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: about 5 years ago

10.7717/peerj.9847

Prognostic implications of metabolism-associated gene signatures in colorectal cancer
Cited by: 21
Author(s): Yifei Miao, Qiutian Li, Jiangtao Wang, Wuxia Quan, Chen Li, Yuan Yang, Denghai Mi
Software Mentions: 12
Published: about 6 years ago

10.1093/gigascience/gix037

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics
Cited by: 48
Author(s): Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R. Fernie
Software Mentions: 12
Published: over 9 years ago

10.1371/journal.pone.0225900

PyRates—A Python framework for rate-based neural simulations
Cited by: 10
Author(s): Richard Gast, Daniel Rose, Christoph Salomon, Harald E. Möller, Nikolaus Weiskopf, Thomas R. Knösche
Software Mentions: 12
Published: almost 7 years ago

10.3390/biom11020338

Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations
Cited by: 1
Author(s): Maroua Ben Amira, Mohamed Faize, Magnus Karlsson, Mukesh Dubey, Magdalena Frąc, Jacek Panek, Boris Fumanal, Aurélie Gousset-Dupont, Jean-Louis Julien, Hatem Chaar, Daniel Auguin, Robin Mom, Philippe Label, Jean-Stéphane Venisse
Software Mentions: 12
Published: over 5 years ago

10.7554/eLife.60474

The effect of hybridization on transposable element accumulation in an undomesticated fungal species
Cited by: 26
Author(s): Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R. Landry
Software Mentions: 12
Published: about 6 years ago

10.1007/s12032-017-0963-9

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data
Cited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: over 9 years ago

10.1093/gigascience/giab011

The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets
Cited by: 2
Author(s): Holly C. Beale, Jacquelyn Roger, Matthew Cattle, Liam T. McKay, Drew Thompson, Katrina Learned, A. Geoffrey Lyle, Ellen Kephart, R. Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R. Salama, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 5 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 7 years ago

10.3390/toxins12070433

Low Doses of Mycotoxin Mixtures below EU Regulatory Limits Can Negatively Affect the Performance of Broiler Chickens: A Longitudinal Study
Cited by: 26
Author(s): Oluwatobi Kolawole, A. Graham, Caroline Julie Donaldson, B. Owens, Wilfred A. Abia, Julie Meneely, M. Alcorn, Lisa Connolly, Chris Elliott
Software Mentions: 12
Published: about 6 years ago

10.3897/BDJ.4.e8357

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Cited by: 12
Author(s): Constantinos Varsos, Theodore Patkos, Anastasis Oulas, Christina Pavloudi, Alexandros Gougousis, Umer Zeeshan Ijaz, Irene Filiopoulou, Nikolaos Pattakos, E. Vanden Berghe, Antonio Fernàndez-Guerra, Sarah Faulwetter, Eva Chatzinikolaou, Evangelos Pafilis, Chryssoula Bekiari, Martin Doerr, Christos Arvanitidis
Software Mentions: 12
Published: almost 10 years ago

10.1371/journal.pone.0191956

Carotenoid coloration and health status of urban Eurasian kestrels (Falco tinnunculus)
Cited by: 24
Author(s): Petra Sumasgutner, Marius Adrion, Anita Gamauf
Software Mentions: 12
Published: over 8 years ago

10.1002/aps3.1227

Open‐source data reveal how collections‐based fungal diversity is sensitive to global change
Cited by: 24
Author(s): Carrie Andrew, Ulf Büntgen, Simon Egli, Béatrice Senn-Irlet, John‐Arvid Grytnes, Jacob Heilmann‐Clausen, Lynne Boddy, Claus Bässler, Alan C. Gange, Einar Heegaard, Klaus Høiland, Paul M. Kirk, Irmgard Krisai‐Greilhuber, Thomas W. Kuyper, Håvard Kauserud
Software Mentions: 12
Published: over 7 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: about 6 years ago

10.1186/s12889-021-11065-4

Who or what is to blame? Examining sociodemographic relationships to beliefs about causes, control, and responsibility for cancer and chronic disease prevention in Alberta, Canada
Cited by: 5
Author(s): Kimberley D. Curtin, Mathew Thomson, Candace I. J. Nykiforuk
Software Mentions: 12
Published: over 5 years ago

