10.2196/17110

Predicting Metabolic Syndrome With Machine Learning Models Using a Decision Tree Algorithm: Retrospective Cohort Study
Cited by: 26
Author(s): Cheng Yu, Yu Lin, Chang Hsien Lin, Sen Te Wang, Shiyng Yu Lin, Sanders H. Lin, Jenny L Wu, Shy Shin Chang
Software Mentions: 7
Published: over 6 years ago

10.3758/s13428-017-0862-1

Estimating psychological networks and their accuracy: A tutorial paper
Cited by: 1,743
Author(s): Sacha Epskamp, Denny Borsboom, Eiko I. Fried
Software Mentions: 7
Published: over 9 years ago

10.1186/s12859-015-0568-2

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns
Cited by: 95
Author(s): Tiphaine Martin, İdil Yet, Pei-Chien Tsai, Jordana T. Bell
Software Mentions: 7
Published: about 11 years ago

10.1371/journal.pone.0217708

Nest characteristics determine nest microclimate and affect breeding output in an Antarctic seabird, the Wilson’s storm-petrel
Cited by: 13
Author(s): Rosanne J. Michielsen, Anne N. M. A. Ausems, Dariusz Jakubas, Michał Pętlicki, Joanna Plenzler, Judy Shamoun‐Baranes, Katarzyna Wojczulanis‐Jakubas
Software Mentions: 7
Published: about 7 years ago

10.3389/fnbeh.2019.00157

Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in Adulthood
Cited by: 37
Author(s): Jordan Marrocco, Jason D. Gray, Joshua F. Kogan, Nathan R. Einhorn, Emma M. O’Cinneide, Todd G. Rubin, Thomas Carroll, Eric F. Schmidt, Bruce S. McEwen
Software Mentions: 7
Published: almost 7 years ago

10.3389/fonc.2020.580263

A Prognostic Microenvironment-Related Immune Signature via ESTIMATE (PROMISE Model) Predicts Overall Survival of Patients With Glioma
Cited by: 23
Author(s): Huaide Qiu, Yongqiang Li, Shupeng Cheng, Jiahui Li, Chuan He, Jianan Li
Software Mentions: 7
Published: over 5 years ago

10.1038/s41422-019-0168-1

Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
Cited by: 64
Author(s): Rui Gao, Xingqun Liang, Sirisha Cheedipudi, Julio Cordero, Xiyi Jiang, Qingquan Zhang, Luca Caputo, Stefan Günther, Carsten Kuenne, Yongcheng Ren, Shoumo Bhattacharya, Xuejun Yuan, Guillermo Barreto, Yihan Chen, Thomas Braun, Sylvia M. Evans, Yunfu Sun, Gergana Dobreva
Software Mentions: 7
Published: about 7 years ago

10.3389/fcell.2019.00283

A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome
Cited by: 2
Author(s): Selma L van Esveld, Şirin Cansız-Arda, Fenna Hensen, Robin van der Lee, Martijn Huynen, Johannes N. Spelbrink
Software Mentions: 7
Published: over 6 years ago

10.1186/1472-6807-13-2

Designing and benchmarking the MULTICOM protein structure prediction system
Cited by: 25
Author(s): Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng
Software Mentions: 7
Published: over 13 years ago

10.1038/s41598-018-34138-8

A network analysis of female sexual function: comparing symptom networks in women with decreased, increased, and stable sexual desire
Cited by: 8
Author(s): Annika Gunst, Marlene Werner, Lourens J. Waldorp, Ellen Laan, Marianne Källström, Patrick Jern
Software Mentions: 7
Published: over 7 years ago

10.3389/fonc.2020.596318

Single-Cell RNA-Seq Analysis Reveals Microenvironmental Infiltration of Plasma Cells and Hepatocytic Prognostic Markers in HCC With Cirrhosis
Cited by: 40
Author(s): Siwen Zhang, Zhenhao Liu, Dan Wu, Lanming Chen, Lu Xie
Software Mentions: 7
Published: over 5 years ago

