Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

10.1186/s13059-020-02136-7

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Cited by: 53
Author(s): Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
Software Mentions: 21
Published: about 4 years ago

10.1186/s12868-019-0538-0

28th Annual Computational Neuroscience Meeting: CNS*2019
Cited by: 3
Author(s):
Software Mentions: 13
Published: about 5 years ago

10.3389/fgene.2019.01079

HiCeekR: A Novel Shiny App for Hi-C Data Analysis
Cited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: about 5 years ago

10.1186/s12859-018-2296-x

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
Cited by: 47
Author(s): Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele Calogero
Software Mentions: 10
Published: about 6 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: almost 4 years ago

10.18632/aging.203040

Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension
Cited by: 16
Author(s): Haoru Dong, Xiuchun Li, Mengsi Cai, Chi Zhang, Mao Wei-qi, Ying Wang, Qinying Xu, Mayun Chen, Liangxing Wang, Xiaoying Huang
Software Mentions: 9
Published: over 3 years ago

10.3389/fpls.2019.01645

Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply
Cited by: 15
Author(s): Paula Pongrac, Sina Fischer, Jacqueline Thompson, G. M. Wright, Philip J. White
Software Mentions: 7
Published: almost 5 years ago

10.1111/jcmm.15472

Transcriptomic landscape profiling of metformin‐treated healthy mice: Implication for potential hypertension risk when prophylactically used
Cited by: 4
Author(s): Yuhuan Meng, Rui Xiang, Han Yan, Yiran Zhou, Yuntao Hu, Jichun Yang, Yuan Zhou, Qinghua Cui
Software Mentions: 7
Published: over 4 years ago

10.3390/metabo10030088

Analysis and Simulation of Glioblastoma Cell Lines-Derived Extracellular Vesicles Metabolome
Cited by: 25
Author(s): Miroslava Čuperlović-Culf, Nam Huan Khieu, Anuradha Surendra, Melissa Hewitt, Claudie Charlebois, Jagdeep K. Sandhu
Software Mentions: 6
Published: over 4 years ago

10.1002/ece3.2206

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?
Cited by: 14
Author(s): Albert Rivas‐Ubach, José A. Hódar, Jordi Sardans, Jennifer Kyle, Young Mo Kim, Michal Oravec, Otmar Urban, Alex Guenther, Josep Peñuelas
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0068826

SIMS: A Hybrid Method for Rapid Conformational Analysis
Cited by: 14
Author(s): Bryant Gipson, Mark Moll, Lydia E. Kavraki
Software Mentions: 6
Published: over 11 years ago

10.1186/s12864-017-3630-9

Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients
Cited by: 42
Author(s): Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller‐Brüsselbach, Silke Reinartz, Rolf Müller
Software Mentions: 6
Published: over 7 years ago

10.3389/fncel.2020.00245

A Primer on Constructing Plasticity Phenotypes to Classify Experience-Dependent Development of the Visual Cortex
Cited by: 2
Author(s): Justin L. Balsor, Dezi Ahuja, David Jones, Kathryn Murphy
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.54540

A Matlab-based toolbox for characterizing behavior of rodents engaged in string-pulling
Cited by: 13
Author(s): Samsoon Inayat, Surjeet Singh, Arashk Ghasroddashti, Qandeel, Pramuka Egodage, Ian Q. Whishaw, Majid H. Mohajerani
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0214311

ukbtools: An R package to manage and query UK Biobank data
Cited by: 33
Author(s): Ken B. Hanscombe, Jonathan R. I. Coleman, Matthew Traylor, Cathryn M. Lewis
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0126911

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data
Cited by: 18
Author(s): David Wood, Kátia Nones, Anita L Steptoe, Angelika N. Christ, Ivon Harliwong, Felicity Newell, Timothy J. C. Bruxner, David Miller, Nicole Cloonan, Sean M. Grimmond
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0032394

pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data
Cited by: 24
Author(s): Morten Hansen, Thomas Alexander Gerds, Ole Haagen Nielsen, Jakob Benedict Seidelin, Jesper T. Troelsen, Jørgen Olsen
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0036161

