Ecosyste.ms: Papers

10.7717/peerj.5661

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
Cited by: 17
Author(s): Camila Duarte Ritter, Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher J. Barnes, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0195065

Dengue forecasting in São Paulo city with generalized additive models, artificial neural networks and seasonal autoregressive integrated moving average models
Cited by: 48
Author(s): Oswaldo Santos Baquero, Lidia Maria Reis Santana, Francisco Chiaravalloti Neto
Software Mentions: 12
Published: over 6 years ago

10.1093/conphys/coaa047

Changes in physiology and microbial diversity in larval ornate chorus frogs are associated with habitat quality
Cited by: 9
Author(s): Cory B. Goff, Susan C. Walls, David Rodríguez, Caitlin R. Gabor
Software Mentions: 12
Published: almost 5 years ago

10.1002/ece3.7625

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab <i>Scylla olivacea</i> (Herbst, 1796) in the Sulu Sea
Cited by: 4
Author(s): Michael John Mendiola, Rachel Ravago-Gotanco
Software Mentions: 12
Published: over 3 years ago

10.3390/plants10050879

Multivariate Analysis of Morpho-Physiological Traits Reveals Differential Drought Tolerance Potential of Bread Wheat Genotypes at the Seedling Stage
Cited by: 26
Author(s): Mohammed Mohi-Ud-Din, Md. Alamgir Hossain, Md. Motiar Rohman, Md. Nesar Uddin, Md. Sabibul Haque, Jalal Uddin Ahmed, Akbar Hossain, Mohamed M. Hassan, Mohammad Golam Mostofa
Software Mentions: 12
Published: over 3 years ago

10.3389/fgene.2021.689159

Analyzing Roles of NUSAP1 From Clinical, Molecular Mechanism and Immune Perspectives in Hepatocellular Carcinoma
Cited by: 3
Author(s): Wenjie Zhu, Jian Xu, Zehao Chen, Jianxin Jiang
Software Mentions: 12
Published: over 3 years ago

10.7554/eLife.65751

Visualizing anatomically registered data with brainrender
Cited by: 64
Author(s): Federico Claudi, Adam L. Tyson, Luigi Petrucco, Troy W. Margrie, Rubén Portugues, Tiago Branco
Software Mentions: 12
Published: over 3 years ago

10.1186/s40462-017-0096-y

Movement of leopard tortoises in response to environmental and climatic variables in a semi-arid environment
Cited by: 6
Author(s): Martyn Drabik-Hamshare, Colleen T. Downs
Software Mentions: 12
Published: over 7 years ago

10.1186/s12974-021-02235-7

Sex differences and similarities in the neuroimmune response to central administration of poly I:C
Cited by: 14
Author(s): Caitlin K. Posillico, Rosa E. Garcia-Hernandez, Natalie C. Tronson
Software Mentions: 12
Published: about 3 years ago

10.1111/gcb.15637

Impacts of climate change on aquatic insects in temperate alpine regions: Complementary modeling approaches applied to Swiss rivers
Cited by: 6
Author(s): Pablo Timoner, Marc Fasel, Seyed Saeid Ashraf Vaghefi, Pierre Marle, Emmanuel Castella, Frédéric Moser, Anthony Lehmann
Software Mentions: 12
Published: over 3 years ago

10.1186/s13148-019-0729-7

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease
Cited by: 26
Author(s): Mikko Konki, Maia Malonzo, Ida Karlsson, Noora Lindgrén, Bishwa Ghimire, Johannes Smolander, Noora M. Scheinin, Miina Ollikainen, Asta Laiho, Laura L. Elo, Tapio Lönnberg, Matias Röyttä, Nancy L. Pedersen, Jaakko Kaprio, Harri Lähdesmäki, Juha O. Rinne, Riikka Lund
Software Mentions: 12
Published: about 5 years ago

10.1002/cam4.4126

Hypoxia‐related lncRNAs to build prognostic classifier and reveal the immune characteristics of EGFR wild type and low expression of PD‐L1 squamous and adenocarcinoma NSCLC
Cited by: 4
Author(s): Fang Zhao, Min Wang, Jie Zhu
Software Mentions: 12
Published: over 3 years ago

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: about 6 years ago

10.3389/fimmu.2021.647832

Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection
Cited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 3 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: about 11 years ago

10.1371/journal.pone.0251323

The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases
Cited by: 2
Author(s): Weijun Shi, Xincan Li, Shuai Xu, Hexin Wen, Tianwen Chen, Huazhang Wu, Mulin Liu
Software Mentions: 12
Published: over 3 years ago