10.3390/nu12102934

Dietary Sodium Intake and Risk of Cardiovascular Disease: A Systematic Review and Dose-Response Meta-Analysis
Cited by: 64
Author(s): Yijie Wang, Tzu‐Lin Yeh, Ming‐Chieh Shih, Yu‐Kang Tu, Kuo–Liong Chien
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12864-019-6155-6

A framework using topological pathways for deeper analysis of transcriptome data
Cited by: 0
Author(s): Yue Zhao, Stephanie Piekos, Tham H. Hoang, Dong-Guk Shin
Software Mentions: 7
Published: over 6 years ago

10.1038/s41419-021-04067-y

Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4
Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: almost 5 years ago

10.3389/fonc.2021.618187

CCR4, CCR8, and P2RY14 as Prognostic Factors in Head and Neck Squamous Cell Carcinoma Are Involved in the Remodeling of the Tumor Microenvironment
Cited by: 9
Author(s): Liangliang Meng, Xiaoxi He, Hong Qin, Bo Qiao, Xiao Zhang, Bin Wu, Xiaobo Zhang, Yingtian Wei, Jing Li, Zhaoxiang Ye, Yueyong Xiao
Software Mentions: 7
Published: over 5 years ago

10.1155/2021/2628824

A Potential ceRNA Network for Neurological Damage in Preterm Infants
Cited by: 7
Author(s): Hui‐Zi Jin, Xinlan Liang, Zhenyu Cai
Software Mentions: 7
Published: almost 5 years ago

10.1186/1471-2105-12-267

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
Cited by: 39
Author(s): Xutao Deng
Software Mentions: 7
Published: about 15 years ago

10.12688/f1000research.19410.1

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
Cited by: 0
Author(s): Shian Su, Vincent J. Carey, Lori Shepherd, Matthew E. Ritchie, Martin Morgan, Sean Davis
Software Mentions: 7
Published: about 7 years ago

10.3389/fphar.2020.00076

Efficacy of Chinese Herbal Formula Sini Zuojin Decoction in Treating Gastroesophageal Reflux Disease: Clinical Evidence and Potential Mechanisms
Cited by: 10
Author(s): Shaowei Li, Mengfen Huang, Guojing Wu, Wei-Han Huang, Zhanhui Huang, Xiaoqian Yang, Jinming Ou, Qipeng Wei, Chengli Liu, YU Shaoyuan
Software Mentions: 7
Published: over 6 years ago

10.1107/S2059798320003769

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries
Cited by: 0
Author(s): J.M. de la Rosa-Trevín, Pedro Alberto Hernández Viga, Joaquı́n Otón, Erik Lindahl
Software Mentions: 7
Published: over 6 years ago

10.1002/ece3.7810

Visitation of artificial watering points by the red fox (<i>Vulpes vulpes</i>) in semiarid Australia
Cited by: 2
Author(s): David A. Roshier, Johannes Signer, Andrew Carter
Software Mentions: 7
Published: about 5 years ago

10.3390/ijerph15122893

Comorbidity of Symptoms of Alcohol and Cannabis Use Disorders among a Population-Based Sample of Simultaneous Users. Insight from a Network Perspective
Cited by: 9
Author(s): Stéphanie Baggio, Marlène Sapin, Yasser Khazaal, Joseph Studer, Hans Wolff, Gerhard Gmel
Software Mentions: 7
Published: over 7 years ago

10.3389/fpsyt.2021.680811

TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatry
Cited by: 55
Author(s): Stefan Frässle, Eduardo A. Aponte, Saskia Bollmann, Kay H. Brodersen, Ting Cao, Olivia K. Harrison, Sarah M. Harrison, Jakob Heinzle, Sandra Iglesias, Lars Kasper, Ekaterina I. Lomakina, Christoph Mathys, Matthias Müller-Schrader, Inês Pereira, Frederike H. Petzschner, Sudhir Raman, Dario Schöbi, Birte Toussaint, Lilian Weber, Yu Yao, Klaas Enno Stephan
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pbio.3000301

Proteome-wide analysis of chaperone-mediated autophagy targeting motifs
Cited by: 125
Author(s): Philipp Kirchner, Mathieu Bourdenx, Julio Madrigal‐Matute, Simoni Tiano, Antonio Díaz, Boris Bartholdy, Britta Will, Ana María Cuervo
Software Mentions: 7
Published: about 7 years ago

