Scientific Papers with Software Mentions

10.1186/s12885-021-08559-0

A novel ferroptosis-related 12-gene signature predicts clinical prognosis and reveals immune relevancy in clear cell renal cell carcinoma
Cited by: 42
Author(s): Ying‐Kai Hong, Mingen Lin, Dehua Ou, Zhuangkai Huang, Peilin Shen
Software Mentions: 15
Published: over 3 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: about 5 years ago

10.1371/journal.pcbi.1008625

mbkmeans: Fast clustering for single cell data using mini-batch k-means
Cited by: 27
Author(s): Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso
Software Mentions: 15
Published: almost 4 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago

10.12688/f1000research.11622.3

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
Cited by: 205
Author(s): Małgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Software Mentions: 15
Published: over 5 years ago

10.1038/s41598-020-72571-w

Persistent fire foci in all biomes undermine the Paris Agreement in Brazil
Cited by: 51
Author(s): Carlos Antônio da Silva, Paulo Eduardo Teodoro, Rafael Coll Delgado, Larissa Pereira Ribeiro Teodoro, Mendelson Lima, Ariane de Andréa Pantaleão, Fábio Henrique Rojo Baio, Gileno Brito de Azevedo, Glauce Táıs de Oliveira Sousa Azevedo, Guilherme Fernando Capristo-Silva, Damien Arvor, Cassiele Uliana Facco
Software Mentions: 15
Published: about 4 years ago

10.1186/s12859-017-1994-0

PIVOT: platform for interactive analysis and visualization of transcriptomics data
Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: almost 7 years ago

10.2196/12875

Developing the National Usability-Focused Health Information System Scale for Physicians: Validation Study
Cited by: 26
Author(s): Hannele Hyppönen, Johanna Kaipio, Tarja Heponiemi, Tinja Lääveri, Anna Mari Aalto, Jukka Vänskä, Marko Elovainio
Software Mentions: 15
Published: over 5 years ago

10.3389/fcell.2021.671736

Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Endometrial Carcinoma to Immunotherapy and Chemotherapy
Cited by: 6
Author(s): Jinhui Liu, Yichun Wang, Jie Mei, Song Nie, Yan Zhang
Software Mentions: 15
Published: over 3 years ago

10.3390/microorganisms9051050

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum
Cited by: 5
Author(s): Jing Zhu, Xiang Sun, Zhidong Zhang, Qi-Yong Tang, Minghong Gu, Lijuan Zhang, Min Hou, Amir Sharon, Hongli Yuan
Software Mentions: 15
Published: over 3 years ago

10.3390/cells8111321

Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets
Cited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: about 5 years ago

10.3389/fneur.2019.01366

Prediction of Early TBI Mortality Using a Machine Learning Approach in a LMIC Population
Cited by: 39
Author(s): Robson Luís Oliveira de Amorim, Louise Makarem Oliveira, Luis Marcelo Malbouisson, Márcia Mitie Nagumo, Marcela Simoes, Leandro Miranda, Edson Bor‐Seng‐Shu, André Beer‐Furlan, Almir Ferreira de Andrade, Andrés M. Rubiano, Manoel Jacobsen Teixeira, Angelos G. Kolias, Wellingson Silva Paiva
Software Mentions: 15
Published: almost 5 years ago

10.1111/tran.12131

Regional surnames and genetic structure in Great Britain
Cited by: 14
Author(s): Jens Kandt, James Cheshire, Paul Longley
Software Mentions: 15
Published: over 8 years ago

10.1371/journal.pone.0188955

Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning
Cited by: 19
Author(s): Simon Dedman, Rick Officer, Maurice Clarke, David G. Reid, Deirdre Brophy
Software Mentions: 15
Published: almost 7 years ago

10.1038/s41598-019-46510-3

Differential prognostic impact of platelet-derived growth factor receptor expression in NSCLC
Cited by: 19
Author(s): Thomas K. Kilvaer, Mehrdad Rakaee, Turid Hellevik, Jørg Vik, Luigi De Petris, Tom Dønnem, Carina Strell, Arne Östman, Lill-Tove Busund, Iñigo Martínez-Zubiaurre
Software Mentions: 15
Published: over 5 years ago

