Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: IMP

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/IMP

Interactive Model Performance Evaluation
2 versions
Latest release: almost 9 years ago
131 downloads last month

Papers Mentioning IMP 172

10.1186/s13059-019-1819-8
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago
10.1038/srep35903
Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: about 8 years ago
10.1155/2015/693193
Genetic Geostatistical Framework for Spatial Analysis of Fine-Scale Genetic Heterogeneity in Modern Populations: Results from the KORA Study
Cited by: 2
Author(s): Amalia Diaz‐Lacava, Maja Walier, Daniela Höller, Michael Steffens, Christian Gieger, Cesare Furlanello, Claudia Lamina, H‐Erich Wichmann, Tim Becker
Software Mentions: 8
Published: almost 10 years ago
10.1186/s40168-020-00993-9
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data
Cited by: 61
Author(s): Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz‐Buschart, Cédric Christian Laczny, Patrick May, Paul Wilmes
Software Mentions: 7
Published: over 3 years ago
10.1093/bioinformatics/btaa177
Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: over 4 years ago
10.1186/s13059-021-02435-7
DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
Cited by: 15
Author(s): Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Software Mentions: 6
Published: over 3 years ago
10.12688/f1000research.28608.2
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: over 3 years ago
10.3389/fgene.2019.00904
Advances and Challenges in Metatranscriptomic Analysis
Cited by: 217
Author(s): Migun Shakya, Chien‐Chi Lo, Patrick Chain
Software Mentions: 6
Published: about 5 years ago
10.1186/s12864-020-07013-y
Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework
Cited by: 3
Author(s): Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars, H. Peter Hofstee
Software Mentions: 6
Published: about 4 years ago
10.1186/s41512-018-0036-3
Methods for Evaluation of medical prediction Models, Tests And Biomarkers (MEMTAB) 2018 Symposium
Cited by: 3
Author(s):
Software Mentions: 6
Published: over 6 years ago
10.1673/031.012.3001
Multi–predator Effects Produced by Functionally Distinct Species Vary with Prey Density
Cited by: 15
Author(s): Ben P. Werling, David M. Lowenstein, Cory S. Straub, Claudio Gratton
Software Mentions: 5
Published: almost 13 years ago
10.1371/journal.pone.0193925
From top to bottom: Do Lake Trout diversify along a depth gradient in Great Bear Lake, NT, Canada?
Cited by: 13
Author(s): Louise Chavarie, Kimberly L. Howland, Les N. Harris, Michael J. Hansen, William J. Harford, Colin P. Gallagher, Shauna M. Baillie, Brendan K. Malley, William M. Tonn, Andrew M. Muir, Charles C. Krueger
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0160001
Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)
Cited by: 31
Author(s): Ljiljana Šašić, Jelena Ačanski, Ante Vujić, Gunilla Ståhls, Snežana Radenković, Dubravka Milić, Dragana Obreht Vidaković, Dan Mo
Software Mentions: 4
Published: about 8 years ago
10.3389/fimmu.2020.583013
Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures
Cited by: 10
Author(s): David Roe, Rui Kuang
Software Mentions: 4
Published: almost 4 years ago
10.3390/s17020403
Towards a Semantic Web of Things: A Hybrid Semantic Annotation, Extraction, and Reasoning Framework for Cyber-Physical System
Cited by: 27
Author(s): Zhenyu Wu, Yuan Xu, Yunong Yang, Chunhong Zhang, Xinning Zhu, Yang Ji
Software Mentions: 4
Published: over 7 years ago
10.3390/s18114029
Sensor Fusion for Recognition of Activities of Daily Living
Cited by: 51
Author(s): Jiaxuan Wu, Yunfei Feng, Peng Sun
Software Mentions: 4
Published: almost 6 years ago
10.1186/s13059-016-1116-8
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Cited by: 112