10.1002/ece3.7992

Using Delaunay triangulation to sample whole‐specimen color from digital images
Cited by: 5
Author(s): Jennifer J Valvo, J. David Aponte, Mitch J Daniel, Kenna Dwinell, Helen Rodd, David Houle, Kimberly A. Hughes
Software Mentions: 12
Published: over 3 years ago

10.3389/fgene.2020.00968

Systematic Transcriptome Analysis of Noise-Induced Hearing Loss Pathogenesis Suggests Inflammatory Activities and Multiple Susceptible Molecules and Pathways
Cited by: 6
Author(s): Quan Wang, Yilin Shen, Hongbo Hu, Fan Cui, Andi Zhang, Rui Ding, Bin Ye, Ming Xiang
Software Mentions: 12
Published: over 4 years ago

10.7717/peerj.11923

Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery
Cited by: 2
Author(s): Peng Han, Jiaqi Yue, Kangle Kong, Shan Huang, Pei Cao, Yu Deng, Ли Фан, Bo Zhao
Software Mentions: 12
Published: over 3 years ago

10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Cited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: about 7 years ago

10.1371/journal.pone.0205742

The calm during the storm: Snowfall events decrease the movement rates of grey wolves (Canis lupus)
Cited by: 10
Author(s): Amanda Droghini, Stan Boutin
Software Mentions: 12
Published: about 6 years ago

10.3389/fgene.2020.00363

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma
Cited by: 114
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Qiuyu Zhang, Jinsheng Hong
Software Mentions: 12
Published: over 4 years ago

10.1111/1462-2920.14621

Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes
Cited by: 22
Author(s): Pavla Debeljak, Ève Toulza, Sara Beier, Stéphane Blain, Ingrid Obernosterer
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2017.01553

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves
Cited by: 58
Author(s): Juliana Dias, Marcos Inácio Marcondes, Melline Fontes Noronha, Rafael Tassinari Resende, F. S. Machado, Hilário Cuquetto Mantovani, Kimberly A. Dill‐McFarland, Garret Suen
Software Mentions: 12
Published: over 7 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: almost 7 years ago

10.12688/f1000research.27893.1

A guide to creating design matrices for gene expression experiments
Cited by: 18
Author(s): Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 12
Published: almost 4 years ago

10.1186/s12935-021-01900-4

Role of tumor mutation burden-related signatures in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma
Cited by: 16
Author(s): Rong Tang, Xiaomeng Liu, Wei Wang, Jie Hua, Jin Xu, Chen Liang, Qingcai Meng, Jiang Liu, Bo Zhang, Yu Lei, Si Shi
Software Mentions: 12
Published: over 3 years ago

10.1371/journal.pntd.0007061

Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae)
Cited by: 2
Author(s): Stephen W. Attwood, Liang Liu, Guan-Nan Huo
Software Mentions: 12
Published: almost 6 years ago

10.1002/ece3.7130

QuoVidi: An open‐source web application for the organization of large‐scale biological treasure hunts
Cited by: 8
Author(s): Guillaume Lobet, Charlotte Descamps, Lola Leveau, Alain Guillet, Jean-François Rees
Software Mentions: 12
Published: almost 4 years ago

10.1002/ece3.7294

Determinants of habitat suitability models transferability across geographically disjunct populations: Insights from <i>Vipera ursinii urs</i> <i>inii</i>
Cited by: 8
Author(s): Francesco Cerasoli, Aurélien Besnard, Marc-Antoine Marchand, Paola D’Alessandro, Mattia Iannella, Maurizio Biondi
Software Mentions: 12
Published: over 3 years ago

10.7717/peerj.11534

<i>AlleleShift:</i> an R package to predict and visualize population-level changes in allele frequencies in response to climate change
Cited by: 5
Author(s): Roeland Kindt
Software Mentions: 12
Published: over 3 years ago

10.1002/ece3.5295

<i>Acacia dealbata</i> invasion in Chile: Surprises from climatic niche and species distribution models
Cited by: 12
Author(s): Bárbara Langdon, Aníbal Pauchard, Ramiro O. Bustamante
Software Mentions: 12
Published: over 5 years ago

