Ecosyste.ms: Papers

10.2196/26412

Recursive partitioning vs computerized adaptive testing to reduce the burden of health assessment in cleft lip and/or palate: a comparative simulation study (Preprint)
Cited by: 1
Author(s): Conrad Harrison, Chris Sidey‐Gibbons, Anne F. Klassen, Karen W. Y. Wong Riff, Dominic Furniss, Marc C. Swan, Jeremy Rodrigues
Software Mentions: 10
Published: almost 4 years ago

10.3389/fpls.2020.00136

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato
Cited by: 17
Author(s): Araceli Lamelas, Damaris Desgarennes, Daniel López-Lima, Luc Villain, Alexandro Alonso-Sánchez, Alejandro Artacho, Amparo Latorre, Andrés Moya, Gloria Carrión
Software Mentions: 10
Published: almost 5 years ago

10.3389/fnins.2019.00494

Automated, Efficient, and Accelerated Knowledge Modeling of the Cognitive Neuroimaging Literature Using the ATHENA Toolkit
Cited by: 6
Author(s): Michael C. Riedel, Taylor Salo, Jason Hays, Matthew D. Turner, Matthew T. Sutherland, Jessica A. Turner, Angela R. Laird
Software Mentions: 10
Published: over 5 years ago

10.7554/eLife.62250

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells
Cited by: 11
Author(s): Helen M Tauc, Imilce A. Rodriguez‐Fernandez, Jason A. Hackney, Michał Pawlak, Tal Oron, Jerome Korzelius, Hagar F. Moussa, Subhra Chaudhuri, Zora Modrušan, Bruce A Edgar, Heinrich Jasper
Software Mentions: 10
Published: over 3 years ago

10.3389/fmed.2020.00247

Growth Rate and Acceleration Analysis of the COVID-19 Pandemic Reveals the Effect of Public Health Measures in Real Time
Cited by: 34
Author(s): Yuri Tani Utsunomiya, Adam Taiti Harth Utsunomiya, Rafaela Beatriz Pintor Torrecilha, Silvana de Cássia Paulan, Marco Milanesi, José Fernando Garcia
Software Mentions: 10
Published: over 4 years ago

10.3389/fonc.2021.671171

Development of a Prognostic Scoring System for Hepatocellular Carcinoma Patients With Main Portal Vein Tumor Thrombus Undergoing Conventional Transarterial Chemoembolization: An Analysis of 173 Patients
Cited by: 3
Author(s): Jinghuan Li, Xin Yin, Fan Yan Wei, Lan Zhang, Rongxin Chen, Yi Chen, Lixin Li, Ning Ge, Yuhong Gan, Yanhong Wang, Zhigang Ren
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.10421

Loss of HOXB3 correlates with the development of hormone receptor negative breast cancer
Cited by: 6
Author(s): Lizhe Zhu, Shibo Yu, Siyuan Jiang, Ge Gao, Yan Yu, Yong Jin Zhou, Ligang Niu, Jing He, Yu Ren, Bin Wang
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.ppat.1007945

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype
Cited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: over 5 years ago

10.1186/s12940-021-00693-3

Examining the role of wind in human illness due to pesticide drift in Washington state, 2000–2015
Cited by: 3
Author(s): Edward J. Kasner, Joanne Bonnar Prado, Michael G. Yost, Richard A. Fenske
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-020-03795-w

optimalFlow: optimal transport approach to flow cytometry gating and population matching
Cited by: 11
Author(s): Eustasio del Barrio, Hristo Inouzhe, Jean-Michel Loubès, Carlos Matrán, Agustín Mayo-Íscar
Software Mentions: 10
Published: about 4 years ago

10.1093/molbev/msu269

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
Cited by: 488
Author(s): Simon H. Martin, John W. Davey, Chris D. Jiggins
Software Mentions: 10
Published: about 10 years ago

10.1371/journal.pcbi.1006369

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks
Cited by: 35
Author(s): Rong Zhang, Zhao Ren, Wei Chen
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pone.0185171

