10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-018-31154-6

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis
Cited by: 156
Author(s): Hendrik Nolte, Thomas MacVicar, Frederik Tellkamp, Marcus Krüger
Software Mentions: 11
Published: almost 8 years ago

10.1242/bio.018713

3D for the people: multi-camera motion capture in the field with consumer-grade cameras and open source software
Cited by: 65
Author(s): Brandon E. Jackson, Dennis Evangelista, Dylan D. Ray, Tyson L. Hedrick
Software Mentions: 11
Published: almost 10 years ago

10.3389/fphys.2020.00845

Dynamic Courtship Signals and Mate Preferences in Sepia plangon
Cited by: 5
Author(s): Alejandra López Galán, Wen-Sung Chung, N. Justin Marshall
Software Mentions: 11
Published: almost 6 years ago

10.3389/fpls.2021.657796

Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat
Cited by: 8
Author(s): Eva C Henningsen, Vahid Omidvar, Rafael Della Coletta, Jean Michel Michno, Erin Gilbert, Feng Li, Marisa E. Miller, Chad L. Myers, Sean P. Gordon, John P. Vogel, Brian J. Steffenson, Shahryar F. Kianian, Cory D. Hirsch, Melania Figueroa
Software Mentions: 11
Published: about 5 years ago

10.3389/fimmu.2021.599207

Molecular and Clinical Characterization of LAG3 in Breast Cancer Through 2994 Samples
Cited by: 15
Author(s): Qiang Liu, Yihang Qi, Jie Zhai, Xiangyi Kong, Xiangyu Wang, Zhongzhao Wang, Yi Fang, Jing Wang
Software Mentions: 11
Published: almost 5 years ago

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: over 6 years ago

10.1038/s41598-021-94656-w

A global assessment of surveillance methods for dominant malaria vectors
Cited by: 4
Author(s): Bram van de Straat, Tanya L. Russell, Kyran M. Staunton, Marianne Sinka, Thomas R. Burkot
Software Mentions: 11
Published: almost 5 years ago

10.1186/s12859-018-2105-6

Building protein-protein interaction networks for Leishmania species through protein structural information
Cited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 8 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 16 years ago

10.1038/s41598-021-82043-4

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: over 5 years ago

10.3390/cancers12030692

Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles
Cited by: 29
Author(s): Geoffroy Walbrecq, Odile Lecha, Anthoula Gaigneaux, Miriam Rebecca Fougeras, Demetra Philippidou, Christiane Margue, Miléne Tetsi Nomigni, François Bernardin, Gunnar Dittmar, Iris Behrmann, Stephanie Kreis
Software Mentions: 11
Published: over 6 years ago

10.1002/ece3.6904

Light might suppress both types of sound‐evoked antipredator flight in moths
Cited by: 2
Author(s): Theresa Hügel, Holger R. Goerlitz
Software Mentions: 11
Published: over 5 years ago

10.3389/fbioe.2020.00101

The Integrated Transcriptome Bioinformatics Analysis Identifies Key Genes and Cellular Components for Spinal Cord Injury-Related Neuropathic Pain
Cited by: 8
Author(s): Runzhi Huang, Tong Meng, Rui Zhu, Lijuan Zhao, Dianwen Song, Huabin Yin, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.3389/fpsyg.2018.02251

Disabled or Cyborg? How Bionics Affect Stereotypes Toward People With Physical Disabilities
Cited by: 28
Author(s): Bertolt Meyer, Frank Asbrock
Software Mentions: 11
Published: over 7 years ago

10.3389/fmicb.2019.01770

Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder
Cited by: 55
Author(s): Bingdong Liu, Win Lin, Shujie Chen, Ting Xiang, Yifan Yang, Yulong Yin, Guohuan Xu, Zhihong Liu, Li Liu, Jiyang Pan, Liwei Xie
Software Mentions: 11
Published: almost 7 years ago

10.1186/s41235-018-0133-4

App icon similarity and its impact on visual search efficiency on mobile touch devices
Cited by: 5
Author(s): Anna Trapp, Carolin Wienrich
Software Mentions: 11
Published: over 7 years ago

10.1111/mec.13636

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event
Cited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: about 10 years ago

10.1371/journal.pone.0151959

Physiological Limits along an Elevational Gradient in a Radiation of Montane Ground Beetles
Cited by: 28
Author(s): R. O. Slatyer, Sean D. Schoville
Software Mentions: 11
Published: about 10 years ago

