moore, Sally R. Littau, Wayne F. Peate, Nathan A. Ellis, Peter Lance, Yin Chen, Jefferey L. Burgess
Software Mentions: 4
Published: over 7 years ago

10.3390/vaccines9060664

In Vitro Characterization of the Innate Immune Pathways Engaged by Live and Inactivated Tick-Borne Encephalitis Virus
Cited by: 3
Author(s): Aurora Signorazzi, Jeroen L. A. Pennings, Marilena P. Etna, Malou Noya, Eliana M. Coccia, Anke Huckriede
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2018.00182

Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota
Cited by: 160
Author(s): Helen Groves, Leah Cuthbertson, Phillip James, Miriam F. Moffatt, Michael J. Cox, John S. Tregoning
Software Mentions: 4
Published: over 8 years ago

10.1007/s00216-021-03393-6

Sample preparation strategy for the detection of steroid-like compounds using MALDI mass spectrometry imaging: pulmonary distribution of budesonide as a case study
Cited by: 11
Author(s): Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Davide Amidani, Chiara Catozzi, Francesca Ricci, Fabrizio Salomone, Giuseppe Pieraccini, Barbara Pioselli, Valentina Mileo
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-15-191

Efficient design of meganucleases using a machine learning approach
Cited by: 9
Author(s): Mikhail Zaslavskiy, Claudia Bertonati, Philippe Duchâteau, Aymeric Duclert, George H. Silva
Software Mentions: 4
Published: about 12 years ago

10.1038/s41598-021-89741-z

Differential features of chronic cough according to etiology and the simple decision tree for predicting causes
Cited by: 2
Author(s): Hyeon Kyoung Koo, Woo Kyung Bae, Joon-Shik Moon, Hyun Lee, Jin Woo Kim, Seung Hun Jang, Hyoung Kyu Yoon, Deog Kyeom Kim
Software Mentions: 4
Published: about 5 years ago

10.3389/fendo.2021.705154

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

10.1038/s41416-020-0796-8

Molecular subtypes of oropharyngeal cancer show distinct immune microenvironment related with immune checkpoint blockade response
Cited by: 16
Author(s): Min Hwan Kim, Jaehwan Kim, Ji Min Lee, Jae Woo Choi, Dongmin Jung, Hojin Cho, Hyundeok Kang, Min Hee Hong, Su Jin Heo, Se Heon Kim, Eun Chang Choi, Da Hee Kim, Young Min Park, Sang Woo Kim, Sun Och Yoon, Yoon Woo Koh, Byoung Chul Cho, Hye Ryun Kim
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-019-2789-2

Neural sentence embedding models for semantic similarity estimation in the biomedical domain
Cited by: 18
Author(s): Kathrin Blagec, Hong Xu, Asan Agibetov, Matthias Samwald
Software Mentions: 4
Published: over 7 years ago

10.3389/fendo.2020.581768

Identification of the Biomarkers and Pathological Process of Heterotopic Ossification: Weighted Gene Co-Expression Network Analysis
Cited by: 7
Author(s): Shuang Wang, Jun Tian, Jianzhong Wang, Sizhu Liu, Lianwei Ke, Chaojiang Shang, Jichun Yang, Lin Wang
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.2367

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species
Cited by: 74
Author(s): Isabelle Laforest‐Lapointe, Christian Messier, Steven W. Kembel
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0164461

Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Cited by: 40
Author(s): M. Malvisi, Fiorentina Palazzo, Nicola Morandi, Barbara Lazzari, J. L. Williams, G. Pagnacco, Giulietta Minozzi
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-018-31640-x

Cell type-resolved human lung lipidome reveals cellular cooperation in lung function
Cited by: 28
Author(s): Jennifer Kyle, Gérémy Clair, Gautam Bandyopadhyay, Ravi S. Misra, Erika Zink, Kent Bloodsworth, Anil Shukla, Yina Du, Jacquelyn Lillis, Jason Myers, John M. Ashton, Timothy Bushnell, Matthew Cochran, Gail H. Deutsch, Erin Baker, James P. Carson, Thomas J. Mariani, Yan Xu, Jeffrey A. Whitsett, Gloria S. Pryhuber, Charles Ansong
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0232372

Clinical feasibility of ultrafast intracranial vessel imaging with non-Cartesian spiral 3D time-of-flight MR angiography at 1.5T: An intra-individual comparison study
Cited by: 10
Author(s): Thomas Sartoretti, Elisabeth Sartoretti, Árpád Schwenk, Luuk van Smoorenburg, Manoj Mannil, André Euler, Anton S. Becker, Alex Alfieri, Arash Najafi, Christoph A. Binkert, Michael Wyss, Sabine Sartoretti‐Schefer
Software Mentions: 4
Published: over 6 years ago

10.1007/s00438-020-01735-0

Major latex protein-like encoding genes contribute to Rhizoctonia solani defense responses in sugar beet
Cited by: 16
Author(s): Louise Holmquist, Fredrik Dölfors, Johan Fogelqvist, Jonathan Cohn, Thomas Kraft, Christina Dixelius
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2018.01693

Immunophenotype and Transcriptome Profile of Patients With Multiple Sclerosis Treated With Fingolimod: Setting Up a Model for Prediction of Response in a 2-Year Translational Study
Cited by: 28
Author(s): Ivo Torres, C. Garcı́a, Marco Marconi, Aránzazu García-Grande, Luis Rodríguez‐Esparragoza, Vı́ctor Elvira, Elvira Ramil, Lucía Campos-Ruíz, Ruth García-Hernández, Fátima Al‐Shahrour, Coral Fustero-Torre, Alicia Sánchez-Sanz, Antonio Garcı́a-Merino, A.J. Sánchez López
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-61273-y

Comprehensive transcriptome profiling of Taiwanese colorectal cancer implicates an ethnic basis for pathogenesis
Cited by: 8
Author(s): Shao‐Min Wu, Wen‐Sy Tsai, Sum-Fu Chiang, Yi-Hsuan Lai, Chung‐Pei Ma, Jianhua Wang, Jeng-Feng Lin, Pei-Shan Lu, Chao-Ping Yang, Bertrand Chin‐Ming Tan, Hsuan Liu
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2017.00175

Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury
Cited by: 21
Author(s): Arko Sen, Katherine Gurdziel, Jenney Liu, Qian Wen, Oluwademi O Nuga, Rayanne B. Burl, Maik Hüttemann, Roger Piqué-Regi, Douglas M. Ruden
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-020-6722-x

MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression
Cited by: 15
Author(s): Chin-Sheng Teng, Bing-Heng Wu, Ming‐Ren Yen, Pao‐Yang Chen
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.2575

Monte Carlo simulation of OLS and linear mixed model inference of phenotypic effects on gene expression
Cited by: 1
Author(s): Jeffrey A. Walker
Software Mentions: 4
Published: almost 10 years ago

10.3389/fpls.2021.612382

High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum
Cited by: 15
Author(s): Aleksey A. Penin, Artem S. Kasianov, Anna V. Klepikova, Ilya Kirov, Evgeny S. Gerasimov, А Н Фесенко, Maria D. Logacheva
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-31545-9

Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species
Cited by: 21
Author(s): Giulia Magoga, D. Coral Şahin, Diego Fontaneto, Matteo Montagna
Software Mentions: 4
Published: almost 8 years ago