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes
Cited by: 29
Author(s): Tuulia Mali, Jaana Kuuskeri, Firoz Shah, Taina Lundell
Software Mentions: 10
Published: about 7 years ago

10.1371/journal.pone.0224947

Does caching strategy vary with microclimate in endangered Mt. Graham red squirrels?
Cited by: 1
Author(s): Calebe P. Mendes, John L. Koprowski
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.pcbi.1007803

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pntd.0009540

Sexual selection theory meets disease vector control: Testing harmonic convergence as a “good genes” signal in Aedes aegypti mosquitoes
Cited by: 6
Author(s): Garrett P. League, Laura C. Harrington, Sylvie A. Pitcher, Julie K. Geyer, Lindsay L. Baxter, Julian Montijo, John G. Rowland, Lynn M. Johnson, Courtney C. Murdock, Lauren J. Cator
Software Mentions: 10
Published: over 3 years ago

10.1534/g3.120.401309

CeMbio - The<i>Caenorhabditis elegans</i>Microbiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: over 4 years ago

10.3390/microorganisms8121887

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
Cited by: 13
Author(s): Laurin Christopher Gierse, Alexander Meene, Daniel Schultz, Theresa Schwaiger, Claudia Karte, Charlotte Schröder, Haitao Wang, Christine Wünsche, Karen Methling, Bernd Kreikemeyer, Stephan Fuchs, Jörg Bernhardt, Dörte Becher, Michael Lalk, Tim Urich, Katharina Riedel
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pgen.1008530

Genetic variation in GC and CYP2R1 affects 25-hydroxyvitamin D concentration and skeletal parameters: A genome-wide association study in 24-month-old Finnish children
Cited by: 12
Author(s): Anders Kämpe, Maria Enlund-Cerullo, Saara Valkama, Elisa Holmlund-Suila, Jenni Rosendahl, Helena Hauta-alus, Minna Pekkinen, Sture Andersson, Outi Mäkitie
Software Mentions: 10
Published: almost 5 years ago

10.1111/eva.13209

Mixed‐stock analysis using Rapture genotyping to evaluate stock‐specific exploitation of a walleye population despite weak genetic structure
Cited by: 17
Author(s): Peter T. Euclide, Tom MacDougall, Jason M. Robinson, Matthew D. Faust, Chris C. Wilson, Kuan‐Yu Chen, Elizabeth A. Marschall, Wesley A. Larson, Stuart A. Ludsin
Software Mentions: 10
Published: over 3 years ago

10.7554/eLife.43257

Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures
Cited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0216611

Combined effects of nutritional, biochemical and environmental stimuli on growth performance and fatty acid composition of gilthead sea bream (Sparus aurata)
Cited by: 3
Author(s): Claudia Torno, Stefanie Staats, Anna Fickler, Sonia de Pascual‐Teresa, M.S. Izquierdo, Gerald Rimbach, Carsten Schulz
Software Mentions: 10
Published: over 5 years ago

10.3390/insects10030065

Multi-Scenario Species Distribution Modeling
Cited by: 12
Author(s): Senait D. Senay, Susan P. Worner
Software Mentions: 10
Published: almost 6 years ago

10.1186/cc13914

Higher clinical success in patients with ventilator-associated pneumonia due to methicillin-resistant Staphylococcus aureus treated with linezolid compared with vancomycin: results from the IMPACT-HAP study
Cited by: 37
Author(s): Paula Peyrani, Timothy Wiemken, Robert Kelley, Marcus J. Zervos, Daniel H. Kett, Thomas M. File, Gary E. Stein, Kimbal D. Ford, Ernesto G. Scerpella, Verna L Welch, Julio A. Ramirez
Software Mentions: 10
Published: almost 11 years ago

10.1186/s12864-015-2356-9

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
Cited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: almost 9 years ago

10.7717/peerj.10871

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula
Cited by: 2
Author(s): Anastasiia K. Kimeklis, Grigory Gladkov, Aleksei Zverev, Arina Kichko, Evgeny Andronov, E. I. Ergina, I. V. Kostenko
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pgen.1009376

Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: almost 4 years ago

10.3390/microorganisms9071487

Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: over 3 years ago

10.1007/s00228-020-03052-2

Potentially inappropriate prescribing in older hospitalized Dutch patients according to the STOPP/START criteria v2: a longitudinal study
Cited by: 9
Author(s): Birgit A. Damoiseaux-Volman, Stephanie Medlock, Kimmy Raven, Danielle Sent, Johannes A. Romijn, Nathalie van der Velde, Ameen Abu‐Hanna
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13059-021-02316-z

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
Cited by: 24
Author(s): Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd Richmond, Donald J. Johann, Halil Bişğin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee S Basehore, Anne Bergstrom Lucas, Daniel L. Burgess, Daniel Butler, Simon Cawley, Chia Jung Chang, Guangchun Chen, Tao Chen, Yun Ching Chen, Daniel J. Craig, Ángela del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, You-Zeng Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff S. Jasper, Giuseppe Jurman, David P. Kreil, Paweł P. Łabaj, Kevin Lai, Jianying Li, Quan Zhen Li, Yulong Li, Chi Kong Li, Zhichao Liu, Mario Solís-López, Kelci Miclaus, Raymond D. Miller, Vinay Kumar Mittal, Marghoob Mohiyuddin, Carlos Pabón-Peña, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy M. Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Leming Shi, Joshua Xu
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0250231

Changing parental feeding practices through web-based interventions: A systematic review and meta-analysis
Cited by: 15
Author(s): Ana Coelho Gomes, Ana Isabel Pereira, Magda Sofia Roberto, Klara Boraska, Luísa Barros
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-70722-7

Active and social life is associated with lower non-social fearfulness in pet dogs
Cited by: 15
Author(s): Emma Hakanen, Salla Mikkola, Milla Salonen, Jenni Puurunen, Sini Sulkama, Cynthia Gobbi Alves Araújo, Hannes Lohi
Software Mentions: 10
Published: over 4 years ago

10.18632/aging.102434

Development and validation of a metastasis-associated prognostic signature based on single-cell RNA-seq in clear cell renal cell carcinoma
Cited by: 28
Author(s): Chuanjie Zhang, Hongchao He, Xin Hu, Ao Liu, Da Huang, Yu Xu, Lu Chen, Danfeng Xu
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.pone.0138031

The Effect of Host-Plant Phylogenetic Isolation on Species Richness, Composition and Specialization of Insect Herbivores: A Comparison between Native and Exotic Hosts
Cited by: 16
Author(s): Julio Miguel Grandez-Rios, Leonardo Lima Bergamini, Walter Santos de Araújo, Fabricio Villalobos, Mário Almeida‐Neto
Software Mentions: 10
Published: about 9 years ago

10.3389/fonc.2021.615321

Development and Validation of a Prognostic Nomogram for Colorectal Cancer Patients With Synchronous Peritoneal Metastasis
Cited by: 8
Author(s): Zifeng Yang, Li Yong, Xiusen Qin, Zejian Lv, Huaiming Wang, Deqing Wu, Zixu Yuan
Software Mentions: 10
Published: over 3 years ago

10.1186/s12935-021-01965-1

Elevated expression of LPCAT1 predicts a poor prognosis and is correlated with the tumour microenvironment in endometrial cancer
Cited by: 9
Author(s): Tianyi Zhao, Min Han, Xiaohong Ma, Lina Wei, Yixin Hou, Rui Sun, Jie Jiang
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2021.616686

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests
Cited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: over 4 years ago

10.1017/S0950268821000091

How to improve infectious disease prediction by integrating environmental data: an application of a novel ensemble analysis strategy to predict HFMD
Cited by: 1
Author(s): Junwen Tao, Yue Ma, Xuefei Zhuang, Qiang Lv, Yaqiong Liu, Tao Zhang, Fei Yin
Software Mentions: 10
Published: almost 4 years ago

10.1093/biostatistics/kxz034

Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
Cited by: 10
Author(s): Britta Velten, Wolfgang Huber
Software Mentions: 10
Published: about 5 years ago

