Ecosyste.ms: Papers

10.1186/s12859-021-03970-7

stochprofML: stochastic profiling using maximum likelihood estimation in R
Cited by: 3
Author(s): Lisa Amrhein, Christiane Fuchs
Software Mentions: 14
Published: over 3 years ago

10.1186/s12864-016-3278-x

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
Cited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: almost 8 years ago

10.1038/s41598-020-69361-9

Effects of different intracranial volume correction methods on univariate sex differences in grey matter volume and multivariate sex prediction
Cited by: 28
Author(s): Carles Sanchis‐Segura, M.V. Ibáñez-Gual, Naiara Aguirre, Álvaro Javier Cruz-Gómez, Cristina Forn
Software Mentions: 14
Published: over 4 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

10.1523/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

10.1186/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

10.3389/fcell.2021.657667

Identification of the Prognostic Significance of Somatic Mutation-Derived LncRNA Signatures of Genomic Instability in Lung Adenocarcinoma
Cited by: 31
Author(s): Geng Wang, Zhi Lv, Jinshuo Fan, Jing Xu, Kaimin Mao, Zhengrong Yin, Wanlu Qing, Yang Jin
Software Mentions: 14
Published: over 3 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

10.1186/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

10.1371/journal.pgen.1008405

Causal relationships between obesity and the leading causes of death in women and men
Cited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: about 5 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

10.1186/s13059-021-02349-4

PEPPRO: quality control and processing of nascent RNA profiling data
Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: over 3 years ago

10.1186/s42523-020-00027-7

Domesticated equine species and their derived hybrids differ in their fecal microbiota
Cited by: 18
Author(s): Joan E. Edwards, A. Schennink, Faith Burden, Stuart A. Long, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Edoardo Saccenti, Hauke Smidt
Software Mentions: 14
Published: over 4 years ago

10.3390/ijms22115751

Multi-Omics Model Applied to Cancer Genetics
Cited by: 14
Author(s): Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
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

10.1371/journal.pone.0249268

Outdoor cycling activity affected by COVID-19 related epidemic-control-decisions
Cited by: 38
Author(s): Anne-Maria Schweizer, Anna Leiderer, Veronika Mitterwallner, Anna Walentowitz, Gregor Mathes, Manuel J. Steinbauer
Software Mentions: 14
Published: over 3 years ago

10.7554/eLife.55913

An image-based data-driven analysis of cellular architecture in a developing tissue
Cited by: 22
Author(s): Jonas Hartmann, Mie Wong, Elisa Cristina de Proença Rodrigues Gallo, Darren Gilmour
Software Mentions: 14
Published: over 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

10.3390/microorganisms7120680

EpiExploreR: A Shiny Web Application for the Analysis of Animal Disease Data
Cited by: 4
Author(s): Lara Savini, Luca Candeloro, Samuel Perticara, Annamaria Conte
Software Mentions: 14
Published: almost 5 years ago

10.3389/fgene.2021.689406

Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing
Cited by: 26
Author(s): Júber Herrera-Uribe, Jayne E Wiarda, Sathesh K Sivasankaran, Lance Daharsh, Haibo Li, Kristen A Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 14
Published: over 3 years ago

10.3389/fgene.2020.522125

Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles
Cited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: about 4 years ago

10.1186/s12859-016-0971-3

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
Cited by: 20
Author(s): Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew Parnell, Stephen V. Gordon, David E. MacHugh
Software Mentions: 14
Published: over 8 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

10.1186/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

10.1371/journal.pone.0243467

Predicting self-harm within six months after initial presentation to youth mental health services: A machine learning study
Cited by: 16
Author(s): Frank Iorfino, Nicholas Ho, Joanne S. Carpenter, Shane Cross, Tracey A Davenport, Daniel F. Hermens, Hannah Yee, Alissa Nichles, Natalia Zmicerevska, Adam J. Guastella, Elizabeth Scott, Ian B. Hickie
Software Mentions: 14
Published: almost 4 years ago