10.1002/ece3.6784

Ecomorphology of the pectoral girdle in anurans (Amphibia, Anura): Shape diversity and biomechanical considerations
Cited by: 10
Author(s): Karolin Engelkes, Lena Kath, Thomas Kleinteich, Jörg U. Hammel, André Beerlink, Alexander Haas
Software Mentions: 12
Published: about 4 years ago

10.26508/lsa.202000770

In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer
Cited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: about 4 years ago

10.1111/test.12258

Some teaching resources using R with illustrative examples exploring COVID ‐19 data
Cited by: 0
Author(s): Arthur Berg, Nour Hawila
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: about 6 years ago

10.3389/pore.2021.1609852

Identification of a Gene Prognostic Model of Gastric Cancer Based on Analysis of Tumor Mutation Burden
Cited by: 9
Author(s): Weijun Ma, Weidong Li, Xu Liu, Lu Liu, Xinbing Yu, Liping Yang, Mingxu Da
Software Mentions: 11
Published: about 3 years ago

10.1371/journal.pone.0234503

Nest boxes buffer the effects of climate on breeding performance in an African urban raptor
Cited by: 17
Author(s): Petra Sumasgutner, Andrew R. Jenkins, Arjun Amar, Res Altwegg
Software Mentions: 11
Published: over 4 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 5 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 3 years ago

10.1042/BSR20210527

Construction of a prognostic model for non-small-cell lung cancer based on ferroptosis-related genes
Cited by: 10
Author(s): Ke Han, Jukun Wang, Kun Qian, Teng Zhao, Xingsheng Liu, Yi Zhang
Software Mentions: 11
Published: over 3 years ago

10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Cited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 8 years ago

10.1016/j.mex.2018.07.003

A practical method to control spatiotemporal confounding in environmental impact studies
Cited by: 4
Author(s): Rezvan Hatami
Software Mentions: 11
Published: almost 7 years ago

10.1534/g3.120.401612

A Reference Genome Sequence for Giant Sequoia
Cited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: about 4 years ago

10.1186/s12859-019-2706-8

svist4get: a simple visualization tool for genomic tracks from sequencing experiments
Cited by: 32
Author(s): Artyom A. Egorov, Ekaterina Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy
Software Mentions: 11
Published: over 5 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago

10.1038/s41598-018-20825-z

Mosquito community influences West Nile virus seroprevalence in wild birds: implications for the risk of spillover into human populations
Cited by: 30
Author(s): Josué Martínez‐de la Puente, Martina Ferraguti, Santiago Ruíz, David Roiz, Francisco Rubio Llorente, Elisa Pérez‐Ramírez, Miguel Ángel Jiménez‐Clavero, Ramón C. Soriguer, Jordi Figuerola
Software Mentions: 11
Published: almost 7 years ago

10.2196/25124

Enhancing Obstructive Sleep Apnea Diagnosis With Screening Through Disease Phenotypes: Algorithm Development and Validation
Cited by: 2
Author(s): Daniela Ferreira-Santos, Pedro Pereira Rodrigues
Software Mentions: 11
Published: over 3 years ago

10.3389/fimmu.2021.664845

CD2 Is a Novel Immune-Related Prognostic Biomarker of Invasive Breast Carcinoma That Modulates the Tumor Microenvironment
Cited by: 24
Author(s): Yanzhu Chen, Zhishang Meng, Lin Zhang, Feng Liu
Software Mentions: 11
Published: over 3 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: over 4 years ago

10.1038/s41598-019-46850-0

Deep Learning using Convolutional LSTM estimates Biological Age from Physical Activity
Cited by: 56
Author(s): Syed Ashiqur Rahman, Donald A. Adjeroh
Software Mentions: 11
Published: over 5 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: almost 4 years ago

10.1038/srep44348

Major shifts at the range edge of marine forests: the combined effects of climate changes and limited dispersal
Cited by: 70
Author(s): Jorge Assis, Estíbaliz Berecibar, Bruno Claro, Filipe Alberto, Daniel C. Reed, Peter T. Raimondi, Ester Á. Serrão
Software Mentions: 11
Published: over 7 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: almost 9 years ago

10.3389/fmicb.2021.633659

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast
Cited by: 14
Author(s): Maria Luis de Vilar Correia Brito Bôto, Catarina Magalhães, Rafaela Perdigão, Diogo A. M. Alexandrino, Joana P. Fernandes, Ana M. Bernabéu, Sandra Ramos, Maria F. Carvalho, Miguel Semedo, Julie LaRoche, C. Marisa R. Almeida, Ana P. Mucha
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0245127