10.1098/rspb.2021.0394

Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework
Cited by: 7
Author(s): Orlin S. Todorov, Simone P. Blomberg, Anjali Goswami, Karen E. Sears, Patrik Drhlík, James Peters, Vera Weisbecker
Software Mentions: 12
Published: over 5 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: about 5 years ago

10.1002/ece3.8020

Functional groups in piscivorous fishes
Cited by: 8
Author(s): Michalis Mihalitsis, David R. Bellwood
Software Mentions: 12
Published: about 5 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 5 years ago

10.3389/fonc.2020.596822

Predictive Model and Precaution for Oral Mucositis During Chemo-Radiotherapy in Nasopharyngeal Carcinoma Patients
Cited by: 10
Author(s): Peijing Li, Kaixin Li, Tengchuan Jin, Hua Lin, Jun Fang, Shengchun Yang, Wei‐Chih Shen, Jia Chen, Jiang Zhang, Xiaozhong Chen, Ming Chen, Yuanyuan Chen
Software Mentions: 12
Published: almost 6 years ago

10.1186/s13059-019-1790-4

Identifying significantly impacted pathways: a comprehensive review and assessment
Cited by: 113
Author(s): Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen, Sorin Drăghici
Software Mentions: 12
Published: almost 7 years ago

10.1186/s12911-017-0500-y

Predicting two-year survival versus non-survival after first myocardial infarction using machine learning and Swedish national register data
Cited by: 53
Author(s): John Wallert, Mattia Tomasoni, Guy Madison, Claes Held
Software Mentions: 12
Published: about 9 years ago

10.1371/journal.pone.0204123

Prediction of early breast cancer patient survival using ensembles of hypoxia signatures
Cited by: 8
Author(s): Inna Y. Gong, Natalie S. Fox, Vincent Huang, Paul C. Boutros
Software Mentions: 12
Published: about 8 years ago

10.1038/srep26451

Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes
Cited by: 52
Author(s): Jahanshah Ashkani, Kevin J. Naidoo
Software Mentions: 12
Published: over 10 years ago

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: over 9 years ago

10.1371/journal.pone.0197176

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation
Cited by: 12
Author(s): Selçuk Korkmaz, José M. Duarte, Andreas Prlić, Dinçer Göksülük, Gökmen Zararsız, Osman Saraçbaşı, S.K. Burley, Peter W. Rose
Software Mentions: 12
Published: over 8 years ago

10.1186/s12885-021-07788-7

Comprehensive analysis of genomic mutation signature and tumor mutation burden for prognosis of intrahepatic cholangiocarcinoma
Cited by: 14
Author(s): Rui Zhang, Qi Li, Jiao Fu, Z C Jin, Jingbo Su, Jian Zhang, Chen Chen, Zhimin Geng, Dong Zhang
Software Mentions: 12
Published: over 5 years ago

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: almost 8 years ago

10.1186/s12859-018-2367-z

Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: almost 8 years ago

10.1186/s13567-021-00981-3

Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogens
Cited by: 8
Author(s): Christine Weiße, Denise Dittmar, Beata Jakóbczak, Volker Florian, Nicole Schütze, Gottfried Alber, Kristin Klose, Stephan Michalik, Peter Valentin‐Weigand, Uwe Völker, Christoph Georg Baums
Software Mentions: 12
Published: about 5 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 5 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 7 years ago

10.1371/journal.pone.0229330

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis
Cited by: 22
Author(s): Nicola G. Criscuolo, Claudia Angelini
Software Mentions: 12
Published: over 6 years ago

10.1002/ece3.7972

Elevated temperature increases reproductive investment in less preferred mates in the invasive European corn borer moth
Cited by: 4
Author(s): Arielle N. Enos, Genevieve M. Kozak
Software Mentions: 12
Published: about 5 years ago

10.3389/fgene.2020.00906

Construction and Validation of Novel Diagnostic and Prognostic DNA Methylation Signatures for Hepatocellular Carcinoma
Cited by: 7
Author(s): Ran Li, Liyan Shui, Junling Jia, Chao Wu
Software Mentions: 12
Published: about 6 years ago