10.1111/mec.15366

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts
Cited by: 36
Author(s): María Lucena-Pérez, Elena Marmesat, Daniel Kleinman‐Ruiz, Begoña Martínez‐Cruz, Karolina Wȩcek, Alexander P. Saveljev, Ivan V. Seryodkin, И. М. Охлопков, Mikhail G. Dvornikov, Jurijs Ozoliņš, Naranbaatar Galsandorj, Milan Paunović, Mirosław Ratkiewicz, Krzysztof Schmidt, José A. Godoy
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2021.732211

A Ferroptosis-Related Prognostic Signature Based on Antitumor Immunity and Tumor Protein p53 Mutation Exploration for Guiding Treatment in Patients With Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Xin Fan, YangShaobo Ou, Huijie Liu, Liangzhen Zhan, Xiaohui Zhu, Mingyang Cheng, Qun Li, Dongmei Yin, Lan Liao
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12885-017-3689-3

GRcalculator: an online tool for calculating and mining dose–response data
Cited by: 57
Author(s): Nicholas Clark, Marc Hafner, Michal Kouril, Liz Williams, Jeremy Muhlich, Marcin Pilarczyk, Mario Niepel, Peter K. Sorger, Mario Medvedovic
Software Mentions: 7
Published: over 8 years ago

10.1038/s41416-019-0571-x

Prognosis and modulation mechanisms of COMMD6 in human tumours based on expression profiling and comprehensive bioinformatics analysis
Cited by: 24
Author(s): Mi Yang, Weiqiang Huang, Yaling Sun, Huazhen Liang, Min Chen, Xixi Wu, Xiaoqing Wang, Longshan Zhang, Xiaobin Cheng, Yu Fan, Hua Pan, Longhua Chen, Jian Guan
Software Mentions: 7
Published: almost 7 years ago

10.3389/fimmu.2021.639634

Development and Validation of a Novel Prognostic Model for Acute Myeloid Leukemia Based on Immune-Related Genes
Cited by: 10
Author(s): Ran Li, Zuoyou Ding, Peng Jin, Shishuang Wu, Ge Jiang, Rufang Xiang, Wenfang Wang, Zhen Jin, Xiaoyang Li, Kai Xue, Xiaolu Wu, Junmin Li
Software Mentions: 7
Published: about 5 years ago

10.3389/fninf.2018.00030

Information-Theoretical Analysis of EEG Microstate Sequences in Python
Cited by: 13
Author(s): Frederic von Wegner, Helmut Laufs
Software Mentions: 7
Published: about 8 years ago

10.1186/1471-2105-14-145

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform
Cited by: 10
Author(s): Josh Eckels, Cory Nathe, Elizabeth Nelson, Sara G Shoemaker, Elizabeth Van Nostrand, Nicole L. Yates, Vicki C. Ashley, Linda J. Harris, Mark Bollenbeck, Youyi Fong, Georgia D. Tomaras, Britt Piehler
Software Mentions: 7
Published: about 13 years ago

10.1098/rsos.170073

Predictors and immunological correlates of sublethal mercury exposure in vampire bats
Cited by: 44
Author(s): Daniel J. Becker, Matthew M. Chumchal, Alexandra B. Bentz, Steven G. Platt, Gábor Á. Czirják, Thomas R. Rainwater, Sonia Altizer, Daniel G. Streicker
Software Mentions: 7
Published: about 9 years ago

10.1080/19490976.2020.1794466

Alterations of gut microbiota composition in neonates conceived by assisted reproductive technology and its relation to infant growth
Cited by: 6
Author(s): Qun Lü, Yuan Lin, Ting Chen, Hong Lv, Feiyang Diao, Cong Liu, Meijuan Peng, Xiufeng Ling, Hong Li, Yun Wang, Yongyue Wei, Jiangbo Du, Guangfu Jin, Yankai Xia, Hongxia Ma, Xingyin Liu, Hongbing Shen, Zhibin Hu
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0171072