Adaptation and validation of a German version of the Strengths Use and Deficit Correction (SUDCO) questionnaire
Cited by: 2
Author(s): Timo Lorenz, Kathrin Heinitz, Clemens Beer, Marianne van Woerkom
Software Mentions: 11
Published: almost 4 years ago

10.7717/peerj.4395

COREMIC: a web-tool to search for a niche associated CORE MICrobiome
Cited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: almost 7 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: over 4 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 5 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: over 3 years ago

10.1186/s12935-020-01393-7

Small nucleolar RNAs signature (SNORS) identified clinical outcome and prognosis of bladder cancer (BLCA)
Cited by: 5
Author(s): Rui Cao, Bo Ma, Lushun Yuan, Gang Wang, Ye Tian
Software Mentions: 11
Published: over 4 years ago

10.1038/s41598-017-17728-w

Enclaves of genetic diversity resisted Inca impacts on population history
Cited by: 28
Author(s): Chiara Barbieri, José R. Sandoval, Jairo Valqui, Aviva Shimelman, Stefan Ziemendorff, Roland Schröder, Martin Geppert, Lutz Roewer, Russell D. Gray, Mark Stoneking, Ricardo Fujita, Paul Heggarty
Software Mentions: 11
Published: almost 7 years ago

10.18632/oncotarget.22928

Comparing the genomes of cutaneous melanoma tumors to commercially available cell lines
Cited by: 10
Author(s): Stephen A. Luebker, Weiwei Zhang, Scott A. Koepsell
Software Mentions: 11
Published: almost 7 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: over 9 years ago

10.18632/aging.203242

Glycolysis- and immune-related novel prognostic biomarkers of Ewing's sarcoma: glucuronic acid epimerase and triosephosphate isomerase 1
Cited by: 9
Author(s): Jie Jiang, Xinli Zhan, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Yuanlin Yao, Chong Liu
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-020-59494-2

Unstable crop yields reveal opportunities for site-specific adaptations to climate variability
Cited by: 30
Author(s): Rafael A. Martinez-Feria, Bruno Basso
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pgen.1009240

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior
Cited by: 5
Author(s): Colleen M Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G Brovero, Michelle N. Arbeitman
Software Mentions: 11
Published: over 3 years ago

10.1098/rspb.2021.0616

Juvenile ecology drives adult morphology in two insect orders
Cited by: 4
Author(s): Peter T. Rühr, Thomas van de Kamp, Tomáš Faragó, Jörg U. Hammel, Fabian Wilde, Elena Borisova, Carina Edel, Melina Frenzel, Tilo Baumbach, Alexander Blanke
Software Mentions: 11
Published: over 3 years ago

10.3389/fpsyg.2021.638659

Syllable Complexity and Morphological Synthesis: A Well-Motivated Positive Complexity Correlation Across Subdomains
Cited by: 2
Author(s): Shelece Easterday, Matthew Stave, Marc Allassonnière-Tang, Frank Seifart
Software Mentions: 11
Published: over 3 years ago

10.1016/j.isci.2021.102882

Integrated analysis of glycan and RNA in single cells
Cited by: 22
Author(s): Fumi Minoshima, Haruka Ozaki, Haruki Odaka, Hiroaki Tateno
Software Mentions: 11
Published: over 3 years ago

10.3389/fmolb.2019.00025

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Cited by: 22
Author(s): Dalibor Trapl, Izabela Horvacanin, Václav Mareška, Furkan Özçelik, Gözde Ünal, Vojtěch Spiwok
Software Mentions: 11
Published: over 5 years ago

10.1093/beheco/araa104

Sequential organization of birdsong: relationships with individual quality and fitness
Cited by: 8
Author(s): Sándor Zsebők, Gábor Herczeg, Miklós Laczi, Gergely Nagy, Éva Vaskúti, Rita Hargitai, Gergely Hegyi, Márton Herényi, Gábor Markó, Balázs Rosivall, Eszter Szász, Eszter Szöllősi, János Török, László Zsolt Garamszegi
Software Mentions: 11
Published: about 4 years ago

10.1080/0886022X.2021.1960563

Derivation and validation of a model to predict acute kidney injury following cardiac surgery in patients with normal renal function
Cited by: 8
Author(s): Penghua Hu, Zhiming Mo, Yuanhan Chen, Yanhua Wu, Li Song, Li Zhang, Zhilian Li, Lei Fu, Huaban Liang, Yiming Tao, Shuangxin Liu, Zhiming Ye, Xinling Liang
Software Mentions: 11
Published: almost 4 years ago