10.1002/ece3.6786

<i>SDMtune</i>: 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

10.1186/s12888-020-02645-6

Depression, anxiety, and burnout among medical students and residents of a medical school in Nepal: a cross-sectional study
Cited by: 66
Author(s): Nishan Babu Pokhrel, Ramesh Khadayat, P Tulachan
Software Mentions: 14
Published: over 4 years ago

10.1186/s12859-021-04261-x

Machine learning-based prediction of survival prognosis in cervical cancer
Cited by: 16
Author(s): Dongyan Ding, Tingyuan Lang, Dongling Zou, Jianrong Tan, Jia Chen, Lei Zhou, Dong Wang, Rong Li, Yunzhe Li, Jingshu Liu, Cui Ma, Qi Zhou
Software Mentions: 14
Published: over 3 years ago

10.3389/fonc.2020.573295

Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal Cancer
Cited by: 11
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Zheng Liu, Qian Liu
Software Mentions: 14
Published: about 4 years ago

10.3390/cancers13174348

Histological Grade of Endometrioid Endometrial Cancer and Relapse Risk Can Be Predicted with Machine Learning from Gene Expression Data
Cited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: about 3 years ago

10.1038/s41598-021-97071-3

Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions
Cited by: 10
Author(s): Ankit T. Hinsu, Ketankumar Panchal, Ramesh Pandit, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 14
Published: about 3 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

10.1186/s12859-016-0884-1

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

10.3390/pathogens9100841

Diverse Epidemiology of Leptospira Serovars Notified in New Zealand, 1999–2017
Cited by: 12
Author(s): Shahista Nisa, David A. Wilkinson, Olivia Angelin‐Bonnet, Shevaun Paine, Karen Weber Cullen, Jackie Wight, Michael G Baker, Jackie Benschop
Software Mentions: 14
Published: about 4 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

10.3389/fnins.2014.00067

Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRF
Cited by: 11
Author(s): Vincent Thomas, Solveig Badillo, Laurent Risser, Lotfi Chaâri, Christine Bakhous, Florence Forbes, Philippe Ciuciu
Software Mentions: 14
Published: over 10 years ago

10.3390/microorganisms9061167

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad
Cited by: 10
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 14
Published: over 3 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

10.7717/peerj.3472

Using high-throughput sequencing of ITS2 to describe <i>Symbiodinium</i> 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

10.1371/journal.pntd.0002045

Drivers of Echinococcus multilocularis Transmission in China: Small Mammal Diversity, Landscape or Climate?
Cited by: 65
Author(s): Patrick Giraudoux, Francis Raoul, David Pleydell, Tiaoying Li, Xiuming Han, Jiamin Qiu, Yan Xie, Wang Hu, Akira Itō, Philip S. Craig
Software Mentions: 14
Published: over 11 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

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.1186/s12967-021-02894-3

Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responses
Cited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: over 3 years ago

10.12688/f1000research.24956.2

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Cited by: 274
Author(s): Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Software Mentions: 14
Published: about 4 years ago

10.1186/s40679-016-0031-0

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: almost 8 years ago

10.1186/s12859-018-2486-6

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Cited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: almost 6 years ago

10.1186/s13148-021-01173-8

Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism
Cited by: 5
Author(s): Kristyna Kupkova, Savera J. Shetty, Rashidul Haque, William A. Petri, David T. Auble
Software Mentions: 14
Published: about 3 years ago

10.1186/s12916-020-01686-8

In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children
Cited by: 19
Author(s): Marta Vives-Usano, Carles Hernández-Ferrer, Léa Maitre, Carlos Ruiz‐Arenas, Sandra Andrušaitytė, Eva Borràs, Ángel Carracedo, Maribel Casas, Leda Chatzi, Muireann Coen, Xavier Estivill, Juan R. González, Kristine B. Gützkow, Hector C. Keun, Chung-Ho E Lau, Solène Cadiou, Johanna Lepeule, Dan Mason, Inés Quintela, Oliver Robinson, Eduard Sabidó, Gillian Santorelli, Per E. Schwarze, Alexandros P. Siskos, Rémy Slama, Marina Vafeiadi, Eulàlia Martı́, Martine Vrijheid, Mariona Bustamante
Software Mentions: 14
Published: over 4 years ago