10.3390/insects11080535

Impacts of Dietary Nutritional Composition on Larval Development and Adult Body Composition in the Yellow Fever Mosquito (Aedes aegypti)
Cited by: 15
Author(s): Tess van Schoor, Erin Taylor Kelly, Nicole Tam, Geoffrey M. Attardo
Software Mentions: 12
Published: about 6 years ago

10.3389/fonc.2021.654076

A Novel Ferroptosis Related Gene Signature for Prognosis Prediction in Patients With Colon Cancer
Cited by: 29
Author(s): Jianhua Nie, Dan Shan, Shun Li, Shuyuan Zhang, Xiaolin Zi, Fan Xing, Jiaqi Shi, Caiqi Liu, Tianjiao Wang, Xiankai Sun, Qian Zhang, Meng Zhou, Sai Luo, Hongxue Meng, Yanqiao Zhang, Tongsen Zheng
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-021-85155-z

Validating machine learning approaches for prediction of donor related complication in microsurgical breast reconstruction: a retrospective cohort study
Cited by: 6
Author(s): Yujin Myung, Sungmi Jeon, Chan Yeong Heo, Eun‐Kyu Kim, Eunyoung Kang, Hee-Chul Shin, Eun Joo Yang, Jae Hoon Jeong
Software Mentions: 12
Published: over 5 years ago

10.3389/fphar.2020.563751

Countrywide Survey of Plants Used for Liver Disease Management by Traditional Healers in Burkina Faso
Cited by: 1
Author(s): André Tibiri, Sébastien Boria, Tata Kadiatou Traoré, Noufou Ouédraogo, Aude Nikièma, Souleymane Ganaba, J. Compaoré, Issiaka Ouédraogo, Innocent Pierre Guissou, M Carraz
Software Mentions: 12
Published: almost 6 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: almost 6 years ago

10.1186/s41073-017-0030-2

Concern noted: a descriptive study of editorial expressions of concern in PubMed and PubMed Central
Cited by: 15
Author(s): Melissa Vaught, Diana C. Jordan, Hilda Bastian
Software Mentions: 12
Published: over 9 years ago

10.1128/mSystems.00903-19

manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: over 6 years ago

10.1186/s13059-018-1563-5

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: almost 8 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: over 7 years ago

10.3389/fmicb.2019.00144

Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges
Cited by: 70
Author(s): Laura M. Carroll, Manjarí Mukherjee, David Nicholas, Lisa A. Mingle, Nellie B. Dumas, Jocelyn A. Cole, Jasna Kovač
Software Mentions: 12
Published: over 7 years ago

10.7717/peerj.9850

lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time
Cited by: 5
Author(s): Thiago Pires Oliveira, Rafael de Andrade Moral, Sílvio Sandoval Zocchi, Clarice Garcia Borges Demétrio, John Hinde
Software Mentions: 12
Published: about 6 years ago

10.1038/s41421-021-00321-x

Dynamics of TCR repertoire and T cell function in COVID-19 convalescent individuals
Cited by: 23
Author(s): Lingjie Luo, Wenhua Liang, Jianfeng Pang, Gang Xu, Yingying Chen, Xinrong Guo, Xin Wang, Yi Zhao, Yang-dian Lai, Yang Liu, Bin Li, Bing Su, Shuye Zhang, Michal Baniyash, Lei Shen, Lei Chen, Yun Ling, Ying Wang, Qiming Liang, Hongzhou Lu, Zheng Zhang, Feng Wang
Software Mentions: 12
Published: almost 5 years ago

10.7554/eLife.48994

Self-assembling manifolds in single-cell RNA sequencing data
Cited by: 48
Author(s): Alexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang
Software Mentions: 12
Published: about 7 years ago

10.15252/embj.2020106388

Unraveling the features of somatic transposition in the <i>Drosophila</i> intestine
Cited by: 25
Author(s): Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Software Mentions: 12
Published: over 5 years ago