10.1002/1878-0261.12134

Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma
Cited by: 21
Author(s): Merrina Anugraham, Francis Jacob, Arun Everest‐Dass, Andreas Schoetzau, Sheri Nixdorf, Neville F. Hacker, Daniel Fink, Viola Heinzelmann‐Schwarz, Nicolle H. Packer
Software Mentions: 11
Published: about 7 years ago

10.1111/eva.13274

SNP analyses and acoustic tagging reveal multiple origins and widespread dispersal of invasive brown trout in the Falkland Islands
Cited by: 2
Author(s): Jessica F. Minett, Carlos García de Leániz, Halina Sobolewska, Paul Brickle, Glenn T. Crossin, Sofía Consuegra
Software Mentions: 11
Published: over 3 years ago

10.1002/ece3.7881

Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola
Cited by: 4
Author(s): Winda Ika Susanti, Tamara Bartels, Valentyna Krashevska, Rahayu Widyastuti, Louis Deharveng, Stefan Scheu, Anton M. Potapov
Software Mentions: 11
Published: over 3 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 10 years ago

10.1038/s41598-021-96712-x

Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
Cited by: 12
Author(s): César A. Medina, Deborah A. Samac, Long‐Xi Yu
Software Mentions: 11
Published: over 3 years ago

10.3389/fmicb.2019.02904

Fungal Traits Important for Soil Aggregation
Cited by: 68
Author(s): Anika Lehmann, Weiguo Zheng, Masahiro Ryo, Katharina Soutschek, Julien Roy, Rebecca Rongstock, Stefanie Maaß, Matthias C. Rillig
Software Mentions: 11
Published: almost 5 years ago

10.1007/s40300-021-00213-w

Editorial, special issue on “Advances in Robust Statistics”
Cited by: 1
Author(s): Marco Riani, Mia Hubert
Software Mentions: 11
Published: over 3 years ago

10.7717/peerj.4251

Sicegar: R package for sigmoidal and double-sigmoidal curve fitting
Cited by: 28
Author(s): Mehmet Umut Caglar, Ashley I. Teufel, Claus O. Wilke
Software Mentions: 11
Published: almost 7 years ago

10.1186/s12859-019-2968-1

Visualization methods for differential expression analysis
Cited by: 6
Author(s): Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0235283

Targeting the oral plaque microbiome with immobilized anti-biofilm peptides at tooth-restoration interfaces
Cited by: 18
Author(s): Dina G. Moussa, Conrado Aparicio
Software Mentions: 11
Published: over 4 years ago

10.1128/mSphere.00481-19

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
Cited by: 15
Author(s): Ryan B. Ghannam, Laura G. Schaerer, Timothy Butler, Stephen M. Techtmann
Software Mentions: 11
Published: almost 5 years ago

10.1016/j.celrep.2020.107908

Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
Cited by: 174
Author(s): Ying-Wooi Wan, Rami Al‐Ouran, Carl Grant Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine S. Allison, Vivek Swarup, Cory C. Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M. Neuner, Catherine C. Kaczorowski, Vivek Philip, Gareth R. Howell, Heidi Martini‐Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L. Dawson, Ted M. Dawson, Ping‐Chieh Pao, Li‐Huei Tsai, Jean‐Vianney Haure‐Mirande, Michelle E. Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen K. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuß, Ayla Ergün, Philip J. Ebert, David Airey, Sara Mostafavi, Lei Yu, Hans‐Ulrich Klein, Gregory W. Carter, David A. Collier, Todd E. Golde, Aĺlan I. Levey, David A. Bennett, Karol Estrada, T. Matthew Townsend, Bin Zhang, Eric E. Schadt, Philip L. De Jager, Nathan D. Price, Nilüfer Ertekin-Taner, Zhandong Liu, Zhandong Liu, Lara M. Mangravite, Benjamin A. Logsdon
Software Mentions: 11
Published: over 4 years ago

10.1111/jcmm.15939

Prognostic value and immune cell infiltration of hypoxic phenotype‐related gene signatures in glioblastoma microenvironment
Cited by: 10
Author(s): Kai Xiao, Jun Tan, Jian Yuan, Gang Peng, Wenyong Long, Jun Su, Yao Xiao, Qian Xiao, Changwu Wu, Chaoying Qin, Lili Hu, Kaili Liu, Shunlian Liu, Hao Zhou, Yichong Ning, Xiaojuan Ding, Qing Liu
Software Mentions: 11
Published: about 4 years ago