10.1186/s12882-021-02267-4

Low plasma magnesium concentration and future abdominal aortic calcifications in moderate chronic kidney disease
Cited by: 2
Author(s): Anique D. ter Braake, Larissa P. Govers, Mieke J. Peeters, Arjan D. van Zuilen, Jack F.M. Wetzels, Peter J. Blankenstijn, Joost G. J. Hoenderop, Jeroen H. F. de Baaij, Jan van den Brand
Software Mentions: 15
Published: over 3 years ago

10.1038/s41598-021-81200-z

MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies
Cited by: 11
Author(s): Mario Zanfardino, Rossana Castaldo, Katia Pane, Ornella Affinito, Marco Aiello, Marco Salvatore, Monica Franzese
Software Mentions: 15
Published: almost 4 years ago

10.3390/ijms21239157

NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC)
Cited by: 16
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Roberto Mantovani, Diletta Dolfini
Software Mentions: 15
Published: almost 4 years ago

10.3389/fonc.2021.650153

Identification and Validation of a Prognostic Immune-Related Alternative Splicing Events Signature for Glioma
Cited by: 5
Author(s): Minjie Wang, Zhongqiang Zhou, Jianglin Zheng, Wenjun Xiao, Jun Zhu, Chaocai Zhang, Xueshi Jiang
Software Mentions: 15
Published: over 3 years ago

10.7717/peerj.6876

Hierarchical generalized additive models in ecology: an introduction with mgcv
Cited by: 443
Author(s): Eric J. Pedersen, David L. Miller, Gavin L. Simpson, Noam Ross
Software Mentions: 15
Published: over 5 years ago

10.3389/fchem.2021.734132

The “DOLPHINS” Project: A Low-Cost Real-Time Multivariate Process Control From Large Sensor Arrays Providing Sparse Binary Data
Cited by: 1
Author(s): Eugenio Alladio, Marcello Baricco, Vincenzo Leogrande, Renato Pagliari, Fabio Pozzi, Paolo Foglio, Marco Vincenti
Software Mentions: 15
Published: about 3 years ago

10.1098/rsos.191609

Spatial heterogeneity of the shorebird gastrointestinal microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: almost 5 years ago

10.1186/s12885-021-08598-7

Cannabinoid exposure as a major driver of pediatric acute lymphoid Leukaemia rates across the USA: combined geospatial, multiple imputation and causal inference study
Cited by: 24
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 15
Published: about 3 years ago

10.3390/cells10061292

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cited by: 1
Author(s): Axel Künstner, Rédouane Aherrahrou, Misa Hirose, Petra Bruse, Saleh M. Ibrahim, Hauke Busch, Jeanette Erdmann, Zouhair Aherrahrou
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-020-03860-4

Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: almost 4 years ago

10.3389/fimmu.2021.668391

A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma
Cited by: 21
Author(s): Yuhan Sun, Alexander James Sedgwick, Yaseelan Palarasah, Stefano Mangiola, Alexander D. Barrow
Software Mentions: 15
Published: about 3 years ago

10.3389/fmicb.2020.580691

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
Cited by: 20
Author(s): Laura M. Carroll, Rachel A. Cheng, Jasna Kovač
Software Mentions: 15
Published: about 4 years ago

10.1038/s41598-020-63428-3

No evidence of spontaneous preference for slowly moving objects in visually naïve chicks
Cited by: 7
Author(s): Bastien S. Lemaire
Software Mentions: 15
Published: over 4 years ago

10.1371/journal.pone.0091650

rAvis: An R-Package for Downloading Information Stored in Proyecto AVIS, a Citizen Science Bird Project
Cited by: 6
Author(s): Sara Varela, Javier González-Hernández, Eduardo Casabella, Rafael Barrientos
Software Mentions: 15
Published: over 10 years ago

10.1007/s00204-021-03031-1

Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neurons
Cited by: 26
Author(s): Dominik Loser, María G. Hinojosa, John D. Blum, Jasmin Schaefer, Markus Brüll, Ylva Johansson, Ilinca Suciu, Karin Grillberger, Timm Danker, Clemens Möller, Iain Gardner, Gerhard Ecker, Susanne Hougaard Bennekou, Anna Forsby, Udo Kraushaar, Marcel Leist
Software Mentions: 15
Published: over 3 years ago

10.1186/1471-2105-16-S11-S2

VisRseq: R-based visual framework for analysis of sequencing data
Cited by: 59
Author(s): Hamid Younesy, Torsten B. Möller, Matthew C. Lorincz, Mehdi Karimi, Steven J.M. Jones
Software Mentions: 15
Published: over 9 years ago