Effect of Age on Variability in the Production of Text-Based Global Inferences
Cited by: 9
Author(s): Lynne J. Williams, Joseph Dunlop, Hervé Abdi
Software Mentions: 4
Published: over 12 years ago

10.1186/s12967-018-1755-5

Serum protein signature of coronary artery disease in type 2 diabetes mellitus
Cited by: 28
Author(s): Ramu Adela, Podduturu Naveen Chander Reddy, Tarini Shankar Ghosh, Suruchi Aggarwal, Amit Kumar Yadav, Bhabatosh Das, Sanjay K. Banerjee
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0247028

How similar is “similar,” or what is the best measure of soil spectral and physiochemical similarity?
Cited by: 2
Author(s): Rong Zeng, J P Zhang, Kaiyong Cai, Weichang Gao, Wenjie Pan, Chaoying Jiang, P Y Zhang, Bing Wu, C H Wang, Xing Jin, Daixun Li
Software Mentions: 4
Published: over 3 years ago

10.26508/lsa.201900561

Refining the adipose progenitor cell landscape in healthy and obese visceral adipose tissue using single-cell gene expression profiling
Cited by: 40
Author(s): Dong Seong Cho, Bolim Lee, Jason D. Doles
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pntd.0007382

Identification of divergent Leishmania (Viannia) braziliensis ecotypes derived from a geographically restricted area through whole genome analysis
Cited by: 11
Author(s): Bruna Santos Lima Figueiredo de Sá, Antônio Mauro Rezende, Osvaldo P. de Melo Neto, Maria Edileuza Felinto de Brito, Sinval Pinto Brandão-Filho
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms7100426

Peroxynitrite Generation and Increased Heterotrophic Capacity Are Linked to the Disruption of the Coral–Dinoflagellate Symbiosis in a Scleractinian and Hydrocoral Species
Cited by: 19
Author(s): Laura Fernandes de Barros Marangoni, Miguel Mies, Arthur Z. Güth, Thomás N. S. Banha, Alex Inague, Juliana da Silva Fonseca, Camila Dalmolin, Samuel Coelho Faria, Christine Ferrier‐Pagès, Adalto Bianchini
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1005728

Population FBA predicts metabolic phenotypes in yeast
Cited by: 18
Author(s): Piyush Labhsetwar, Marcelo C.R. Melo, John A. Cole, Zaida Luthey‐Schulten
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0240429

Detecting inversions with PCA in the presence of population structure
Cited by: 7
Author(s): Ronald J. Nowling, Krystal R. Manke, Scott J. Emrich
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0040425

The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization
Cited by: 92
Author(s): Benjamin Smith, Thomas McAndrew, Zigui Chen, Ariana Harari, David M. Barris, Viswanathan Shankar, Ana Cecilia Rodríguez, Phillip E. Castle, Rolando Herrero, Mark Schiffman, Robert D. Burk
Software Mentions: 3
Published: over 12 years ago

10.18632/oncotarget.27732

Novel combination therapy for melanoma induces apoptosis via a gap junction positive feedback mechanism
Cited by: 3
Author(s): Archis Bagati, Timothy C. Hutcherson, Zethan Koch, Joseph Pechette, Hossein Dianat, Cory Higley, Lisa Chiu, Yesul Song, Jay B. Shah, Elana Chazen, Andrew Nicolais, Peter Casey, Kyle Thompson, K. Burke, Mikhail A. Nikiforov, J. Zirnheld, Shoshanna N. Zucker
Software Mentions: 3
Published: about 4 years ago

10.1016/j.jsb.2021.107729

Structure of the cytoplasmic domain of SctV (SsaV) from the Salmonella SPI-2 injectisome and implications for a pH sensing mechanism
Cited by: 12
Author(s): Teige R. S. Matthews-Palmer, Nayim Gonzalez-Rodriguez, Thomas Calcraft, Signe Lagercrantz, Tobias Zachs, Xiu-Jun Yu, Grzegorz Grabe, David W. Holden, Andrea Nans, Peter B. Rosenthal, Sarah L. Rouse, Morgan Beeby
Software Mentions: 3
Published: over 3 years ago