10.1038/s41375-018-0360-1

Immune cell constitution in bone marrow microenvironment predicts outcome in adult ALL
Cited by: 39
Author(s): Helena Hohtari, Oscar Brück, Sami Blom, Riku Turkki, Marjatta Sinisalo, Panu E. Kovanen, Olli Kallioniemi, Teijo Pellinen, Kimmo Porkka, Satu Mustjoki
Software Mentions: 14
Published: almost 6 years ago

10.3390/ijms22073681

Circulating miRNAs as Biomarkers for Mitochondrial Neuro-Gastrointestinal Encephalomyopathy
Cited by: 4
Author(s): Mark Mencias, Michelle Levene, Kevin Blighe, Bridget E. Bax
Software Mentions: 14
Published: over 3 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

10.1186/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

10.1371/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

10.1007/s00204-020-02956-3

Human neuronal signaling and communication assays to assess functional neurotoxicity
Cited by: 13
Author(s): Dominik Loser, Jasmin Schaefer, Timm Danker, Clemens Möller, Markus Brüll, Ilinca Suciu, Anna‐Katharina Ückert, Stefanie Klima, Marcel Leist, Udo Kraushaar
Software Mentions: 14
Published: almost 4 years ago

10.1111/jcmm.15705

Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma
Cited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: over 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

10.3389/fimmu.2021.557994

Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale Analysis
Cited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: over 3 years ago

10.7150/jca.55970

Characteristics of Infiltrating Immune Cells and a Predictive Immune Model for Cervical Cancer
Cited by: 11
Author(s): Ruanmin Zou, Ruihong Gu, Xinbing Yu, Yingying Hu, Ji Hee Yu, Xiangyang Xue, Xueqiong Zhu
Software Mentions: 14
Published: almost 4 years ago

10.1186/s12859-021-04193-6

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0237368

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?
Cited by: 9
Author(s): Gian Maria Niccolò Benucci, Bryan Rennick, Gregory Bonito
Software Mentions: 14
Published: over 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

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1093/bioinformatics/btx657

heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Cited by: 334
Author(s): Tal Galili, Alan O’Callaghan, Jonathan Savage, Carson Sievert
Software Mentions: 14
Published: about 7 years ago

10.1038/srep30325

In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells
Cited by: 72
Author(s): Joke Robijns, Freya Molenberghs, Tom Sieprath, Tobias Corne, Marlies Verschuuren, Winnok H. De Vos
Software Mentions: 14
Published: over 8 years ago

10.1155/2020/8833972

An Epithelial-Mesenchymal Transition (EMT) Preoperative Nomogram for Prediction of Lymph Node Metastasis in Bladder Cancer (BLCA)
Cited by: 5
Author(s): Rui Cao, Bo Ma, Gang Wang, Yaoyi Xiong, Ye Tian, Lushun Yuan
Software Mentions: 14
Published: about 4 years ago

10.1038/s41598-020-76843-3

Analyzing long-term impacts of ungulate herbivory on forest-recruitment dynamics at community and species level contrasting tree densities versus maximum heights
Cited by: 10
Author(s): Ursula Nopp‐Mayr, Susanne Reimoser, Friedrich Reimoser, Frederik Sachser, Leopold Obermair, Georg Gratzer
Software Mentions: 14
Published: about 4 years ago

10.1186/s12864-016-3038-y

A full-body transcriptome and proteome resource for the European common carp
Cited by: 33
Author(s): Iris Kolder, Suzanne J. van der Plas-Duivesteijn, Ge Tan, G.F. Wiegertjes, Maria Forlenza, Arzu Güler, Dmitrii Y. Travin, Minoru Nakao, Tadaaki Moritomo, Ilgiz Irnazarow, Johan T. den Dunnen, Seyed Yahya Anvar, Hans J. Jansen, Ron P. Dirks, Magnus Palmblad, Boris Lenhard, Christiaan V. Henkel, Herman P. Spaink
Software Mentions: 14
Published: about 8 years ago