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: about 4 years ago

10.12688/f1000research.8987.2

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.21105/joss.03073

mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines
Cited by: 22
Author(s): Begüm D. Topçuoğlu, Zena Lapp, Kelly L Sovacool, Evan S. Snitkin, Jenna Wiens, Patrick D. Schloss
Software Mentions: 15
Published: over 3 years ago

10.1038/s41598-021-87843-2

Bodily ownership and agency sensations in a natural state
Cited by: 1
Author(s): Souta Hidaka, Kyoshiro Sasaki, Toshikazu Kawagoe, Nobuyuki Asai, Wataru Teramoto
Software Mentions: 15
Published: over 3 years ago

10.3389/fimmu.2020.00082

Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection
Cited by: 7
Author(s): Kazuhito Honjo, Woong-Jai Won, R. Glenn King, Lara Ianov, David K. Crossman, Juliet Easlick, Mikhail A. Shakhmatov, Mohamed Khass, André M. Vale, Robert P. Stephan, Ran Li, Randall S. Davis
Software Mentions: 15
Published: almost 5 years ago

10.1371/journal.pone.0018850

Multiplexed Immunoassay Panel Identifies Novel CSF Biomarkers for Alzheimer's Disease Diagnosis and Prognosis
Cited by: 199
Author(s): Rebecca Craig‐Schapiro, Max Kühn, Chengjie Xiong, Eve H. Pickering, Jingxia Liu, Thomas P. Misko, Richard J. Perrin, Kelly R. Bales, Holly Soares, Anne M. Fagan, David M. Holtzman
Software Mentions: 15
Published: over 13 years ago

10.3389/fcell.2020.00790

The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer
Cited by: 4
Author(s): Runzhi Huang, Jian Guo, Penghui Yan, Suna Zhai, Peng Hu, Xiaolong Zhu, Jiayao Zhang, Yannan Qiao, Yu Zhang, Hui Liu, Ling Huang, Jie Zhang, Daoke Yang, Zongqiang Huang
Software Mentions: 15
Published: about 4 years ago

10.1371/journal.pntd.0009232

Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-Bissau
Cited by: 8
Author(s): Sebastian von Huth, Louise B. Thingholm, Poul Erik Kofoed, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 15
Published: over 3 years ago

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: over 3 years ago

10.3390/biomedicines9020144

Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation
Cited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago

10.3389/fpls.2021.618028

Floral UV Features of Plant Species From a Neotropical Savanna
Cited by: 6
Author(s): Priscila Tunes, Maria Gabriela Gutierrez Camargo, Elza Guimarães
Software Mentions: 15
Published: over 3 years ago

10.1186/s40168-020-00961-3

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Cited by: 30
Author(s): Wang Ya, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pone.0240935

The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Cited by: 24
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Dionne Sakhrani, Carlo A. Biagi, Anne-Marie Flores, Ruth E. Withler, Scott A. Pavey, Terry D. Beacham, Theresa Godin, Eric B. Taylor, Michael A. Russello, Robert H. Devlin, Ben F. Koop
Software Mentions: 15
Published: about 4 years ago

10.3390/cancers13123089

A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer
Cited by: 12
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 15
Published: over 3 years ago

10.1371/journal.pone.0183417

Association of gene expression with biomass content and composition in sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: over 7 years ago

10.3389/fgene.2021.559998

Gene Size Matters: An Analysis of Gene Length in the Human Genome
Cited by: 55
Author(s): Inês Lopes, Gulam Altab, Priyanka Raina, João Pedro de Magalhães
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pgen.1009538

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
Cited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: over 3 years ago

10.1111/eva.13202

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation
Cited by: 15
Author(s): Felix Vaux, Sandra Bohn, John R. Hyde, Kathleen G. O’Malley
Software Mentions: 15
Published: over 3 years ago

10.1128/mBio.00034-20

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes
Cited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: over 4 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 years ago

10.3389/fmicb.2015.00104

Long-term forest soil warming alters microbial communities in temperate forest soils
Cited by: 237
Author(s): Kristen M. DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T. A. van Diepen, Rebecca Varney, Jeffrey L. Blanchard, Jerry M. Melillo, Serita D. Frey
Software Mentions: 15
Published: almost 10 years ago