10.1038/cr.2016.128

DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
Cited by: 87
Author(s): Hongshan Guo, Boqiang Hu, Liying Yan, Jun Yong, Yan Wu, Yun Gao, Fan Guo, Yu Hou, Xiaoying Fan, Ji Dong, Xiaoye Wang, Xiaohui Zhu, Jie Yan, Wei Yuan, Hongyan Jin, Wenxin Zhang, Lu Wen, Fuchou Tang
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2021.666689

Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov.
Cited by: 20
Author(s): James T. Tambong, Ran Xu, Suzanne Gerdis, Greg C. Daniels, Denise Chabot, Keith Hubbard, Michael W. Harding
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0017900

Transcriptome Analysis of the Vernalization Response in Barley (Hordeum vulgare) Seedlings
Cited by: 53
Author(s): Aaron G. Greenup, Shahryar Sasani, Sandra N. Oliver, Sally A. Walford, Anthony A. Millar, Ben Trevaskis
Software Mentions: 2
Published: over 13 years ago

10.3389/fpls.2017.00632

Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size
Cited by: 28
Author(s): Jérôme Grimplet, Javier Tello, Natalia Laguna, Javier Ibáñez
Software Mentions: 2
Published: over 7 years ago

10.1186/s12968-015-0108-2

T2 mapping of the heart with a double-inversion radial fast spin-echo method with indirect echo compensation
Cited by: 11
Author(s): Tomoe Hagio, Chuan-Chin Huang, Aiden Abidov, Jaspreet Singh, Bujji Ainapurapu, Scott Squire, Denise Bruck, María I. Altbach
Software Mentions: 2
Published: over 9 years ago

10.1186/s13068-016-0572-4

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type
Cited by: 52
Author(s): Robert Heyer, Dirk Benndorf, Fabian Kohrs, Jo De Vrieze, Nico Boon, Marcus Hoffmann, Erdmann Rapp, Andreas Schlüter, Alexander Sczyrba, Udo Reichl
Software Mentions: 2
Published: over 8 years ago

10.1038/srep25444

Specific Cues Associated With Honey Bee Social Defence against Varroa destructor Infested Brood
Cited by: 63
Author(s): Fanny Mondet, Seo Hyun Kim, Joachim Rodrigues De Miranda, Dominique Beslay, Yves Le Conte, Alison R. Mercer
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.29593

Natural variation in stochastic photoreceptor specification and color preference in Drosophila
Cited by: 25
Author(s): Caitlin Anderson, India Reiss, Cyrus Zhou, Annie Cho, Haziq Siddiqi, Benjamin Mormann, Cameron M. Avelis, Peter DeFord, Alan O. Bergland, Elijah Roberts, James Taylor, Daniel Vasiliauskas, Robert J. Johnston
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.32373

Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron
Cited by: 31
Author(s): Elisa Galliano, Eleonora Franzoni, Marine Breton, Annisa Chand, Darren J Byrne, Venkatesh N. Murthy, Matthew S. Grubb
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms151018162

Towards Global QSAR Model Building for Acute Toxicity: Munro Database Case Study
Cited by: 33
Author(s): Swapnil Chavan, Ian A. Nicholls, Britt Karlsson, Annika M. Rosengren, Davide Ballabio, Viviana Consonni, Roberto Todeschini
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2156-9-14

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
Cited by: 35
Author(s): Adam B. Olshen, Bert Gold, Kirk E. Lohmueller, Jeffery P. Struewing, Jaya M. Satagopan, Стефан Стефанов, Eleazar Eskin, Tomas Kirchhoff, James A. Lautenberger, Robert J. Klein, Eitan Friedman, Larry Norton, Nathan A. Ellis, Agnès Viale, Catherine S. Lee, Patrick I. Borgen, Andrew G. Clark, Kenneth Offit, Jeff Boyd
Software Mentions: 2
Published: over 16 years ago