Author(s): Shaman Narayanasamy, Yohan Jarosz, Emilie Muller, Anna Heintz‐Buschart, Malte Herold, Anne Kaysen, Cédric Christian Laczny, Nicolás Pinel, Patrick May, Paul Wilmes
Software Mentions: 4
Published: almost 8 years ago
10.1186/s13059-016-1146-2
Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Cited by: 148
Author(s): Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Software Mentions: 4
Published: almost 8 years ago
10.1186/s13072-017-0142-4
Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
Cited by: 18
Author(s): Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim Imakaev, Nezar Abdennur, Mikhail S. Gelfand, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 4
Published: over 7 years ago
10.1016/j.csbj.2016.11.005
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Cited by: 102
Author(s): Karel Sedlář, Kristyna Kupkova, Ivo Provazník
Software Mentions: 4
Published: almost 8 years ago
10.1093/gigascience/giz096
To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)
Cited by: 24
Author(s): Muhammad Zohaib Anwar, Anders Lanzén, Toke Bang‐Andreasen, Carsten Suhr Jacobsen
Software Mentions: 4
Published: over 5 years ago
10.1186/s12859-019-2659-y
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis
Cited by: 2
Author(s): Mohieddin Jafari, Payman Nickchi, Soheil Jahangiri, Abdollah Safari, Mehdi Mirzaie, Mohieddin Jafari
Software Mentions: 4
Published: over 5 years ago
10.1002/ece3.7158
Among‐individual diet variation within a lake trout ecotype: Lack of stability of niche use
Cited by: 4
Author(s): Louise Chavarie, Kimberly L. Howland, Les N. Harris, Colin P. Gallagher, Michael J. Hansen, William M. Tonn, Andrew M. Muir, Charles C. Krueger
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1004005
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
Cited by: 110
Author(s): James Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique Hinchcliff, Michael L. Whitfield
Software Mentions: 4
Published: almost 10 years ago
10.1002/ece3.3138
Snails in the desert: Species diversification of <i>Theba</i> (Gastropoda: Helicidae) along the Atlantic coast of <scp>NW</scp> Africa
Cited by: 7
Author(s): Carola Greve, Martín Haase, Rainer Hutterer, Dennis Rödder, Flora Ihlow, Bernhard Misof
Software Mentions: 3
Published: over 7 years ago
10.1186/1471-2164-15-852
Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models
Cited by: 10
Author(s): Sophie Rodius, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Céline Jeanty, Juan Manuel González‐Rosa, Mark Ibberson, Ricardo Costa, Ioannis Xénarios, Nadia Mercader, Francisco Azuaje
Software Mentions: 3
Published: about 10 years ago
10.1016/j.jbc.2021.100743
From integrative structural biology to cell biology
Cited by: 38
Author(s): Andrej Šali
Software Mentions: 3
Published: almost 4 years ago
10.3390/microorganisms8121861
Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community
Cited by: 3
Author(s): Claudia Sala, Hanne Mordhorst, Josephine Grützke, Annika Brinkmann, Thomas Nordahl Petersen, Casper Sahl Poulsen, Paul D. Cotter, Fiona Crispie, Richard J. Ellis, Gastone Castellani, Clara Amid, Mikhayil Hakhverdyan, Soizick Le Guyader, Gerardo Manfreda, Joël Mossong, Andreas Nitsche, Catherine Ragimbeau, Julien Schaeffer, Jørgen Schlundt, Moon Y. F. Tay, Frank Møller Aarestrup, René S. Hendriksen, Sünje Johanna Pamp, Alessandra De Cesare
Software Mentions: 3
Published: almost 4 years ago
10.7554/eLife.08719
Molecular architecture of the yeast Mediator complex
Cited by: 133
Author(s): Philip J. Robinson, Michael J. Trnka, Riccardo Pellarin, Charles H. Greenberg, David Bushnell, Roger T. Davis, Alma L. Burlingame, Andrej Šali, Roger D. Kornberg
Software Mentions: 3
Published: about 9 years ago
10.1111/eva.13188
Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?