10.1186/s13059-020-02116-x

Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Cited by: 107
Author(s): Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry W. Long, Tao Liu, X. Shirley Liu
Software Mentions: 15
Published: over 4 years ago

10.1038/s42003-021-01796-w

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Cited by: 73
Author(s): Rong Xu, Renfei Lu, Tao Zhang, Qian Wu, Wei Cai, Xudong Han, Zhenzhou Wan, Xia Jin, Zhigang Zhang, Chiyu Zhang
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-016-1455-1

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Cited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: almost 8 years ago

10.1002/ece3.6786

SDMtune: An R package to tune and evaluate species distribution models
Cited by: 68
Author(s): Sergio Vignali, Arnaud Barras, Raphaël Arlettaz, Veronika Braunisch
Software Mentions: 14
Published: about 4 years ago

10.3390/ijerph18179227

Multivariate Analysis of Risk Factors of the COVID-19 Pandemic in the Community of Madrid, Spain
Cited by: 2
Author(s): Víctor Pérez-Segura, Raquel Caro Carretero, António Rua
Software Mentions: 14
Published: about 3 years ago

10.1038/s41598-020-80165-9

Multi-level remodelling of chromatin underlying activation of human T cells
Cited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: almost 4 years ago

10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: almost 5 years ago

10.1038/s42003-019-0554-8

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome
Cited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: over 5 years ago

10.1371/journal.pcbi.1003118

Software for Computing and Annotating Genomic Ranges
Cited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: over 11 years ago

10.1186/s12920-017-0261-6

CVE: an R package for interactive variant prioritisation in precision oncology
Cited by: 6
Author(s): Andreas Möck, Suzanne Murphy, James A. Morris, Francesco Marass, Nitzan Rosenfeld, Charles E. Massie
Software Mentions: 14
Published: over 7 years ago

10.1002/1873-3468.12684

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.3390/insects10100321

Evaluation of NEON Data to Model Spatio-Temporal Tick Dynamics in Florida
Cited by: 5
Author(s): Geraldine Klarenberg, Samantha M. Wisely
Software Mentions: 14
Published: about 5 years ago

10.1371/journal.pcbi.1005158

Machine Learning for Characterization of Insect Vector Feeding
Cited by: 25
Author(s): Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe
Software Mentions: 14
Published: about 8 years ago

10.3390/microorganisms9061222

Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study
Cited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: over 3 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1186/s13742-016-0147-0

2015 Brainhack Proceedings
Cited by: 6
Author(s): R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller, AmanPreet Badhwar, David Kennedy, Jean‐Baptiste Poline, Roberto Toro, Ben Cipollini, Ariel Rokem, Daniel J. Clark, Krzysztof J. Gorgolewski, Daniel J. Clark, Samir Das, Cécile Madjar, Ayan Sengupta, Zia Mohades, Sébastien Déry, Weiran Deng, Eric Earl, Damion V. Demeter, Kate Mills, Glad Mihai, Luka Ružić, Nick Ketz, Andrew E. Reineberg, Marianne C. Reddan, Anne-Lise Goddings, Javier Gonzalez‐Castillo, Caroline Froehlich, Gil Dekel, Daniel S. Margulies, Ben D. Fulcher, Tristan Glatard, Reza Adalat, Natacha Beck, R. Bernard, Najmeh Khalili-Mahani, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans, Yaroslav Halchenko, Matteo Visconti di Oleggio Castello, Raúl Hernández-Pérez, Edgar Abarca Morales, Laura V. Cuaya, Kaori Ito, Sook‐Lei Liew, Hans J. Johnson, Erik Kan, Julia Anglin, Michael R. Borich, Neda Jahanshad, Paul Thompson, Marcel Falkiewicz, Julia M. Huntenburg, David O’Connor, Michael P. Milham, Ramon Fraga Pereira, Anibal Sólon Heinsfeld, Alexandre R. Franco, Augusto Buchweitz, Felipe Meneguzzi, Rickson C. Mesquita, Luis C. T. Herrera, Daniela Dentico, Vanessa Sochat, Julio E. Villalon‐Reina, Eleftherios Garyfallidis
Software Mentions: 14
Published: about 8 years ago

10.7717/peerj.3472

Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands
Cited by: 50
Author(s): Ross Cunning, Ruth D. Gates, Peter J. Edmunds
Software Mentions: 14
Published: over 7 years ago