10.1038/s41396-020-00798-6

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations
Cited by: 48
Author(s): Kali M. Pruss, Ángela Marcobal, Audrey Southwick, Dylan Dahan, Sam Smits, Jessica A. Ferreyra, Steven K. Higginbottom, Erica D. Sonnenburg, Purna C. Kashyap, Biswa Choudhury, Lars Bode, Justin L. Sonnenburg
Software Mentions: 14
Published: about 4 years ago

10.3390/cells10030620

Measuring Pre- and Post-Copulatory Sexual Selection and Their Interaction in Socially Monogamous Species with Extra-Pair Paternity
Cited by: 6
Author(s): Emily R. A. Cramer
Software Mentions: 14
Published: over 3 years ago

10.1186/s12864-018-4559-3

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Cited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: over 6 years ago

10.1038/s41598-021-97362-9

N6-methylandenosine-related lncRNAs play an important role in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Yuhai Hu, Yiping Chen
Software Mentions: 14
Published: about 3 years ago

10.1371/journal.pone.0248185

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis
Cited by: 15
Author(s): Laura Vega, Giovanny Herrera, Marina Muñoz, Manuel A. Patarroyo, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 14
Published: over 3 years ago

10.1186/s13059-021-02264-8

GeneWalk identifies relevant gene functions for a biological context using network representation learning
Cited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: almost 4 years ago

10.18632/aging.203353

Development and validation of an intra-tumor heterogeneity-related signature to predict prognosis of bladder cancer: a study based on single-cell RNA-seq
Cited by: 7
Author(s): Ranran Zhou, Jingjing Liang, Qi Chen, Haijun Tian, Cheng Yang, Cundong Liu
Software Mentions: 14
Published: over 3 years ago

10.3389/fgene.2021.723360

Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens
Cited by: 7
Author(s): Fasil Getachew Kebede, Hans Komen, Tadelle Dessie, Setegn Worku Alemu, Olivier Hanotte, J.W.M. Bastiaansen
Software Mentions: 14
Published: about 3 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

10.7717/peerj.11880

Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of <i>NEDD4L</i> in clear-cell renal cell cancer
Cited by: 6
Author(s): Hui Zhao, Junjun Zhang, Xiaoliang Fu, Dongdong Mao, Xuesen Qi, Shuai Liang, Gang Ma, Zewen Song, Ru Yang, Zhenni Guo, Binghua Tong, Meiqing Sun, Baile Zuo, Guoyin Li
Software Mentions: 14
Published: over 3 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

10.1186/s13059-019-1851-8

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
Cited by: 44
Author(s): Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
Software Mentions: 14
Published: about 5 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

10.1186/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/fgene.2021.702072

Characterization of Modification Patterns, Biological Function, Clinical Implication, and Immune Microenvironment Association of m6A Regulators in Pancreatic Cancer
Cited by: 5
Author(s): Kun Fang, Hairong Qu, Jiapei Wang, Desheng Tang, Changsheng Yan, Jiamin Ma, Lei Gao
Software Mentions: 14
Published: about 3 years ago