Forest biomass density across large climate gradients in northern South America is related to water availability but not with temperature
Cited by: 67
Author(s): Esteban Álvarez-Dávila, Luis Cayuela, Sebastián González‐Caro, Ana M. Aldana, Pablo R. Stevenson, Oliver L. Phillips, Álvaro Cogollo, M. C. Peñuela, Patricio von Hildebrand, Eliana Jiménez, Omar Melo, Ana Catalina Londoño-Vega, Irina Mendoza, Oswaldo Velásquez, Fernando Fernández, Marcela Serna, Cesar Velázquez-Rua, Doris Benítez, José María Rey‐Benayas
Software Mentions: 7
Published: over 9 years ago

10.3390/s20174741

Use of Predicted Behavior from Accelerometer Data Combined with GPS Data to Explore the Relationship between Dairy Cow Behavior and Pasture Characteristics
Cited by: 20
Author(s): Lucile Riaboff, Sébastien Couvreur, Aurélien Madouasse, Marie Roig-Pons, Sébastien Aubin, Patrick Massabie, Alain Chauvin, Nicolas Bédère, Guy Plantier
Software Mentions: 7
Published: almost 6 years ago

10.3389/fgene.2020.590660

Identification of Key Genes and Potential New Biomarkers for Ovarian Aging: A Study Based on RNA-Sequencing Data
Cited by: 14
Author(s): Lingwei Ma, Huan Lu, Runhua Chen, Meng Wu, Yan Jin, Jinjin Zhang, Shixuan Wang
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.635863

Identification and Validation of a Novel DNA Damage and DNA Repair Related Genes Based Signature for Colon Cancer Prognosis
Cited by: 16
Author(s): Xuequan Wang, Shiwen Xu, Wei Wang, Shang Guo Piao, Xin-Li Mao, Xian-Bin Zhou, Yi Wang, Weidan Wu, Liping Ye, Shaowei Li
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.739470

Construction on of a Ferroptosis-Related lncRNA-Based Model to Improve the Prognostic Evaluation of Gastric Cancer Patients Based on Bioinformatics
Cited by: 19
Author(s): Jing Pan, Xinyue Zhang, Xuedong Fang, Zhuoyuan Xin
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmicb.2018.01620

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory
Cited by: 26
Author(s): Flora Jane Mary O'Brien, Marc G. Dumont, Jeremy S. Webb, Guy M. Poppy
Software Mentions: 7
Published: almost 8 years ago

10.1002/ece3.6479

Generation and application of river network analogues for use in ecology and evolution
Cited by: 38
Author(s): Luca Carraro, Enrico Bertuzzo, Emanuel A. Fronhofer, Reinhard Furrer, Isabelle Gounand, Andrea Rinaldo, Florian Altermatt
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0258157

Dynamically expressed genes provide candidate viability biomarkers in a model coccidian
Cited by: 4
Author(s): Matthew S. Tucker, Celia O’Brien, Mark C. Jenkins, Benjamin M. Rosenthal
Software Mentions: 7
Published: over 4 years ago

10.1128/mSphere.00737-20

Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus <i>Cryphonectria</i>
Cited by: 16
Author(s): Lea Stauber, Simone Prospero, Daniel Croll
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1008354

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
Cited by: 5
Author(s): Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Škrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz
Software Mentions: 7
Published: over 5 years ago

10.1002/ece3.2824

Canada lynx use of burned areas: Conservation implications of changing fire regimes
Cited by: 26
Author(s): Carmen Vanbianchi, Melanie A. Murphy, Karen E. Hodges
Software Mentions: 7
Published: over 9 years ago

10.1038/srep29532

Delineation of autoantibody repertoire through differential proteogenomics in hepatitis C virus-induced cryoglobulinemia
Cited by: 12
Author(s): Masato Ogishi, Hiroshi Yotsuyanagi, Kyoji Moriya, Kazuhiko Koike
Software Mentions: 7
Published: almost 10 years ago

10.1371/journal.pone.0242191

EZH2 is a negative prognostic biomarker associated with immunosuppression in hepatocellular carcinoma
Cited by: 20
Author(s): Baoqiang Guo, Xiaohong Tan, Hong Cen
Software Mentions: 7
Published: over 5 years ago