10.1098/rsif.2020.0476

A comparison of metrics for quantifying cranial suture complexity
Cited by: 10
Author(s): Heather E White, Julien Clavel, Abigail S. Tucker, Anjali Goswami
Software Mentions: 2
Published: about 4 years ago

10.1016/j.dib.2018.02.071

Microstructural data of six recent brachiopod species: SEM, EBSD, morphometric and statistical analyses
Cited by: 11
Author(s): Facheng Ye, Gaia Crippa, Claudio Garbelli, Erika Griesshaber
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1005485

Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host Apoplast
Cited by: 71
Author(s): Yan Zhang, Juan He, Lei-Jie Jia, Ting Yuan, Dong Zhang, Yan Guo, Yufeng Wang, Wei Tang
Software Mentions: 1
Published: over 8 years ago

10.1186/s40659-021-00336-4

NOD1 rs2075820 (p.E266K) polymorphism is associated with gastric cancer among individuals infected with cagPAI-positive H. pylori
Cited by: 4
Author(s): Patricio González‐Hormazábal, Diana Pelaez, Maher Musleh, Marco Bustamante, Juan Stambuk, R Pisano, H Valladares, Enrique Lanzarini, Hector Chiong, José Suazo, Luis A. Quiñones, Nelson Varela, Victor Castro, Lilian Jara, Zoltán Berger
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.42746

State transitions in the substantia nigra reticulata predict the onset of motor deficits in models of progressive dopamine depletion in mice
Cited by: 41
Author(s): Amanda M Willard, Brian R. Isett, Timothy C Whalen, Kevin J Mastro, Chris S Ki, Xiaobo Mao, Aryn H. Gittis
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-15915-3

Genetic polymorphism related to monocyte-macrophage function is associated with graft-versus-host disease
Cited by: 17
Author(s): Kati Hyvärinen, Jarmo Ritari, Satu Koskela, Riitta Niittyvuopio, Anne Nihtinen, Liisa Volin, David Gallardo, Jukka Partanen
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-019-42987-0

A systematic approach re-analyzing the effects of temperature disturbance on the microbial community of mesophilic anaerobic digestion
Cited by: 11
Author(s): Grace Tzun-Wen Shaw, Chieh-Yin Weng, Cheng-Yu Chen, Francis Cheng-Hsuan Weng, Daryi Wang
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.00623-19

Metabolic Remodeling during Biofilm Development of Bacillus subtilis
Cited by: 82
Author(s): Tippapha Pisithkul, Jeremy W. Schroeder, Edna A. Trujillo, Ponlkrit Yeesin, David Stevenson, Tai Chaiamarit, Joshua J. Coon, Jue D. Wang, Daniel Amador‐Noguez
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2020.00019

Meta-Analysis of Genome-Wide Association and Gene Expression Studies Implicates Donor T Cell Function and Cytokine Pathways in Acute GvHD
Cited by: 4
Author(s): Kati Hyvärinen, Satu Koskela, Riitta Niittyvuopio, Anne Nihtinen, Liisa Volin, Urpu Salmenniemi, Matti Putkonen, Ismael Buño, David Gallardo, Maija Itälä‐Remes, Jukka Partanen, Jarmo Ritari
Software Mentions: 1
Published: almost 5 years ago

10.5812/ijem.3058

Advantage of Applying OSC to 1H NMR-Based Metabonomic Data of Celiac Disease
Cited by: 15
Author(s): Mostafa Rezaei‐Tavirani, Fariba Fathi, Fatemeh Darvizeh, Mohammad Reza Zali, Mohammad Rostami‐Nejad, Kamran Rostami, Mohsen Tafazzoli, Afsaneh Arefi Oskouie, Seyed Abdolreza Mortazavi-Tabatabaei
Software Mentions: 1
Published: over 12 years ago