10.1128/mSystems.00316-20

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
Cited by: 8
Author(s): Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
Software Mentions: 11
Published: over 5 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 10 years ago

10.3389/fninf.2019.00012

A Serverless Tool for Platform Agnostic Computational Experiment Management
Cited by: 13
Author(s): Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
Software Mentions: 11
Published: over 7 years ago

10.12688/f1000research.18458.2

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Cited by: 15
Author(s): Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Software Mentions: 11
Published: about 7 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: almost 5 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: over 6 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: about 14 years ago

10.1093/bioinformatics/btz889

<i>CellBench</i>: <i>R/Bioconductor</i> software for comparing single-cell RNA-seq analysis methods
Cited by: 17
Author(s): Shian Su, Luyi Tian, Xueyi Dong, Peter Hickey, Saskia Freytag, Matthew E. Ritchie
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0258031

High site-fidelity in common bottlenose dolphins despite low salinity exposure and associated indicators of compromised health
Cited by: 6
Author(s): Ryan Takeshita, Brian C. Balmer, Francesca Messina, Eric S. Zolman, Len Thomas, Randall S. Wells, Cynthia R. Smith, Teresa K. Rowles, Lori H. Schwacke
Software Mentions: 11
Published: over 4 years ago

10.1111/jcmm.16773

Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA‐Seq
Cited by: 3
Author(s): Qi Zhang, Manchao Kuang, Haiyin An, Yajing Zhang, Kai Zhang, Feng Li, Lei Zhang, Shujun Cheng
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0188079

Episodic future thinking reduces temporal discounting in healthy adolescents
Cited by: 35
Author(s): Uli Bromberg, Maria Lobatcheva, Jan Peters
Software Mentions: 11
Published: over 8 years ago

10.1098/rsif.2010.0230

Multi-camera real-time three-dimensional tracking of multiple flying animals
Cited by: 164
Author(s): Andrew Straw, Kristin Branson, Titus R. Neumann, Michael H. Dickinson
Software Mentions: 11
Published: almost 16 years ago

10.1186/s40064-015-0795-z

Rapid publication-ready MS-Word tables for two-way ANOVA
Cited by: 56
Author(s): Houssein Assaad, Yongqing Hou, Lan Zhou, Raymond J. Carroll, Guoyao Wu
Software Mentions: 11
Published: over 11 years ago

10.3389/fonc.2020.570654

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis
Cited by: 16
Author(s): Junya Yan, Xiaowen Wu, Jiayi Yu, Yanyan Zhu, Shundong Cang
Software Mentions: 11
Published: over 5 years ago

10.1080/21623945.2019.1697563

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: over 7 years ago

10.3390/jcm9082591

Risk of Adverse Drug Events Following the Virtual Addition of COVID-19 Repurposed Drugs to Drug Regimens of Frail Older Adults with Polypharmacy
Cited by: 14
Author(s): Sweilem B. Al Rihani, Matt K. Smith, Ravil Bikmetov, Malavika Deodhar, Pamela Dow, Jacques Turgeon, Véronique Michaud
Software Mentions: 11
Published: almost 6 years ago

10.3390/diagnostics10030171

GRB10 and E2F3 as Diagnostic Markers of Osteoarthritis and Their Correlation with Immune Infiltration
Cited by: 56
Author(s): Yajun Deng, Enhui Ren, Wenhua Yuan, Guang-Zhi Zhang, Zhi-Xi Wu, Qiqi Xie
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0256694

Factors contributing to farm-level productivity and household income generation in coastal Bangladesh’s rice-based farming systems
Cited by: 18
Author(s): Shah Al Emran, Timothy J. Krupnik, Sreejith Aravindakshan, Virender Kumar, Cameron M. Pittelkow
Software Mentions: 11
Published: almost 5 years ago

10.1186/1756-0500-3-10

A collection of bioconductor methods to visualize gene-list annotations
Cited by: 46
Author(s): Gang Feng, Pan Du, Nancy L. Krett, Michael A. Tessel, Steven T. Rosen, Warren A. Kibbe, Simon Lin
Software Mentions: 11
Published: over 16 years ago