10.1038/srep28657

Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood
Cited by: 57
Author(s): Kristian Almstrup, Marie Johansen, Alexander Busch, Casper P Hagen, John Nielsen, Jørgen Holm Petersen, Anders Juul
Software Mentions: 7
Published: about 10 years ago

10.1038/s41598-020-66404-z

Does entry to center-based childcare affect gut microbial colonization in young infants?
Cited by: 9
Author(s): Gerben D. A. Hermes, Henrik Eckermann, Willem M. de Vos, Carolina de Weerth
Software Mentions: 7
Published: about 6 years ago

10.1186/s13148-019-0651-z

Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
Cited by: 18
Author(s): Shivani Kamdar, Ruth Isserlin, Theodorus van der Kwast, Alexandre R. Zlotta, Gary D. Bader, Neil Fleshner, Bharati Bapat
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0221617

Free will beliefs are better predicted by dualism than determinism beliefs across different cultures
Cited by: 19
Author(s): David Wisniewski, Robert Deutschländer, John‐Dylan Haynes
Software Mentions: 7
Published: almost 7 years ago

10.3389/fmicb.2021.658116

Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of “Cherry-Red” Tobacco
Cited by: 4
Author(s): Yonglei Jiang, Xing Chen, Gaokun Zhao, Jiahong Liu, Yan Xie, Yong Li, Huaguo Gu, Congming Zou
Software Mentions: 7
Published: almost 5 years ago

10.1186/s40168-019-0684-8

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Cited by: 38
Author(s): Luís Pedro Coelho, Renato Alves, Paulo P. Monteiro, Jaime Huerta-Cepas, Ana T. Freitas, Peer Bork
Software Mentions: 7
Published: about 7 years ago

10.3389/fmicb.2017.00358

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions
Cited by: 38
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: over 9 years ago

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: over 6 years ago

10.1186/s13148-018-0510-3

Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception
Cited by: 25
Author(s): Davide Gentilini, Edgardo Somigliana, Luca Pagliardini, Elisa Rabellotti, Paolo Garagnani, Luisa Bernardinelli, Enrico Papaleo, Massimo Candiani, Anna Maria Di Blasio, Paola Viganò
Software Mentions: 7
Published: about 8 years ago

10.12688/f1000research.16032.3

epiflows: an R package for risk assessment of travel-related spread of disease
Cited by: 3
Author(s): Paula Moraga, Ilaria Dorigatti, Zhian N. Kamvar, Paweł Piątkowski, Salla Toikkanen, VP Nagraj, Christl A. Donnelly, Thibaut Jombart
Software Mentions: 7
Published: almost 7 years ago

10.3390/brainsci11060735

Statistical and Machine Learning Link Selection Methods for Brain Functional Networks: Review and Comparison
Cited by: 3
Author(s): Ilinka Ivanoska, Kire Trivodaliev, Slobodan Kalajdziski, Massimiliano Zanin
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.53281

Feedback inhibition and its control in an insect olfactory circuit
Cited by: 8
Author(s): Subhasis Ray, Zane Aldworth, Mark Stopfer
Software Mentions: 7
Published: over 6 years ago

10.3390/ijerph17217771

The Quality of Work Index and the Quality of Employment Index: A Multidimensional Approach of Job Quality and Its Links to Well-Being at Work
Cited by: 23
Author(s): Georges Steffgen, Philipp Sischka, Martha Fernandez de Henestrosa
Software Mentions: 7
Published: over 5 years ago

10.1007/s00401-021-02263-w

Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease
Cited by: 143
Author(s): Emma Gerrits, Nieske Brouwer, Susanne M. Kooistra, Maya E. Woodbury, Yannick Vermeiren, Mirjam Lambourne, Jan Mulder, Markus P. Kummer, Thomas Möller, Knut Biber, Wilfred F. A. den Dunnen, Peter Paul De Deyn, Bart J. L. Eggen, Erik Boddeke
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0236142

Diet flexibility and growth of the early herbivorous juvenile crown-of-thorns sea star, implications for its boom-bust population dynamics
Cited by: 17
Author(s): Dione J. Deaker, Benjamin Mos, Huang-An Lin, Corinne Lawson, Claire Budden, Symon A. Dworjanyn, Maria Byrne
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-020-76207-x