10.3390/cells10051066

Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein’s Anomaly
Cited by: 5
Author(s): Masood Abu‐Halima, Viktoria Wagner, Lea Simone Becker, Basim Ayesh, Mohammed Abd El-Rahman, Ulrike Fischer, Eckart Meese, Hashim Abdul‐Khaliq
Software Mentions: 12
Published: over 5 years ago

10.26508/lsa.201900461

Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion
Cited by: 5
Author(s): Antonio Vitobello, Juliane Perner, Johanna Beil, Jiang Zhu, Alberto Del Río-Espínola, Laurent Morawiec, Magdalena Westphal, Valérie Dubost, Marc Altorfer, Ulrike Naumann, Arne Mueller, Karen Kapur, Mark Borowsky, Colin J. Henderson, Charles Wolf, Michael Schwarz, Jonathan G. Moggs, Rémi Terranova
Software Mentions: 12
Published: almost 7 years ago

10.7717/peerj.11376

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
Cited by: 4
Author(s): Natasha Pavlovikj, João Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson
Software Mentions: 12
Published: over 5 years ago

10.1371/journal.pcbi.1007753

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures
Cited by: 1
Author(s): Jacob Pfeil, Lauren Sanders, Ioannis N. Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 6 years ago

10.7717/peerj.10469

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: almost 6 years ago

10.7554/eLife.37551

Species and cell-type properties of classically defined human and rodent neurons and glia
Cited by: 55
Author(s): Xiao Xu, Elitsa I Stoyanova, Agata E. Lemiesz, Jie Xing, Deborah C. Mash, Nathaniel Heintz
Software Mentions: 12
Published: almost 8 years ago

10.18632/aging.202317

Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer
Cited by: 33
Author(s): Xuening Zhang, Hao Zhao, Xiaoguang Shi, Xiaocan Jia, Yongli Yang
Software Mentions: 12
Published: almost 6 years ago

10.7554/eLife.34409

General decapping activators target different subsets of inefficiently translated mRNAs
Cited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: almost 8 years ago

10.3390/cancers13081788

Analysis of Intra-Tumoral Macrophages and T Cells in Non-Small Cell Lung Cancer (NSCLC) Indicates a Role for Immune Checkpoint and CD200-CD200R Interactions
Cited by: 7
Author(s): Anders Tøndell, Yashwanth Subbannayya, Sissel Gyrid Freim Wahl, Arnar Flatberg, Sveinung Sørhaug, Magne Børset, Markus Haug
Software Mentions: 12
Published: over 5 years ago

10.3389/fgene.2021.687778

Pan-Cancer Analysis of PIMREG as a Biomarker for the Prognostic and Immunological Role
Cited by: 16
Author(s): Hua Zhu, Xinyao Hu, Yingze Ye, Zhihong Jian, Yi Zhong, Lijuan Gu, Xiaoxing Xiong
Software Mentions: 12
Published: about 5 years ago

10.1038/s41416-019-0519-1

Stroma-normalised vessel density predicts benefit from adjuvant fluorouracil-based chemotherapy in patients with stage II/III colon cancer
Cited by: 5
Author(s): Artur Mezheyeuski, Ina Hrynchyk, Mercedes Herrera, Mia Karlberg, Erik Osterman, Peter Ragnhammar, David Edler, Anna Portyanko, Fredrik Pontén, Tobias Sjöblom, Bengt Glimelius, Arne Östman
Software Mentions: 12
Published: about 7 years ago

10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: almost 11 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: about 8 years ago

10.3389/fonc.2021.690324

Predictive Nomogram and Risk Factors for Lymph Node Metastasis in Bladder Cancer
Cited by: 11
Author(s): Zijian Tian, Lingfeng Meng, Xin Wang, Tongxiang Diao, Mao‐Lin Hu, Miao Wang, Yaqun Zhang, Ming Liu
Software Mentions: 12
Published: over 5 years ago

10.1093/gigascience/giaa102

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Cited by: 15
Author(s): Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, D. L. Clements, Fidel Ramírez, Graham Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan Manning, Léa Bellenger, Maria A. Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Björn Grüning
Software Mentions: 12
Published: almost 6 years ago