10.3389/fonc.2021.644956

A New Oxaliplatin Resistance-Related Gene Signature With Strong Predicting Ability in Colon Cancer Identified by Comprehensive Profiling
Cited by: 6
Author(s): Qiu Sheng Lin, Liang Luo, Hua Wang
Software Mentions: 10
Published: over 3 years ago

10.1002/ece3.5599

Linking pollen foraging of megachilid bees to their nest bacterial microbiota
Cited by: 29
Author(s): Anna Voulgari‐Kokota, Markus J. Ankenbrand, Gudrun Grimmer, Ingolf Steffan‐Dewenter, Alexander Keller
Software Mentions: 10
Published: over 5 years ago

10.15252/msb.20188339

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
Cited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pcbi.1006135

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
Cited by: 13
Author(s): Aaron T. L. Lun, Hervé Pagès, Mike L. Smith
Software Mentions: 10
Published: over 6 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: over 4 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: about 4 years ago

10.1093/database/bay033

The tragedy of the biodiversity data commons: a data impediment creeping nigher?
Cited by: 11
Author(s): Nora Escribano, David Galicia, Arturo H. Ariño
Software Mentions: 10
Published: almost 7 years ago

10.1093/bioinformatics/btx392

matter: an R package for rapid prototyping with larger-than-memory datasets on disk
Cited by: 4
Author(s): Kylie A Bemis, Olga Vitek
Software Mentions: 10
Published: over 7 years ago

10.1186/s12859-017-1770-1

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: over 7 years ago

10.12688/f1000research.11997.1

valr: Reproducible genome interval analysis in R
Cited by: 43
Author(s): Kent Riemondy, Ryan M. Sheridan, Austin E. Gillen, Yinni Yu, Christopher Bennett, Jay R. Hesselberth
Software Mentions: 10
Published: over 7 years ago

10.1186/s13059-020-02034-y

APEC: an accesson-based method for single-cell chromatin accessibility analysis
Cited by: 11
Author(s): Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu
Software Mentions: 10
Published: over 4 years ago

10.1111/jcmm.15848

m6A RNA methylation regulators could contribute to the occurrence of chronic obstructive pulmonary disease
Cited by: 43
Author(s): Xinwei Huang, Dongjin Lv, Yao Xiao, Min Li, Hong Zhang
Software Mentions: 10
Published: about 4 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: about 3 years ago

10.12688/f1000research.8759.2

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments
Cited by: 16
Author(s): Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Software Mentions: 10
Published: over 8 years ago

10.7554/eLife.62210

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells
Cited by: 18
Author(s): Balyn W. Zaro, Joseph J. Noh, Victoria L. Mascetti, János Demeter, Benson M. George, Monika Żukowska, Gunsagar S. Gulati, Rahul Sinha, Ryan A. Flynn, Allison Banuelos, Allison Zhang, Adam C. Wilkinson, Peter K. Jackson, Irving L. Weissman
Software Mentions: 10
Published: about 4 years ago

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: about 5 years ago

10.1186/1751-0473-5-3

MADAM - An open source meta-analysis toolbox for R and Bioconductor
Cited by: 20
Author(s): Karl G. Kugler, Laurin A. J. Mueller, Armin Graber
Software Mentions: 10
Published: almost 15 years ago

10.1186/s12859-019-2797-2

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
Cited by: 19
Author(s): Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: about 7 years ago

10.1038/s41598-018-32681-y

Medicinal value of sunflower pollen against bee pathogens
Cited by: 77
Author(s): Jonathan J. Giacomini, Jessica Leslie, David R. Tarpy, Evan C. Palmer‐Young, Rebecca E. Irwin, Lynn S. Adler
Software Mentions: 10
Published: about 6 years ago

10.1038/s41598-020-72369-w

Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology
Cited by: 10
Author(s): Natacha Nikolic, Iratxe Montes, Maxime Lalire, Alexis Puech, Nathalie Bodin, Sophie Arnaud‐Haond, Sven E. Kerwath, Emmanuel Corse, Philippe Gaspar, Stéphanie Hollanda, Jérôme Bourjea, Wendy West, Sylvain Bonhommeau
Software Mentions: 10
Published: about 4 years ago