10.15252/msb.20177697

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations
Cited by: 153
Author(s): Julia Jabs, Franziska Maria Zickgraf, Jeongbin Park, Sven Wagner, Xiaoqi Jiang, Katharina Jechow, Kortine Kleinheinz, Umut Toprak, Marc A. Schneider, Michael Meister, Saskia Spaich, Marc Sütterlin, Matthias Schlesner, Andreas Trumpp, Martin R. Sprick, Roland Eils, Christian Conrad
Software Mentions: 11
Published: over 8 years ago

10.1186/s12859-020-03786-x

IP4M: an integrated platform for mass spectrometry-based metabolomics data mining
Cited by: 32
Author(s): Dandan Liang, Quan Liu, Kejun Zhou, Jia Wang, Guoxiang Xie, Tianlu Chen
Software Mentions: 11
Published: over 5 years ago

10.3390/pharmaceutics13060868

Surfactant-Assisted Distal Pulmonary Distribution of Budesonide Revealed by Mass Spectrometry Imaging
Cited by: 0
Author(s): Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Barbara Pioselli, Valentina Mileo, Xabier Murgia, Fabrizio Salomone, Giuseppe Pieraccini, Haruo Usada, Augusto F. Schmidt, Noah H. Hillman, Matthew W. Kemp, Alan H. Jobe
Software Mentions: 11
Published: about 5 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: over 6 years ago

10.3390/microorganisms8040550

Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering
Cited by: 22
Author(s): Micha Weil, Haitao Wang, Mia M. Bengtsson, Daniel Köhn, Anke Günther, Gerald Jurasinski, John Couwenberg, Wakene Negassa, Dominik Zak, Tim Urich
Software Mentions: 11
Published: about 6 years ago

10.1093/rheumatology/keaa615

Changes in the illness perceptions of patients with rheumatoid arthritis over the first year of methotrexate therapy
Cited by: 7
Author(s): James M Gwinnutt, Sam Norton, Kimme L Hyrich, Mark Lunt, Anne Barton, Lis Cordingley, Suzanne Verstappen, Rams co-investigators
Software Mentions: 11
Published: over 5 years ago

10.3389/fgene.2019.01380

Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma Multiforme
Cited by: 6
Author(s): Runzhi Huang, Zhenyu Li, Chen Li, Guanghua Wang, Penghui Yan, Li P, Jiaqi Wang, Xiaolong Zhu, Peng Hu, Junfang Zhang, Zhengyan Chang, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.3390/cancers13122903

Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma
Cited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0238219

Ground-dwelling arthropods of pinyon-juniper woodlands: Arthropod community patterns are driven by climate and overall plant productivity, not host tree species
Cited by: 6
Author(s): Derek A. Uhey, Hannah Lee Riskas, Aaron D. Smith, Richard W. Hofstetter
Software Mentions: 11
Published: almost 6 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: over 19 years ago

10.1038/s41598-017-02464-y

UROPA: a tool for Universal RObust Peak Annotation
Cited by: 38
Author(s): Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Software Mentions: 11
Published: about 9 years ago

10.1016/j.cels.2018.09.003

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Cited by: 56
Author(s): Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber
Software Mentions: 11
Published: over 7 years ago

10.3897/BDJ.6.e20760

spind: an R Package to Account for Spatial Autocorrelation in the Analysis of Lattice Data
Cited by: 7
Author(s): Gudrun Carl, Sam Levin, Ingolf Kühn
Software Mentions: 11
Published: over 8 years ago

10.1038/s41598-020-66107-5

Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations
Cited by: 5
Author(s): Petra Villette, Eve Afonso, Geoffroy Couval, Aurélien Levret, Maxime Galan, A.-C. Goydadin, Jean-François Cosson, Patrick Giraudoux
Software Mentions: 11
Published: about 6 years ago

10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: over 5 years ago

10.1128/mBio.02699-19

The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: over 6 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: over 17 years ago

10.3390/jcm10184245

Machine-Learning Points at Endoscopic, Quality of Life, and Olfactory Parameters as Outcome Criteria for Endoscopic Paranasal Sinus Surgery in Chronic Rhinosinusitis
Cited by: 4
Author(s): Jörn Lötsch, Constantin A. Hintschich, Petros Petridis, Jürgen Pade, Thomas Hummel
Software Mentions: 11
Published: almost 5 years ago