Protecting nursery areas without fisheries management is not enough to conserve the most endangered parrotfish of the Atlantic Ocean
Cited by: 13
Author(s): Natalia Roos, Guilherme O. Longo, María Grazia Pennino, Ronaldo B. Francini‐Filho, Adriana Rosa Carvalho
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2020.00789

Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach
Cited by: 18
Author(s): Nico Salmaso, Bruno Adriano, Massimo Pindo
Software Mentions: 7
Published: about 6 years ago

10.7554/eLife.64090

Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival
Cited by: 44
Author(s): Paul Guilhamon, Charles Chesnelong, Michelle Kushida, Ana Nikolić, Divya Singhal, Graham MacLeod, Seyed Ali Madani Tonekaboni, Florence M.G. Cavalli, Christopher Arlidge, Nishani Rajakulendran, Naghmeh Rastegar, Xiaoguang Hao, Rozina Hassam, Laura J. Smith, Heather Whetstone, Fiona J. Coutinho, Bettina Nadorp, Katrina Ellestad, H. Artee Luchman, Jennifer A. Chan, Molly S. Shoichet, Michael D. Taylor, Benjamin Haibe‐Kains, Samuel Weiss, Stéphane Angers, Marco Gallo, Peter B. Dirks, Mathieu Lupien
Software Mentions: 7
Published: over 5 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: over 9 years ago

10.1038/s42003-021-02437-y

Neocortical inhibitory interneuron subtypes are differentially attuned to synchrony- and rate-coded information
Cited by: 3
Author(s): Luke Y. Prince, Matthew M Tran, Dorian Grey, Lydia Saad, Helen Chasiotis, Jeehyun Kwag, Michael Köhl, Blake A Richards
Software Mentions: 7
Published: almost 5 years ago

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-021-81668-9

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen
Cited by: 23
Author(s): Laura Glendinning, Buğra Genç, R. J. Wallace, Mick Watson
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2020.566619

Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers
Cited by: 13
Author(s): Anita Dame-Korevaar, Jannigje G. Kers, Jeanet van der Goot, Francisca C. Velkers, Daniela Ceccarelli, Dik Mevius, Arjan Stegeman, E.A.J. Fischer
Software Mentions: 7
Published: over 5 years ago

10.3390/s20154131

Framework and Methodology for Establishing Port-City Policies Based on Real-Time Composite Indicators and IoT: A Practical Use-Case
Cited by: 8
Author(s): Ignacio Lacalle, Andreu Belsa, Rafael Vaño, Carlos E. Palau
Software Mentions: 7
Published: almost 6 years ago

10.3389/fimmu.2020.01166

Non-sterilizing, Infection-Permissive Vaccination With Inactivated Influenza Virus Vaccine Reshapes Subsequent Virus Infection-Induced Protective Heterosubtypic Immunity From Cellular to Humoral Cross-Reactive Immune Responses
Cited by: 6
Author(s): Angela Choi, Lorena Itatí Ibáñez, Shirin Strohmeier, Florian Krammer, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: about 6 years ago

10.3389/fcell.2021.648279

Prognostic Value of a Novel Signature With Nine Hepatitis C Virus-Induced Genes in Hepatic Cancer by Mining GEO and TCGA Databases
Cited by: 5
Author(s): Jianming Wei, Bo Wang, Xibo Gao, Daqing Sun
Software Mentions: 7
Published: almost 5 years ago

10.3389/fimmu.2021.665312

An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells
Cited by: 8
Author(s): James Davies, Andrés F. Vallejo, Sofía Sirvent, Gemma Porter, Kalum Clayton, Yamkela Qumbelo, Patrick S. Stumpf, Jonathan West, Clive M. Gray, Nyaradzo T. L. Chigorimbo‐Murefu, Ben D. MacArthur, Marta E. Polak
Software Mentions: 7
Published: about 5 years ago