10.1007/s15010-021-01656-z

Prediction of COVID-19 deterioration in high-risk patients at diagnosis: an early warning score for advanced COVID-19 developed by machine learning
Cited by: 16
Author(s): Carolin E. M. Jakob, Ujjwal Mukund Mahajan, Marcus Oswald, Melanie Stecher, Maximilian Schons, Julia Mayerle, Siegbert Rieg, Mathias W. Pletz, Uta Merle, Kai Wille, Stefan Borgmann, Christoph D. Spinner, Sebastian Dolff, Clemens Scherer, Lisa Pilgram, Maria Madeleine Rüthrich, Frank Hanses, Martin Hower, Richard Strauß, Steffen Maßberg, Ahmet Er, Norma Jung, Jörg Janne Vehreschild, Hans Stubbe, Lukas Tometten, Rainer König, Lukas Tometten, Siegbert Rieg, Uta Merle, Kai Wille, Stefan Borgmann, Christoph D. Spinner, Sebastian Dolff, Maria Madeleine Rüthrich, Frank Hanses, Martin Hower, Richard Strauß, Murat Akova, Norma Jung, Michael von Bergwelt‐Baildon, Maria J. G. T. Vehreschild, Beate Grüner, Martina Haselberger, Nora Isberner, Christiane Piepel, Kerstin Hellwig, Dominic Rauschning, Lukas Eberwein, Björn Jensen, Claudia Raichle, Gabriele Müller-Jörger, Sven Stieglitz, Thomas Kratz, Christian Degenhardt, Anette Friedrichs, Robert Bals, Susanne Rüger, Katja de With, Katja Rothfuss, Siri Goepel, Jacob Nattermann, Sabine Jordan, Jessica Rüddel, Janina Trauth, Gernot Beutel, Özlem Altuntaş Aydın, Milena Milovanovic, Michael Doll, Jörg Janne Vehreschild, Lisa Pilgram, Melanie Stecher, Carolin E. M. Jakob, Maximilian Schons, Annika Y. Claßen, Sandra Fuhrmann, Susana Nunes de Miranda, Bernd Franke, Nick Schulze, Fabian Praßer, Martin Lablans
Software Mentions: 14
Published: over 3 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

10.1371/journal.pone.0225615

An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery
Cited by: 9
Author(s): Garrett C. McCarthy, Sydney Morgan, Jonathan T. Martiniuk, Brianne L. Newman, Stephanie McCann, Vivien Measday, Daniel M. Durall
Software Mentions: 14
Published: almost 4 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

10.3390/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

10.3389/fimmu.2020.606164

Six Immune Associated Genes Construct Prognostic Model Evaluate Low-Grade Glioma
Cited by: 32
Author(s): Yin Qiu Tan, Yun Tao Li, Teng Feng Yan, Yang Xu, Bao Hui Liu, Ji An Yang, Yang Xue, Qianxue Chen, Hong Bo Zhang
Software Mentions: 14
Published: almost 4 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

10.3389/fonc.2020.575422

A Novel Model Based on CXCL8-Derived Radiomics for Prognosis Prediction in Colorectal Cancer
Cited by: 8
Author(s): Yanpeng Chu, Jie Li, Zong Yuan Zeng, Bin Huang, Jiaojiao Zhao, Qin Liu, Huaping Wu, Jiangping Fu, Zheng Yin, Yefan Zhang, Jianqiang Cai, Fanxin Zeng
Software Mentions: 14
Published: about 4 years ago

10.1186/s12864-021-07542-0

Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: over 3 years ago

10.1038/s41598-020-78747-8

Non-invasive assessment of skeletal muscle fibrosis in mice using nuclear magnetic resonance imaging and ultrasound shear wave elastography
Cited by: 6
Author(s): Aurea B. Martins-Bach, Damien Bachasson, E. Araujo, Lucas Soustelle, Paulo Loureiro de Sousa, Y. Fromes, Pierre Carlier
Software Mentions: 13
Published: almost 4 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: about 3 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 years ago

10.3389/fonc.2020.01317

The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study
Cited by: 17
Author(s): Hao Gu, Lu-Lu Lin, Zhang Chao, Min Yang, Hongshan Zhong, Renxiong Wei
Software Mentions: 13
Published: over 4 years ago

10.1186/s12864-019-5700-7

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pone.0253148

Enhancing monitoring of rewilding progress through wildlife tracking and remote sensing
Cited by: 1
Author(s): Julia Carolina Mata, Robert Buitenwerf, Jens‐Christian Svenning
Software Mentions: 13
Published: over 3 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago

10.1186/s13059-019-1898-6

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 123
Author(s): Shuang Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou
Software Mentions: 13
Published: almost 5 years ago