Cited by: 2
Author(s): Louise Chavarie, Steven L. Voelker, Michael J. Hansen, Charles R. Bronte, Andrew M. Muir, Mara S. Zimmerman, Charles C. Krueger
Software Mentions: 3
Published: almost 4 years ago
10.3390/ijms21114045
Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization
Cited by: 43
Author(s): Bruno Tilocca, Luisa Pieroni, Alessio Soggiu, Domenico Britti, L. Bonizzi, Paola Roncada, Viviana Greco
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0034339
Radiating on Oceanic Islands: Patterns and Processes of Speciation in the Land Snail Genus Theba (Risso 1826)
Cited by: 23
Author(s): Carola Greve, Rainer Hutterer, Bernhard Misof, Martín Haase
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pgen.1005805
Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross
Cited by: 28
Author(s): Anna L. Tyler, Leah Rae Donahue, Gary A. Churchill, Gregory W. Carter
Software Mentions: 3
Published: almost 9 years ago
10.7717/peerj.9973
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams
Cited by: 15
Author(s): Susheel Bhanu Busi, Paraskevi Pramateftaki, Jade Brandani, Stilianos Fodelianakis, Hannes Peter, Rashi Halder, Paul Wilmes, Tom J. Battin
Software Mentions: 3
Published: about 4 years ago
10.3390/proteomes9010015
Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
Cited by: 92
Author(s): Benjamin C. Orsburn
Software Mentions: 3
Published: over 3 years ago
10.1002/ece3.3356
Sexual dimorphism, phenotypic integration, and the evolution of head structure in casque‐headed lizards
Cited by: 8
Author(s): Gregory Taylor, Juan Carlos Santos, Benjamin J. Perrault, Mariana Morando, Carlos Roberto Vásquez Almazán, Jack W. Sites
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pone.0138220
A Framework to Simplify Combined Sampling Strategies in Rosetta
Cited by: 10
Author(s): Justin R. Porter, Brian D. Weitzner, Oliver Lange
Software Mentions: 3
Published: about 9 years ago
10.1016/j.str.2019.09.007
Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes
Cited by: 14
Author(s): Sanchaita Das, Andrew W. Malaby, Agata Nawrotek, Wenhua Zhang, Mahel Zeghouf, Sarah Maslen, Mark Skehel, Srinivas Chakravarthy, Thomas C. Irving, Osman Bilsel, Jacqueline Cherfils, David G. Lambright
Software Mentions: 3
Published: almost 5 years ago
10.1186/1472-6807-11-33
Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria
Cited by: 5
Author(s): Yu Song, A. Vit, Sean R. A. Devenish, H. K. Mahanty, Aymelt Itzen, Roger S. Goody, Wulf Blankenfeldt
Software Mentions: 3
Published: about 13 years ago
10.1016/j.csbj.2017.01.008
Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase
Cited by: 14
Author(s): Katja Venko, Amrita Roy Choudhury, Marjana Novič
Software Mentions: 3
Published: almost 8 years ago
10.1371/journal.pgen.1007054
A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes
Cited by: 25
Author(s): Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, Giovanni Bosco
Software Mentions: 3
Published: about 7 years ago
10.1186/s12859-020-03585-4
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Cited by: 74
Author(s): Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski, Lee Ann McCue
Software Mentions: 3
Published: over 4 years ago
10.18632/aging.103396
Identification of cardiovascular health gene variants related to longevity in a Chinese population
Cited by: 3
Author(s): Li Zhang, Chen Bai, Chao Nie, Xiaoquan Zhu, Huiping Yuan, Liang Sun, Qi Zhou, Xiaoling Li, Xuan Xian, Fan Yang, Guo‐Fang Pang, Yuan Lv, Xiaolin Ni, Chengping Hu, Ze Yang
Software Mentions: 2
Published: about 4 years ago
10.7717/peerj.9925
Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont<i>Diictodon feliceps</i>(Therapsida, Anomodontia)
Cited by: 12
Author(s): Christian F. Kammerer, Michol Deutsch, Jacqueline K. Lungmus, Kenneth D. Angielczyk
Software Mentions: 2
Published: about 4 years ago
10.1111/pbi.13434
Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon
Cited by: 41
Author(s): Shi Liu, Peng Gao, Qianglong Zhu, Zhu Zhang, Hongyu Liu, Xuezheng Wang, Yiqun Weng, Meiling Gao, Feishi Luan
Software Mentions: 2
Published: over 4 years ago
10.3390/antibiotics10091140
Detection of Multidrug-Resistant Enterobacterales—From ESBLs to Carbapenemases
Cited by: 23
Author(s): Janina Noster, Philipp Thelen, Axel Hamprecht
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pcbi.1006030
4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data
Cited by: 9
Author(s): Ibai Irastorza-Azcárate, Rafael D. Acemel, Juan J. Tena, Ignacio Maeso, José Luis Gómez-Skármeta, Damien P. Devos
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pcbi.1004396
Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
Cited by: 32
Author(s): Jonas Paulsen, Odin Gramstad, Philippe Collas
Software Mentions: 2
Published: about 9 years ago
10.3389/fmicb.2018.01235
Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies
Cited by: 13