10.3389/fmicb.2019.01775

Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality
Cited by: 23
Author(s): Hannah E. Epstein, Hillary A. Smith, Neal E. Cantin, Véronique J. L. Mocellin, Gergely Torda, Madeleine J. H. van Oppen
Software Mentions: 14
Published: over 5 years ago

10.1371/journal.pcbi.1009317

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Cited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: about 3 years ago

10.1523/ENEURO.0328-20.2020

Group II Metabotropic Glutamate Receptors Modulate Sound Evoked and Spontaneous Activity in the Mouse Inferior Colliculus
Cited by: 1
Author(s): Inga Kristaponyte, Nichole L. Beebe, Jesse W. Young, Sharad J. Shanbhag, Brett R. Schofield, Alexander V. Galazyuk
Software Mentions: 14
Published: almost 4 years ago

10.3758/s13420-020-00446-1

Response of male and female domestic chicks to change in the number (quantity) of imprinting objects
Cited by: 5
Author(s): Bastien S. Lemaire, Rosa Rugani, Lucia Regolin, Giorgio Vallortígara
Software Mentions: 14
Published: about 4 years ago

10.1007/s43032-020-00438-6

Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition
Cited by: 24
Author(s): Kenetta L. Nunn, Steven S. Witkin, Gudrun Schneider, Allison Boester, Dimitrios Nasioudis, Evelyn Minis, Karol Gliniewicz, Larry J. Forney
Software Mentions: 14
Published: almost 4 years ago

10.1186/s12967-021-02952-w

Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancer
Cited by: 20
Author(s): Daowei Lin, Wenhua Fan, Rongxin Zhang, Enen Zhao, Pansong Li, Wenhao Zhou, Jianhong Peng, Liren Li
Software Mentions: 14
Published: over 3 years ago

10.1186/s13059-019-1783-3

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Cited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: over 5 years ago

10.3389/fimmu.2020.572924

Differential Skewing of Circulating MR1-Restricted and γδ T Cells in Human Psoriasis Vulgaris
Cited by: 7
Author(s): Vera Plužarić, Mario Štefanić, Martina Mihalj, Maja Tolušić Levak, Ivanka Muršić, Ljubica Glavaš‐Obrovac, Martin Petřek, Péter Balogh, Stana Tokić
Software Mentions: 14
Published: almost 4 years ago

10.1080/19490976.2021.1888673

Links between gut microbiome composition and fatty liver disease in a large population sample
Cited by: 31
Author(s): Matti O. Ruuskanen, Fredrik Åberg, Ville Männistö, Aki S. Havulinna, Guillaume Méric, Yang Liu, Rohit Loomba, Yoshiki Vázquez-Baeza, Anupriya Tripathi, Liisa Valsta, Michael Inouye, Pekka Jousilahti, Veikko Salomaa, Mohit Jain, Rob Knight, Leo Lahti, Teemu J. Niiranen
Software Mentions: 14
Published: almost 4 years ago

10.3389/fcell.2020.592490

Transcriptome Sequencing Reveals Potential Roles of ICOS in Primary Sjögren’s Syndrome
Cited by: 19
Author(s): Jing Luo, Xin Liao, Lihe Zhang, Xin Xu, Senhong Ying, Mengjiao Yu, Lixia Zhu, Suxian Lin, Xiaobing Wang
Software Mentions: 14
Published: almost 4 years ago

10.1002/ece3.3204

Habitat selection by Eurasian lynx (Lynx lynx) is primarily driven by avoidance of human activity during day and prey availability during night
Cited by: 50
Author(s): Marc Filla, Joe Premier, Nora Magg, Claudia Dupke, Igor Khorozyan, Matthias Waltert, Luděk Bufka, Marco Heurich
Software Mentions: 14
Published: over 7 years ago

10.15252/msb.20209498

Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans
Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: over 4 years ago

10.3389/fpsyg.2020.564083

Correlates of Health-Protective Behavior During the Initial Days of the COVID-19 Outbreak in Norway
Cited by: 54
Author(s): Janis Zickfeld, Thomas W. Schubert, Anders Kuvaas Herting, Jon Grahe, Kate Faasse
Software Mentions: 14
Published: about 4 years ago

10.1186/s12859-015-0683-0

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Cited by: 172
Author(s): Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 14
Published: over 9 years ago