10.1186/s12918-015-0169-8

Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Cited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: over 9 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: over 6 years ago

10.1186/s12859-017-1498-y

Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysis
Cited by: 15
Author(s): Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano
Software Mentions: 10
Published: almost 8 years ago

10.3389/fpls.2020.587426

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces
Cited by: 13
Author(s): Victor Allan, Mani Vetriventhan, R. Senthil, S. Geetha, Santosh Deshpande, Abhishek Rathore, Vinod Kumar, Prabhat Kumar Singh, Surender Reddymalla, V. C. R. Azevedo
Software Mentions: 10
Published: almost 4 years ago

10.1098/rsos.171218

Tongues on the EDGE: language preservation priorities based on threat and lexical distinctiveness
Cited by: 2
Author(s): Nicolas Perrault, Maxwell J. Farrell, T. Jonathan Davies
Software Mentions: 10
Published: about 7 years ago

10.1126/sciadv.1600760

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia
Cited by: 85
Author(s): S. Picaud, Katharina Leonards, Jean-Philippe Lambert, Oliver M. Dovey, Christopher Wells, Oleg Fedorov, Octovia Monteiro, Takao Fujisawa, Chenyi Wang, Hannah Lingard, C. Tallant, Nikzad Nikbin, Lucie Guetzoyan, Richard J. Ingham, Steven V. Ley, P.E. Brennan, Susanne Müller, Anastasia Samsonova, Anne‐Claude Gingras, Juerg Schwaller, George S. Vassiliou, Stefan Knapp, P. Filippakopoulos
Software Mentions: 10
Published: about 8 years ago

10.3389/fonc.2021.661040

A Novel Prognostic Model and Practical Nomogram for Predicting the Outcomes of Colorectal Cancer: Based on Tumor Biomarkers and Log Odds of Positive Lymph Node Scheme
Cited by: 9
Author(s): Zhu Jun, Jun Hao, Qian Ma, Tong Shi, Shuai Wang, Jingchuan Yan, Rujie Chen, Dong Xu, Yu Jiang, Jian Zhang, Jipeng Li
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-021-04211-7

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Cited by: 6
Author(s): Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-017-1847-x

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Cited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: about 7 years ago

10.1371/journal.pone.0226203

Mating strategy is determinant of adenovirus prevalence in European bats
Cited by: 4
Author(s): Federica Rossetto, María Iglesias-Caballero, H. Christoph Liedtke, Iván Gómez-Mestre, José Miguel Berciano, Gonzalo Pérez-Suárez, Óscar de Paz, Carlos Ibáñez, Juan E. Echevarrı́a, Inmaculada Casas
Software Mentions: 10
Published: almost 5 years ago

10.3389/fneur.2021.683051

An Externally Validated Dynamic Nomogram for Predicting Unfavorable Prognosis in Patients With Aneurysmal Subarachnoid Hemorrhage
Cited by: 8
Author(s): Ping Hu, Yang Xu, Yangfan Liu, Yuntao Li, Liguo Ye, Si Zhang, Xinyi Zhu, Yangzhi Qi, Huikai Zhang, Qian Sun, Yixuan Wang, Gang Deng, Qianxue Chen
Software Mentions: 10
Published: over 3 years ago

10.3389/fimmu.2021.641495

Mitochondrial Reactive Oxygen Species Regulate Immune Responses of Macrophages to Aspergillus fumigatus
Cited by: 15
Author(s): Rémi Hatinguais, Arnab Pradhan, Gordon D. Brown, Alistair J. P. Brown, Adilia Warris, Elena Shekhova
Software Mentions: 10
Published: over 3 years ago

10.1186/s12864-021-07493-6

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Cited by: 19
Author(s): Richard Edwards, Matthew A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina D. Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanović, Robert A. Zammit, E Aiden, Wesley C. Warren, J. William O. Ballard
Software Mentions: 10
Published: over 3 years ago