10.1186/1756-0500-4-546

HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data
Cited by: 20
Author(s): Francesco Mancuso, Magda Montfort, Anna Carreras, Andreu Alibés, Guglielmo Roma
Software Mentions: 11
Published: over 14 years ago

10.1038/s41598-020-60329-3

Neuroestrogen synthesis modifies neural representations of learned song without altering vocal imitation in developing songbirds
Cited by: 11
Author(s): Daniel M. Vahaba, Amelia Hecsh, Luke Remage‐Healey
Software Mentions: 11
Published: over 6 years ago

10.1177/1176934320956575

Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins
Cited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: over 6 years ago

10.1111/jcmm.15615

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme
Cited by: 15
Author(s): Lan Jiang, Min Zhong, Tianbing Chen, Xiaolong Zhu, Hui Yang, Kun Lv
Software Mentions: 11
Published: almost 6 years ago

10.3390/ijerph17031093

Teleconsultations between Patients and Healthcare Professionals in Primary Care in Catalonia: The Evaluation of Text Classification Algorithms Using Supervised Machine Learning
Cited by: 14
Author(s): Francesc López Seguí, Ricardo Ander Egg Aguilar, Gabriel de Maeztu, Anna García‐Altés, Francesc García Cuyàs, Sandra M. Walsh, Marta Sagarra Castro, Josep Vidal-Alaball
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: over 15 years ago

10.3389/fgene.2020.489357

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
Cited by: 13
Author(s): Alejandro Abdala Asbun, Marc Besseling, Sergio Balzano, Judith van Bleijswijk, Harry J. Witte, Laura Villanueva, Julia C. Engelmann
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-89020-x

Gene-environment dependencies lead to collider bias in models with polygenic scores
Cited by: 29
Author(s): Evelina T. Akimova, Richard Breen, David M. Brazel, Melinda Mills
Software Mentions: 11
Published: about 5 years ago

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: over 10 years ago

10.3390/jcm9113643

Diabetic Retinopathy Environment-Wide Association Study (EWAS) in NHANES 2005–2008
Cited by: 10
Author(s): Kevin Blighe, Sarega Gurudas, Ying Lee, Sobha Sivaprasad
Software Mentions: 11
Published: over 5 years ago

10.1186/s12935-021-01795-1

Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinoma
Cited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: over 5 years ago

10.3390/ijerph18041816

Academic Achievement in Spanish Secondary School Students: The Inter-Related Role of Executive Functions, Physical Activity and Gender
Cited by: 7
Author(s): Elena Escolano Pérez, Marta Bestué
Software Mentions: 11
Published: over 5 years ago

10.3389/fmolb.2021.635074

Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks
Cited by: 3
Author(s): Elena Díaz-Santiago, M. Gonzalo Claros, Raquel Yahyaoui, Yolanda de Diego-Otero, Rocío Velasco Calvo, Janet Hoenicka, Francesc Palau, Juan A. G. Ranea, James R. Perkins
Software Mentions: 11
Published: about 5 years ago

10.3389/fimmu.2020.612784

Integrated Analysis of the ETS Family in Melanoma Reveals a Regulatory Role of ETV7 in the Immune Microenvironment
Cited by: 14
Author(s): Hui Qü, Hui Zhao, Xi Zhang, Yang Liu, Feng Li, Li-Yan Sun, Zewen Song
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-018-33986-8

Identification of Novel Genes in Human Airway Epithelial Cells associated with Chronic Obstructive Pulmonary Disease (COPD) using Machine-Based Learning Algorithms
Cited by: 24
Author(s): Shayan Mostafaei, Anoshirvan Kazemnejad, Sadegh Azimzadeh Jamalkandi, Soroush Amirhashchi, Seamas C. Donnelly, Michelle E. Armstrong, Mohammad Doroudian
Software Mentions: 11
Published: over 7 years ago

10.1038/s41598-021-92406-6

Plasma lipidomic analysis shows a disease progression signature in mdx mice
Cited by: 3
Author(s): Roula Tsonaka, Alexandre Seyer, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 11
Published: about 5 years ago

10.3390/biomedicines8110488

TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data
Cited by: 4
Author(s): Carolina Peixoto, Marta B. Lopes, Marta Martins, Luís Costa, Susana Vinga
Software Mentions: 11
Published: over 5 years ago