10.14814/phy2.14880

Animal blood in translational research: How to adjust animal blood viscosity to the human standard
Cited by: 6
Author(s): Paul Ecker, Andreas Sparer, Benjamin Lukitsch, Martin Elenkov, Monika Seltenhammer, Richard Crevenna, Margit Gfoehler, Michael Harasek, Ursula Windberger
Software Mentions: 7
Published: about 5 years ago

10.3389/fimmu.2021.634127

Immunophenotyping of Peripheral Blood Mononuclear Cells in Septic Shock Patients With High-Dimensional Flow Cytometry Analysis Reveals Two Subgroups With Differential Responses to Immunostimulant Drugs
Cited by: 4
Author(s): Ya Wang, Brian Gloss, Benjamin Tang, Suat Dervish, Brigitte Santner-Nanan, Christina Whitehead, Kristy Masters, Kristen K. Skarratt, Sally Teoh, Stephen D. Schibeci, Nicole Fewings, Chrystelle Brignone, Frédéric Triebel, David R. Booth, Anthony S. McLean, Marek Nalos
Software Mentions: 7
Published: over 5 years ago

10.3389/fmolb.2021.624951

Metabolism-Relevant Molecular Classification Identifies Tumor Immune Microenvironment Characterization and Immunotherapeutic Effect in Cervical Cancer
Cited by: 4
Author(s): Luyi Li, Hui Gao, Danhan Wang, Hao Jiang, Hongzhu Wang, Jiajian Yu, Xin Jiang, Changjiang Huang
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13321-019-0338-7

Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview
Cited by: 30
Author(s): Ralf Weiskirchen, Sabine Weiskirchen, Philipp Kim, Robert Winkler
Software Mentions: 7
Published: over 7 years ago

10.12688/f1000research.15830.2

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
Cited by: 2
Author(s): Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael Reich, Jill P. Mesirov
Software Mentions: 7
Published: about 7 years ago

10.3389/fimmu.2021.691811

Immune Infiltrating Cells-Derived Risk Signature Based on Large-scale Analysis Defines Immune Landscape and Predicts Immunotherapy Responses in Glioma Tumor Microenvironment
Cited by: 36
Author(s): Nan Zhang, Hao Zhang, Zeyu Wang, Ziyu Dai, Xun Zhang, Quan Cheng, Zhixiong Liu
Software Mentions: 7
Published: almost 5 years ago

10.1111/1365-2656.12765

Using host species traits to understand the consequences of resource provisioning for host-parasite interactions
Cited by: 46
Author(s): Daniel J. Becker, Daniel G. Streicker, Sonia Altizer
Software Mentions: 7
Published: over 8 years ago

10.1002/ece3.5188

Invasive species removal increases species and phylogenetic diversity of wetland plant communities
Cited by: 12
Author(s): Shane C. Lishawa, Beth A. Lawrence, Dennis A. Albert, Daniel J. Larkin, Nancy C. Tuchman
Software Mentions: 7
Published: about 7 years ago

10.3389/fonc.2021.636565

Identification and Development of Subtypes With Poor Prognosis in Pan-Gynecological Cancer Based on Gene Expression in the Glycolysis-Cholesterol Synthesis Axis
Cited by: 6
Author(s): Guangwei Wang, Xiaofei Liu, Dandan Wang, Meige Sun, Qing Yang
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-43758-7

In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival
Cited by: 2
Author(s): Danish Memon, Jing Bi, Crispin Miller
Software Mentions: 7
Published: about 7 years ago

10.1038/s41598-017-15712-y

Genome-wide analyses of long noncoding RNA expression profiles in lung adenocarcinoma
Cited by: 20
Author(s): Peng Zhang, Jun Wang, Bin Shan, Fulai Yuan, Bin Li, Yeping Dong, Wei Peng, Weisong Shi, Yuanda Cheng, Yang Gao, Chunfang Zhang, Chaojun Duan
Software Mentions: 7
Published: over 8 years ago

10.1016/j.molcel.2021.03.013

Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression
Cited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: about 5 years ago