10.1186/s13046-019-1212-1

The kinase inhibitor SI113 induces autophagy and synergizes with quinacrine in hindering the growth of human glioblastoma multiforme cells
Cited by: 23
Author(s): Silvia Matteoni, Claudia Abbruzzese, Paola Matarrese, Gabriele De Luca, Anna Maria Mileo, Stefania Miccadei, Silvia Schenone, Francesca Musumeci, Tobias Haas, Giovanni Sette, Carmine Maria Carapella, Rosario Amato, Nicola Perrotti, Michele Signore, Marco G. Paggi
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-72272-4

Video-assisted thoracoscopic lobectomy is feasible for selected patients with clinical N2 non-small cell lung cancer
Cited by: 7
Author(s): Jae Kwang Yun, Geun Dong Lee, Sehoon Choi, Hyeong Ryul Kim, Yong Hee Kim, Seung-Il Park, Dong Kwan Kim
Software Mentions: 10
Published: about 4 years ago

10.1186/s13059-016-0927-y

Design and computational analysis of single-cell RNA-sequencing experiments
Cited by: 409
Author(s): Rhonda Bacher, Christina Kendziorski
Software Mentions: 10
Published: over 8 years ago

10.1007/s11250-021-02620-7

Risk factors associated with Ctenocephalides felis flea infestation of peri-urban goats: a neglected parasite in an under-appreciated host
Cited by: 4
Author(s): Julia Rose Dahm, Jordana Burdon Bailey, Robert F. Kelly, Patrick Chikungwa, Julius L.C. Chulu, Lívio Martins Costa, Emily June Freeman, Dagmar Mayer, Stella Mazeri, Neil Sargison
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12859-017-1487-1

A systematic comparative evaluation of biclustering techniques
Cited by: 94
Author(s): Victor Alexandre Padilha, Ricardo J. G. B. Campello
Software Mentions: 10
Published: almost 8 years ago

10.1186/s12575-018-0067-8

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results
Cited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 10
Published: almost 7 years ago

10.1017/S0950268820000746

Risk of bacteremia in patients presenting with shaking chills and vomiting - a prospective cohort study
Cited by: 2
Author(s): Madlene Holmqvist, Malin Inghammar, Lisa I. Påhlman, John H. Boyd, Per Åkesson, Adam Linder, Fredrik Kahn
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmicb.2020.00037

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Cited by: 164
Author(s): Arkadiy I. Garber, Kenneth H. Nealson, Akimitsu Okamoto, Sean M. McAllister, Clara S. Chan, Roman A. Barco, Nancy Merino
Software Mentions: 10
Published: almost 5 years ago

10.3389/fmicb.2021.679671

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt
Cited by: 4
Author(s): Junhyeong Kim, A. H. Goldstein, Romy Chakraborty, Kolby Jardine, Robert J. Weber, P. Sørensen, Wang Shi, Boris Faybishenko, Pawel K. Misztal, Eoin L. Brodie
Software Mentions: 10
Published: over 3 years ago

10.1186/s13321-015-0094-2

RRegrs: an R package for computer-aided model selection with multiple regression models
Cited by: 40
Author(s): Georgia Tsiliki, Cristian R. Munteanu, José A. Seoane, Carlos Fernández-Lozano, Haralambos Sarimveis, Egon Willighagen
Software Mentions: 10
Published: about 9 years ago

10.5334/aogh.3278

Derivation of a Contextually-Appropriate COVID-19 Mortality Scale for Low-Resource Settings
Cited by: 5
Author(s): Jennifer L Pigoga, Yasein Omer, Lee Wallis
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.7907

motoRneuron: an open-source R toolbox for time-domain motor unit analyses
Cited by: 0
Author(s): Andrew J. Tweedell, Matthew S. Tenan
Software Mentions: 10
Published: almost 5 years ago

10.1155/2020/5858092

Profiles of Immune Infiltration and Prognostic Immunoscore in Lung Adenocarcinoma
Cited by: 9
Author(s): Yanyan Li, Liping Tao, Weiyang Cai
Software Mentions: 10
Published: over 4 years ago