10.1039/d0sc05337f

A data-driven perspective on the colours of metal–organic frameworks
Cited by: 14
Author(s): Kevin Maik Jablonka, Seyed Mohamad Moosavi, Mehrdad Asgari, Christopher P. Ireland, Luc Patiny, Berend Smit
Software Mentions: 14
Published: almost 4 years ago

10.3390/ijms20174162

SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers
Cited by: 13
Author(s): Fabia Fricke, Malwina Michalak, Uwe Warnken, Ingrid Haußer, Martina Schnölzer, Jürgen Kopitz, Johannes Gebert
Software Mentions: 14
Published: about 5 years ago

10.1186/s41155-021-00194-9

Factor structure, measurement invariance and psychometric properties of the Quality of Life Scale WHOQOL-BREF in the Ecuadorian context
Cited by: 0
Author(s): Sandra Lima-Castro, Paúl Arias-Medina, Alexandra Bueno-Pacheco, Eva Peña-Contreras, Mónica Aguilar-Sizer, Marcela Cabrera-Vélez
Software Mentions: 14
Published: about 3 years ago

10.1186/s12920-017-0274-1

Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Cited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: over 7 years ago

10.1038/s42003-020-01625-6

Mapping the immune environment in clear cell renal carcinoma by single-cell genomics
Cited by: 103
Author(s): Nicholas Borcherding, Ajaykumar Vishwakarma, Andrew P. Voigt, Andrew M. Bellizzi, Jacob Kaplan, Kenneth G. Nepple, Aliasger K. Salem, Russell W. Jenkins, Yousef Zakharia, Weizhou Zhang
Software Mentions: 14
Published: almost 4 years ago

10.1038/s41598-020-66628-z

Impact of a natural disaster on access to care and biopsychosocial outcomes among Hispanic/Latino cancer survivors
Cited by: 15
Author(s): Mary Rodríguez-Rabassa, Ruthmarie Hernandez, Zindie Rodríguez, Claudia B. Colon-Echevarria, Lizette Maldonado, Nelmit Tollinchi, Estefanía Torres-Marrero, Adnil Mulero, Daniela Albors, Jaileene Pérez‐Morales, Idhaliz Flores, Julie Dutil, Heather Jim, Eida Castro, Guillermo N. Armaiz-Peña
Software Mentions: 14
Published: over 4 years ago

10.3390/cancers12051142

Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer
Cited by: 55
Author(s): Marc Clos-García, Koldo Garcia, Cristina Alonso, Marta Iruarrizaga‐Lejarreta, Mauro D’Amato, Anais Crespo, Águeda Iglesias, Joaquín Cubiella, Luís Bujanda, Juan Manuel Falcón‐Pérez
Software Mentions: 14
Published: over 4 years ago

10.3390/ani10071151

Tenebrio molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs
Cited by: 8
Author(s): Sandra De Meyer, Denise K. Geßner, Garima Maheshwari, Julia Röhrig, Theresa Friedhoff, Erika Most, Holger Zorn, Robert Ringseis, Klaus Eder
Software Mentions: 14
Published: over 4 years ago

10.1371/journal.pone.0218310

Evaluating health facility access using Bayesian spatial models and location analysis methods
Cited by: 8
Author(s): Nicholas Tierney, Antonietta Mira, H Reinhold, Giuseppe Arbia, Samuel Clifford, Angelo Auricchio, Tiziano Moccetti, Stefano Peluso, Kerrie Mengersen
Software Mentions: 14
Published: over 5 years ago

10.1007/s00401-021-02343-x

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases
Cited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: over 3 years ago

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 years ago

10.3389/fonc.2021.560136

Screening of miRNAs as Prognostic Biomarkers for Colon Adenocarcinoma and Biological Function Analysis of Their Target Genes
Cited by: 2
Author(s): Guoliang Zheng, Guojun Zhang, Yan Zhao, Zhichao Zheng
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0248202

Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils
Cited by: 1
Author(s): Ava Mackay-Smith, Mary Kate Dornon, R.E. Lucier, Annalisa Okimoto, Flavia Mendonca de Sousa, Marcela Silvina Rodriguero, Viviana A. Confalonieri, Analía Alicia Lanteri, Andrea S. Sequeira
Software Mentions: 14
Published: over 3 years ago