10.3389/fmicb.2017.00682

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Cited by: 314
Author(s): David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, Philip Hugenholtz
Software Mentions: 11
Published: about 9 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0089470

Analytic Programming with fMRI Data: A Quick-Start Guide for Statisticians Using R
Cited by: 9
Author(s): Ani Eloyan, Shanshan Li, John Muschelli, James J. Pekar, Stewart H. Mostofsky, Brian Caffo
Software Mentions: 11
Published: over 12 years ago

10.1038/s41598-020-68780-y

Protecting endangered species in the USA requires both public and private land conservation
Cited by: 15
Author(s): Niall G. Clancy, John P. Draper, J. Marshall Wolf, Umarfarooq A. Abdulwahab, Maya Pendleton, Soren Brothers, Janice Brahney, Jennifer Weathered, Edd Hammill, Trisha B. Atwood
Software Mentions: 11
Published: almost 6 years ago

10.7554/eLife.65372

Image3C, a multimodal image-based and label-independent integrative method for single-cell analysis
Cited by: 6
Author(s): Alice Accorsi, Andrew Box, Robert Peuß, Christopher J. Wood, Alejandro Sánchez Alvarado, Nicolas Rohner
Software Mentions: 11
Published: almost 5 years ago

10.1038/srep43932

Implications of the cattle trade network in Cameroon for regional disease prevention and control
Cited by: 60
Author(s): Paolo Carlo Motta, Thibaud Porphyre, Ian Handel, Saidou M. Hamman, Victor Ngu Ngwa, Vincent N. Tanya, K. L. Morgan, Rob Christley, Barend M. deC. Bronsvoort
Software Mentions: 10
Published: over 9 years ago

10.1128/mSystems.00541-20

Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis
Cited by: 17
Author(s): Luis A. Ibarra-Juárez, Maureen Burton, Peter H. W. Biedermann, Luisa F. Cruz, Damaris Desgarennes, Enrique Ibarra-Laclette, Amparo Latorre, Alexandro Alonso-Sánchez, Emanuel Villafán, Greta Hanako-Rosas, Loredana Lopez, Mirna Vázquez-Rosas-Landa, Gloria Carrión, Daniel Carrillo, Andrés Moya, Araceli Lamelas
Software Mentions: 10
Published: over 5 years ago

10.7554/eLife.66036

A new Heterodontosaurus specimen elucidates the unique ventilatory macroevolution of ornithischian dinosaurs
Cited by: 8
Author(s): Viktor J. Radermacher, Vincent Fernández, Emma R. Schachner, Richard J. Butler, Emese M. Bordy, Michael Naylor Hudgins, William J. De Klerk, Kimberley E. J. Chapelle, Jonah N. Choiniere
Software Mentions: 10
Published: almost 5 years ago

10.3389/fimmu.2021.622563

9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Cited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: about 5 years ago

10.1038/s41598-018-33077-8

Machine-learning based lipid mediator serum concentration patterns allow identification of multiple sclerosis patients with high accuracy
Cited by: 41
Author(s): Jörn Lötsch, Susanne Schiffmann, Katja Schmitz, R. Brunkhorst, F. Javier Lerch, Nerea Ferreirós, Sabine Wicker, Irmgard Tegeder, Gerd Geißlinger, Alfred Ultsch
Software Mentions: 10
Published: over 7 years ago

10.1128/mBio.01105-19

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Cited by: 42
Author(s): Eike J. Steinig, Sebastián Duchêne, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah A. Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Gráinne I. Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Hermı́nia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek S. Sarovich, Simon R. Harris, Julian Parkhill, Ruth C. Massey, Matthew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
Software Mentions: 10
Published: over 6 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: about 7 years ago

10.1038/s41598-020-79875-x

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Cited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
Software Mentions: 10
Published: over 5 years ago

10.1186/s12916-020-01595-w

Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection
Cited by: 30
Author(s): Guoxiang Xie, Xiaoning Wang, Runmin Wei, Jingye Wang, Aihua Zhao, Tianlu Chen, Yixing Wang, Hua Zhang, Zhun Xiao, Xin-Zhu Liu, Youping Deng, Linda L. Wong, Cynthia Rajani, Sandi A. Kwee, Hua Bian, Xin Gao, Ping Liu, Jia Wang
Software Mentions: 10
Published: about 6 years ago