10.3389/fphys.2021.674223

Characterization of Atrial Propagation Patterns and Fibrotic Substrate With a Modified Omnipolar Electrogram Strategy in Multi-Electrode Arrays
Cited by: 4
Author(s): Jennifer Riccio, Alejandro Alcaine, Sara Rocher, Laura Martínez-Mateu, Sérgio Laranjo, Javier Sáiz, Pablo Laguna, Juan Pablo Martínez
Software Mentions: 1
Published: about 3 years ago

10.3389/fpls.2019.01533

The Landscape of Copia and Gypsy Retrotransposon During Maize Domestication and Improvement
Cited by: 6
Author(s): Xiangbo Zhang, Yongwen Qi
Software Mentions: 1
Published: almost 5 years ago

10.2196/14326

Developing the Accuracy of Vital Sign Measurements Using the Lifelight Software Application in Comparison to Standard of Care Methods: Observational Study Protocol
Cited by: 4
Author(s): Thomas Jones, Emily Heiden, Felicity Mitchell, Carole Fogg, Sharon McCready, Laurence Pearce, Melissa Kapoor, Paul Bassett, Anoop Chauhan
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-019-5552-1

Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins
Cited by: 19
Author(s): Mei Liu, Lingzhao Fang, Shuli Liu, Michael G. Pan, Eyal Seroussi, John B. Cole, Li Ma, Hong Chen, George E. Liu
Software Mentions: 1
Published: over 5 years ago

10.3389/fpsyg.2021.678647

Sequential Congruency Effects of Reverse Stroop Interference on Event-Related Potential Components for Go- and Nogo-Stimuli
Cited by: 1
Author(s): Kota Suzuki
Software Mentions: 1
Published: over 3 years ago

10.3390/genes10010020

Polymorphisms in RAS/RAF/MEK/ERK Pathway Are Associated with Gastric Cancer
Cited by: 20
Author(s): Patricio González‐Hormazábal, Maher Musleh, Marco Bustamante, Juan Stambuk, R Pisano, H Valladares, Enrique Lanzarini, Hector Chiong, Jorge Rojas, José Suazo, Victor Castro, Lilian Jara, Zoltán Berger
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1003654

Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks
Cited by: 6
Author(s): Eric Yen, Aaron Tsay, Jérôme Waldispühl, Jackie Vogel
Software Mentions: 1
Published: over 10 years ago

10.1016/j.cub.2020.05.055

Zebrafish Retinal Ganglion Cells Asymmetrically Encode Spectral and Temporal Information across Visual Space
Cited by: 35
Author(s): Mingyi Zhou, John Bear, Paul Roberts, F. Janiak, Julia Lee Semmelhack, Takeshi Yoshimatsu, Tom Baden
Software Mentions: 1
Published: over 4 years ago

10.1186/2040-2392-3-9

Common genetic variants, acting additively, are a major source of risk for autism
Cited by: 354
Author(s): Lambertus Klei, Stephan Sanders, Michael T. Murtha, Vanessa Hus, Jennifer K. Lowe, A. Jeremy Willsey, Daniel Moreno‐De‐Luca, Timothy W. Yu, Éric Fombonne, Daniel H. Geschwind, Dorothy E. Grice, David H. Ledbetter, Catherine Lord, Shrikant Mane, Christa Lese Martin, Donna M. Martin, Eric M. Morrow, Christopher A. Walsh, Nadine M. Melhem, Pauline Chaste, James S. Sutcliffe, Matthew W. State, Edwin H. Cook, Kathryn Roeder, Bernie Devlin
Software Mentions: 1
Published: about 12 years ago

10.1007/s10886-018-0980-y

The Use of Metabolomics to Elucidate Resistance Markers against Damson-Hop Aphid
Cited by: 5
Author(s): Anna K. Undas, Florian Weihrauch, A. Lutz, R. van Tol, Thierry Delatte, Francel Verstappen, Harro J. Bouwmeester
Software Mentions: 1
Published: over 6 years ago