10.1093/gigascience/giz088

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
Cited by: 5
Author(s): Luis Francisco Hernández Sánchez, Bram Burger, Carlos Horro, Antonio Fabregat, Stefan Johansson, Pål Rasmus Njølstad, Harald Barsnes, Henning Hermjakob, Marc Vaudel
Software Mentions: 12
Published: about 7 years ago

10.1093/aobpla/plz054

tealeaves: an R package for modelling leaf temperature using energy budgets
Cited by: 26
Author(s): Christopher D. Muir
Software Mentions: 12
Published: almost 7 years ago

10.1371/journal.pone.0156293

Cryopreservation of Human Mucosal Leukocytes
Cited by: 14
Author(s): Sean M. Hughes, Zhiquan Shu, Claire Levy, April L. Ferre, Heather Hartig, Cifeng Fang, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, Kristina M. Adams Waldorf, Ronald S. Veazey, Anja Germann, Hagen von Briesen, M. Juliana McElrath, Charlene S. Dezzutti, Elizabeth Sinclair, Chris A. R. Baker, Barbara L. Shacklett, Dayong Gao, Florian Hladik
Software Mentions: 12
Published: over 10 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 6 years ago

10.1371/journal.pone.0202824

Allometry predicts trabecular bone structural properties in the carnivoran jaw joint
Cited by: 6
Author(s): Matthew Wysocki, Z. Jack Tseng
Software Mentions: 12
Published: about 8 years ago

10.1371/journal.pone.0184652

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems
Cited by: 48
Author(s): Ana Hranilović, Marina Bely, Isabelle Masneuf‐Pomarède, Vladimir Jiranek, Warren Albertin
Software Mentions: 12
Published: about 9 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: over 5 years ago

10.3389/fcell.2020.618552

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation
Cited by: 12
Author(s): Jenny Ostrop, Rosalie T. Zwiggelaar, Marianne Terndrup Pedersen, François Gerbe, Korbinian Bösl, Håvard T. Lindholm, Alberto Díez-Sánchez, Naveen Parmar, Silke Radetzki, Jens Peter von Kries, Philippe Jay, Kim B. Jensen, C.H. Arrowsmith, Menno J. Oudhoff
Software Mentions: 12
Published: over 5 years ago

10.1038/s42003-021-01941-5

CENP-A overexpression promotes distinct fates in human cells, depending on p53 status
Cited by: 23
Author(s): Daniel Jeffery, Alberto Gatto, Katrina Podsypanina, Charlène Renaud-Pageot, Rebeca Ponce Landete, Lorraine Bonneville, Marie Dumont, Daniele Fachinetti, Geneviève Almouzni
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-019-41592-5

A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion
Cited by: 1
Author(s): Robert F. Rudy, Nareerat Charoenvimolphan, Baogang Qian, Annerose Berndt, Robert M. Friedlander, Scott T. Weiss, Rose Du
Software Mentions: 12
Published: over 7 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: about 9 years ago

10.1186/s40425-019-0764-0

34th Annual Meeting &amp; Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 2
Cited by: 28
Author(s):
Software Mentions: 12
Published: almost 7 years ago

10.3389/fnbeh.2018.00187

Exhaustive Multi-Parametric Assessment of the Behavioral Array of Daily Activities of Mice Using Cluster and Factor Analysis
Cited by: 7
Author(s): Kenzo Yamamoto, Katsiaryna V. Gris, Jesús E. Sotelo Fonseca, Marjan Gharagozloo, Shaimaa Mahmoud, Camille Simard, Daphné Houle-Martel, Theodore Cloutier, Pavel Gris, Denis Gris
Software Mentions: 12
Published: about 8 years ago

10.12688/f1000research.22969.2

clustifyr: an R package for automated single-cell RNA sequencing cluster classification
Cited by: 58
Author(s): Rui Fu, Austin E. Gillen, Ryan M. Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R. Hesselberth, Kent Riemondy
Software Mentions: 12
Published: about 6 years ago

10.3390/genes9120569

NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
Cited by: 13
Author(s): Eduardo Zúñiga-León, Ulises Carrasco-Navarro, Francisco Fierro
Software Mentions: 12
Published: almost 8 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 5 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: over 8 years ago