10.3390/microorganisms9061308

Phenotypic and Genotypic Properties of Fluoroquinolone-Resistant, qnr-Carrying Escherichia coli Isolated from the German Food Chain in 2017
Cited by: 7
Author(s): Katharina Juraschek, Carlus Deneke, Silvia Schmoger, Mirjam Grobbel, Burkhard Malorny, Annemarie Käsbohrer, Štefan Schwarz, Diana Meemken, Jens A. Hammerl
Software Mentions: 10
Published: about 5 years ago

10.7717/peerj.6061

Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
Cited by: 11
Author(s): Zhiqiao Zhang, Qingbo Liu, Peng Wang, Jing Li, Tingshan He, Yanling Ouyang, Yiyan Huang, Weidong Wang
Software Mentions: 10
Published: over 7 years ago

10.1186/s12957-021-02162-0

The preoperative prognostic value of the radiomics nomogram based on CT combined with machine learning in patients with intrahepatic cholangiocarcinoma
Cited by: 16
Author(s): Youyin Tang, Tao Zhang, Xianghong Zhou, Ying Zhao, Hanyue Xu, Yichun Liu, Hang Wang, Zheyu Chen, Xuelei Ma
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41598-020-80308-y

A novel retinal ganglion cell quantification tool based on deep learning
Cited by: 22
Author(s): Luca Masin, Marie Claes, Steven Bergmans, Lien Cools, Lien Andries, Benjamin Davis, Lieve Moons, Lies De Groef
Software Mentions: 10
Published: over 5 years ago

10.1186/s11689-021-09360-7

Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: over 5 years ago

10.1186/s12915-021-01029-w

Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens
Cited by: 36
Author(s): Cengiz Kaya, Tomas N Generalovic, Gunilla Ståhls, Martin Hauser, Ana Clariza Samayoa, Carlos Gustavo Nunes-Silva, Heather Roxburgh, Jens Wohlfahrt, Ebenezer Ato Ewusie, Marc Kenis, Yupa Hanboonsong, Jesús Orozco, Nancy Carrejo, Satoshi Nakamura, Laura Gasco, Santos Rojo, Chrysantus M. Tanga, Rudolf Meier, Clint Rhode, Christine Picard, Chris D. Jiggins, Florian Leiber, Jeffery K. Tomberlin, Martin Hasselmann, Wolf U. Blanckenhorn, Martin Kapun, Christoph Sandrock
Software Mentions: 10
Published: about 5 years ago

10.1186/s13059-014-0413-3

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators
Cited by: 19
Author(s): Laurence D. Hurst, Oxana Sachenkova, Carsten O. Daub, Alistair R.R. Forrest, Łukasz Huminiecki
Software Mentions: 10
Published: almost 12 years ago

10.3389/fpls.2020.587426

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces
Cited by: 13
Author(s): Victor Allan, Mani Vetriventhan, R. Senthil, S. Geetha, Santosh Deshpande, Abhishek Rathore, Vinod Kumar, Prabhat Kumar Singh, Surender Reddymalla, V. C. R. Azevedo
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.ppat.1007945

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype
Cited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: almost 7 years ago

10.1007/s11548-020-02180-5

SciKit-Surgery: compact libraries for surgical navigation
Cited by: 18
Author(s): Stephen A. Thompson, Thomas Dowrick, Mian Asbat Ahmad, Goufang Xiao, Bong-Jin Koo, Ester Bonmati, Kim Kahl, Matthew J. Clarkson
Software Mentions: 10
Published: about 6 years ago

10.1038/s41396-020-00862-1

Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
Cited by: 21
Author(s): Sundy Maurice, Gontran Arnault, Jenni Nordén, Synnøve Smebye Botnen, Otto Miettinen, Håvard Kauserud
Software Mentions: 10
Published: over 5 years ago

10.1186/s13321-015-0094-2

RRegrs: an R package for computer-aided model selection with multiple regression models
Cited by: 40
Author(s): Georgia Tsiliki, Cristian R. Munteanu, José A. Seoane, Carlos Fernández-Lozano, Haralambos Sarimveis, Egon Willighagen
Software Mentions: 10
Published: almost 11 years ago

10.3389/fgene.2021.682475

Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions
Cited by: 10
Author(s): Matthew Johnson, Jason Wallace
Software Mentions: 10
Published: almost 5 years ago