10.1002/ece3.3242

Using digital soil maps to infer edaphic affinities of plant species in Amazonia: Problems and prospects
Cited by: 29
Author(s): Gabriel M. Moulatlet, Gabriela Zuquim, Fernando O. G. Figueiredo, Samuli Lehtonen, Thaíse Emilio, Kalle Ruokolainen, Hanna Tuomisto
Software Mentions: 7
Published: almost 9 years ago

10.7554/eLife.60176

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
Cited by: 21
Author(s): Taro Maeda, Shunichi Takahashi, Takao Yoshida, Shigeru Shimamura, Yoshihiro Takaki, Yukiko Nagai, Atsushi Toyoda, Yutaka Suzuki, Asuka Arimoto, Hisaki Ishii, Nori Satoh, Tomoaki Nishiyama, Mitsuyasu Hasebe, Tadashi Maruyama, Jun Minagawa, Junichi Obokata, Shuji Shigenobu
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2018.01100

nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine
Cited by: 10
Author(s): Prabina Kumar Meher, Tanmaya Kumar Sahu, Jyotilipsa Mohanty, Shachi Gahoi, P. Supriya, Monendra Grover, Atmakuri Ramakrishna Rao
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: over 15 years ago

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: over 5 years ago

10.1186/s13073-016-0334-8

Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer
Cited by: 12
Author(s): Kyle Halliwill, David A. Quigley, Hio Chung Kang, Reyno Del Rosario, David G. Ginzinger, Allan Balmain
Software Mentions: 7
Published: almost 10 years ago

10.1371/journal.pone.0224693

ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells
Cited by: 15
Author(s): Samuel A. Danziger, David L. Gibbs, Ilya Shmulevich, Mark McConnell, Matthew Trotter, Frank Schmitz, David J Reiss, Alexander V. Ratushny
Software Mentions: 7
Published: over 6 years ago

10.3389/fnsys.2021.692152

Age-Related Variations in Regional White Matter Volumetry and Microstructure During the Post-adolescence Period: A Cross-Sectional Study of a Cohort of 1,713 University Students
Cited by: 4
Author(s): Ami Tsuchida, Alexandre Laurent, Fabrice Crivello, Laurent Petit, Antonietta Pepe, Naka Beguedou, Stéphanie Debette, Christophe Tzourio, Bernard Mazoyer
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12859-021-04326-x

SNPxE: SNP-environment interaction pattern identifier
Cited by: 2
Author(s): Hui‐Yi Lin, Po‐Yu Huang, Tung-Sung Tseng, Jong Y. Park
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12859-018-2370-4

GPrank: an R package for detecting dynamic elements from genome-wide time series
Cited by: 7
Author(s): Hande Topa, Antti Honkela
Software Mentions: 7
Published: over 7 years ago

10.3390/plants10010029

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils
Cited by: 6
Author(s): Arfang Badji, Lewis Machida, Daniel Bomet Kwemoi, Frank Kumi, Dennis Okii, Natasha Mwila, Symphorien Agbahoungba, Angele Ibanda, Astère Bararyenya, Selma Ndapewa Nghituwamhata, Thomas Odong, Peter Wasswa, Michael Otim, Mildred Ochwo-Ssemakula, Herbert Talwana, Godfrey Asea, Samuel Kyamanywa, Patrick Rubaihayo
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.8056

Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral
Cited by: 18
Author(s): Mallory M. Rice, Rebecca L. Maher, Rebecca Vega Thurber, Deron E. Burkepile
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2019.00774

A Hybrid Ensemble Approach for Identifying Robust Differentially Methylated Loci in Pan-Cancers
Cited by: 3
Author(s): Qi Tian, Jianxiao Zou, Yuan Fang, Zhongli Yu, Jie Tang, Ying Song, Shicai Fan
Software Mentions: 7
Published: almost 7 years ago

10.1002/ctm2.500

Single‐cell transcriptomes reveal heterogeneity of high‐grade serous ovarian carcinoma
Cited by: 29
Author(s): Qian Hao, Jiajia Li, Qinghua Zhang, Fei Xu, Bangxiang Xie, Hua Lu, Xiaohua Wu, Xiang Zhou
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0132866

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
Cited by: 43
Author(s): Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, Bingyu Chen, Dongsheng Huang
Software Mentions: 7
Published: almost 11 years ago