10.12688/f1000research.15809.2

Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data
Cited by: 90
Author(s): Saskia Freytag, Tian Li, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Software Mentions: 12
Published: almost 8 years ago

10.12688/f1000research.12544.1

Easy and efficient ensemble gene set testing with EGSEA
Cited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: almost 9 years ago

10.1186/s40679-018-0060-y

An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
Cited by: 11
Author(s): Laurent P. René de Cotret, Martin Otto, Mark J. Stern, Bradley J. Siwick
Software Mentions: 12
Published: about 8 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: over 9 years ago

10.3389/fcimb.2021.687607

Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections
Cited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: about 5 years ago

10.3389/fpubh.2020.00425

Political Consequences of COVID-19 and Media Framing in South Korea
Cited by: 13
Author(s): Wonkwang Jo, Daesung Chang
Software Mentions: 12
Published: about 6 years ago

10.3389/fninf.2018.00092

Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0
Cited by: 96
Author(s): Espen Hagen, Solveig Næss, Torbjørn V. Ness, Gaute T. Einevoll
Software Mentions: 12
Published: almost 8 years ago

10.1038/srep26340

Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods
Cited by: 41
Author(s): Jérôme Morinière, Matthew H. Van Dam, Oliver Hawlitschek, Johannes Bergsten, Mariano C. Michat, Lars Hendrich, Ignacio Ribera, Emmanuel F. A. Toussaint, Michael Balke
Software Mentions: 12
Published: over 10 years ago

10.7554/eLife.52465

Navigating the garden of forking paths for data exclusions in fear conditioning research
Cited by: 87
Author(s): Tina B. Lonsdorf, Maren Klingelhöfer-Jens, Marta Andreatta, Tom Beckers, Anastasia Chalkia, Anna Gerlicher, Valerie L. Jentsch, Shira Meir Drexler, Gaëtan Mertens, Jan Richter, Rachel Sjouwerman, Julia Wendt, Christian J. Merz
Software Mentions: 12
Published: almost 7 years ago

10.1016/j.heliyon.2021.e06236

: A neuroscientist's sound toolkit
Cited by: 2
Author(s): N. Jeremy Hill, Scott W.J. Mooney, Glen T. Prusky
Software Mentions: 12
Published: over 5 years ago

10.1186/s12967-017-1285-6

In silico prediction of novel therapeutic targets using gene–disease association data
Cited by: 79
Author(s): Enrico Ferrero, Ian Dunham, Philippe Sanséau
Software Mentions: 12
Published: about 9 years ago

10.3389/fpsyg.2018.00776

Spatial and Verbal Routes to Number Comparison in Young Children
Cited by: 9
Author(s): Francesco Sella, Daniela Lucangeli, Marco Zorzi
Software Mentions: 12
Published: over 8 years ago

10.7717/peerj.10255

Comprehensive genomic analysis of microenvironment phenotypes in ovarian cancer
Cited by: 4
Author(s): Jingshu Wang, Tingting Zhang, Lina Yang, Gong Yang
Software Mentions: 12
Published: almost 6 years ago

10.1186/s13059-019-1766-4

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
Cited by: 74
Author(s): Nelson Johansen, Gerald Quon
Software Mentions: 12
Published: about 7 years ago

10.3389/fgene.2021.655536

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
Cited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 5 years ago

10.18632/aging.103965

Establishing and validating a pathway prognostic signature in pancreatic cancer based on miRNA and mRNA sets using GSVA
Cited by: 8
Author(s): Junfeng Zhang, Jianyou Gu, Shixiang Guo, Wenjie Huang, Yongqiang Zheng, Xianxing Wang, Tao Zhang, Weibo Zhao, Bing Ni, Yingfang Fan, Huaizhi Wang
Software Mentions: 12
Published: almost 6 years ago

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: over 7 years ago

10.1038/s41598-021-86286-z

Construction and validation of a metabolic risk model predicting prognosis of colon cancer
Cited by: 5
Author(s): Didi Zuo, Chao Li, Tao Liu, Meng Yue, Jiantao Zhang, Guang Ning
Software Mentions: 12
Published: over 5 years ago

10.1038/s42003-019-0415-5

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 7 years ago