10.1016/j.celrep.2020.107885

CD4+ T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features
Cited by: 9
Author(s): Alexander Greenshields‐Watson, Meriem Attaf, Bruce J. MacLachlan, Thomas Whalley, Cristina Rius, Aaron Wall, Alun G. Lloyd, Hywel Hughes, Kathryn E. Strange, Georgina H Mason, Andrea J. A. Schauenburg, Sarah Hulin-Curtis, James Geary, Yuan Chen, Sarah N. Lauder, Kathryn Smart, Dhanasekaran Vijaykrishna, Miguel L. Grau, Mikhail Shugay, Robert Andrews, Garry Dolton, P.J. Rizkallah, Awen Gallimore, Andrew K. Sewell, Andrew Godkin, David K. Cole
Software Mentions: 10
Published: over 4 years ago

10.1128/mSphere.00743-20

Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( <i>Chroicocephalus novaehollandiae</i> ) Reveals the Acquisition of Multidrug Resistance Plasmids
Cited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12859-015-0613-1

tcR: an R package for T cell receptor repertoire advanced data analysis
Cited by: 199
Author(s): Vadim Nazarov, Mikhail V. Pogorelyy, Ekaterina A. Komech, Ivan V. Zvyagin, Dmitriy A. Bolotin, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov
Software Mentions: 10
Published: over 9 years ago

10.3389/fmicb.2020.00917

Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets
Cited by: 23
Author(s): Clare H. Gaukroger, Christopher J. Stewart, Sandra Edwards, John Walshaw, Ian Adams, Ι. Kyriazakis
Software Mentions: 10
Published: over 4 years ago

10.1186/s12859-016-0997-6

Unaccounted uncertainty from qPCR efficiency estimates entails uncontrolled false positive rates
Cited by: 5
Author(s): Anders Ellern Bilgrau, Steffen Falgreen, Anders Petersen, Malene Krag Kjeldsen, Julie Støve Bødker, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 10
Published: over 8 years ago

10.1038/s41597-020-00725-6

An annotated dataset of bioacoustic sensing and features of mosquitoes
Cited by: 5
Author(s): Dinarte Vasconcelos, Nuno Nunes, João Gomes
Software Mentions: 10
Published: about 4 years ago

10.7717/peerj.11903

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
Cited by: 10
Author(s): Patricia Sarcinelli Stelzer, Ana Carolina de Azevedo Mazzuco, L.E. de O. Gomes, João Luiz Martins, Sérgio A. Netto, Ângelo F. Bernardino
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pgen.1008126

Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content
Cited by: 14
Author(s): Marco Giovannetti, Christian Göschl, Christof Dietzen, Stig Uggerhøj Andersen, Stanislav Kopriva, Wolfgang Busch
Software Mentions: 10
Published: almost 5 years ago

10.1111/jcmm.14918

An outcome model for human bladder cancer: A comprehensive study based on weighted gene co‐expression network analysis
Cited by: 24
Author(s): Yaoyi Xiong, Lushun Yuan, Jing Xiong, Huimin Xu, Yongwen Luo, Gang Wang, Lingao Ju, Yu Xiao, Xinghuan Wang
Software Mentions: 10
Published: almost 5 years ago

10.3389/fcell.2021.722841

Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution
Cited by: 0
Author(s): Xianxiong Ma, Hengyu Chen, Ming Yang, Zunxiang Ke, Mengyi Wang, Tao Huang, Lei Li
Software Mentions: 10
Published: about 3 years ago

10.3389/fimmu.2016.00372

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts
Cited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: about 8 years ago

10.1038/s41598-019-46168-x

Cytotoxic unsaturated electrophilic compounds commonly target the ubiquitin proteasome system
Cited by: 16
Author(s): Karthik Selvaraju, Arjan Mofers, Paola Pellegrini, Johannes Salomonsson, Alexandra Ahlner, Vivian Morad, Ellin-Kristina Hillert, Belén Espinosa, Elias S.J. Arnér, Lasse Jensen, Jonas Malmström, Maria V. Turkina, Pádraig D’Arcy, Michael A. Walters, Maria Sunnerhagen, Stig Linder
Software Mentions: 10
Published: over 5 years ago