10.1111/jcmm.16552

Identification of autophagy‐related genes signature predicts chemotherapeutic and immunotherapeutic efficiency in bladder cancer (BLCA)
Cited by: 8
Author(s): Rui Cao, Bo Ma, Gang Wang, Yaoyi Xiong, Ye Tian, Lushun Yuan
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pgen.1008748

Polygenic adaptation of rosette growth in Arabidopsis thaliana
Cited by: 19
Author(s): Benedict Wieters, Kim A. Steige, Fei He, Evan Koch, Sebastián E. Ramos-Onsins, Hongya Gu, Ya‐Long Guo, Shamil Sunyaev, Juliette de Meaux
Software Mentions: 11
Published: almost 4 years ago

10.3389/fimmu.2016.00339

IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
Cited by: 38
Author(s): Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie‐Paule Lefranc
Software Mentions: 11
Published: about 8 years ago

10.3390/nu12020302

The Role of Glycemic Index and Glycemic Load in the Development of Real-Time Postprandial Glycemic Response Prediction Models for Patients with Gestational Diabetes
Cited by: 14
Author(s): Evgenii Pustozerov, Aleksandra Tkachuk, Elena Vasukova, А. В. Дронова, Ekaterina S. Shilova, Anna D. Anopova, Faina Piven, Tatiana Pervunina, Elena Vasilieva, Elena Grineva, Polina Popova
Software Mentions: 11
Published: almost 5 years ago

10.3389/fgene.2021.625145

Identification of Tumor Microenvironment-Related Prognostic Biomarkers for Ovarian Serous Cancer 3-Year Mortality Using Targeted Maximum Likelihood Estimation: A TCGA Data Mining Study
Cited by: 2
Author(s): Lu Wang, Xiaoru Sun, Chuandi Jin, Yue Fan, Fuzhong Xue
Software Mentions: 11
Published: over 3 years ago

10.1186/s13321-017-0215-1

ChemSAR: an online pipelining platform for molecular SAR modeling
Cited by: 39
Author(s): Jie Dong, Zhi Jiang Yao, Min Zhu, Ning Ning Wang, Ben Lü, Alex F. Chen, Ai Ping Lu, Hongyu Miao, Wen Zeng, Dong Sheng Cao
Software Mentions: 11
Published: over 7 years ago

10.1093/g3journal/jkab104

Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species
Cited by: 2
Author(s): Astra S. Bryant, Stephanie F. DeMarco, Elissa A. Hallem
Software Mentions: 11
Published: over 3 years ago

10.1038/srep26929

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
Cited by: 43
Author(s): Fábio Pértille, Carlos Guerrero-Bosagna, Vinícius da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, Luiz Lehmann Coutinho
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pone.0207126

Prognostic function to estimate the probability of meaningful clinical improvement after surgery - Results of a prospective multicenter observational cohort study on patients with lumbar spinal stenosis
Cited by: 20
Author(s): Ulrike Held, Jakob M Burgstaller, Maria M. Wertli, Giuseppe Pichierri, Sebastian Winklhofer, Florian Brunner, François Porchet, Mazda Farshad, Johann Steurer
Software Mentions: 11
Published: about 6 years ago

10.7554/eLife.49064

Stepwise polarisation of developing bilayered epidermis is mediated by aPKC and E-cadherin in zebrafish
Cited by: 10
Author(s): Prateek Arora, Shivali Dongre, Renuka Raman, Mahendra Sonawane
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: almost 7 years ago

10.1038/s42003-021-02463-w

Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment
Cited by: 18
Author(s): Kauê de Sousa, Jacob van Etten, Jesse Poland, Carlo Fadda, Jean‐Luc Jannink, Yosef Gebrehawaryat Kidane, Basazen Fantahun, Deȷene K. Mengistu, Mario Enrico Pè, Svein Øivind Solberg, Matteo Dell’Acqua
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-017-1579-y

metaX: a flexible and comprehensive software for processing metabolomics data
Cited by: 402
Author(s): Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
Software Mentions: 11
Published: over 7 years ago

10.1128/mSystems.00404-19

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria <i>In Vitro</i>
Cited by: 13
Author(s): Kaitlyn Oliphant, Kyla Cochrane, Kathleen Schroeter, Michelle Daigneault, Sandi Yen, Elena F. Verdú, Emma Allen‐Vercoe
Software Mentions: 11
Published: almost 5 years ago