Author(s): Maggie C. Y. Lau, Rachel L. Harris, Youmi Oh, Min Joo Yi, Aida Behmard, Tullis C. Onstott
Software Mentions: 2
Published: over 6 years ago
10.3389/fmolb.2019.00102
MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
Cited by: 25
Author(s): Rodrigo Vargas Honorato, Jorge Roel‐Touris, Alexandre Bonvin
Software Mentions: 2
Published: about 5 years ago
10.1186/s13040-015-0050-8
Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study
Cited by: 2
Author(s): Jiang Gui, Casey S. Greene, Claire Sullivan, W. Rowland Taylor, Jason H. Moore, Carol H. Kim
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pcbi.1004619
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
Cited by: 179
Author(s): Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0256604
Link-based influence maximization in networks of health promotion professionals
Cited by: 1
Author(s): Maurits H. W. Oostenbroek, Marco van der Leij, Quinten Meertens, Cees Diks, Heleen M. Wortelboer
Software Mentions: 2
Published: about 3 years ago
10.1186/1745-6150-9-12
Selecting biologically informative genes in co-expression networks with a centrality score
Cited by: 51
Author(s): Francisco Azuaje
Software Mentions: 2
Published: almost 11 years ago
10.1016/j.bpj.2018.02.028
Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy
Cited by: 87
Author(s): Massimiliano Bonomi, Riccardo Pellarin, Michele Vendruscolo
Software Mentions: 2
Published: over 6 years ago
10.1042/BSR20180430
Computational modeling of RNA 3D structure based on experimental data
Cited by: 37
Author(s): Almudena Ponce-Salvatierra, Astha Astha, Katarzyna Merdas, Chandran Nithin, Pritha Ghosh, Sunandan Mukherjee, Janusz Bujnicki
Software Mentions: 2
Published: almost 6 years ago
10.1186/gm550
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity
Cited by: 10
Author(s): Nadia M. Penrod, Casey S. Greene, Jason H. Moore
Software Mentions: 2
Published: almost 11 years ago
10.1186/2047-217X-3-5
Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction
Cited by: 10
Author(s): Marco Mesiti, Matteo Ré, Giorgio Valentini
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0222614
LPS induces inflammatory chemokines via TLR-4 signalling and enhances the Warburg Effect in THP-1 cells
Cited by: 24
Author(s): Philemon Ubanako, Ntombikayise Xelwa, Monde Ntwasa
Software Mentions: 2
Published: about 5 years ago
10.1007/s10858-019-00264-2
Archiving and disseminating integrative structure models
Cited by: 19
Author(s): Brinda Vallat, Benjamin Webb, John D. Westbrook, Andrej Šali, Helen M. Berman
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0175758
Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages
Cited by: 8
Author(s): Qi Chen, Michał Vieth, David E. Timm, Christine Humblet, Dina Stroopinsky, Ilan E. Chemmama, Andrej Šali, Wei Zeng, Jirong Lu, Ling Liu
Software Mentions: 2
Published: over 7 years ago
10.1002/pro.4067
Improving integrative 3D modeling into low‐ to medium‐resolution electron microscopy structures with evolutionary couplings
Cited by: 1
Author(s): Caitlyn L. McCafferty, David W. Taylor, Edward M. Marcotte
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-020-6609-x
Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
Cited by: 4
Author(s): Diego P. Rubert, Fábio Viduani Martinez, Jens Stoye, Daniel Doerr
Software Mentions: 2
Published: over 4 years ago
10.1016/j.mcpro.2021.100139
IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics
Cited by: 4
Author(s): Daniel S. Ziemianowicz, Daniel J. Saltzberg, Troy J. Pells, David A. Crowder, Christoph U. Schräder, Morgan Hepburn, Andrej Šali, David C. Schriemer
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0244967
Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae
Cited by: 16
Author(s): Nousheen Parvaiz, Faisal Ahmad, Wenbo Yu, Alexander D. MacKerell, Syed Sikander Azam
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-019-52162-0
Structure Based Multitargeted Molecular Docking Analysis of Selected Furanocoumarins against Breast Cancer
Cited by: 78
Author(s): Reetuparna Acharya, Shinu Chacko, Pritha Bose, Antonio Lapenna, Shakti Prasad Pattanayak
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0180121
Prevalence of ESBL-producing Pseudomonas aeruginosa isolates in Warsaw, Poland, detected by various phenotypic and genotypic methods
Cited by: 59
Author(s): Agnieszka E. Laudy, Patrycja Róg, Katarzyna Smolińska-Król, Milena Ćmiel, Alicja Słoczyńska, Jan Patzer, D Dzierżanowska, Renata Wolinowska, Bohdan Starościak, Stefan Tyski
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2105-11-429
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
Cited by: 50
Author(s): Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff‐Borg, Thomas Hamelryck
Software Mentions: 2
Published: about 14 years ago
10.1186/s12859-018-2189-z
SAMSA2: a standalone metatranscriptome analysis pipeline
Cited by: 91
Author(s): Samuel T. Westreich, Michelle L. Treiber, David A. Mills, Ian F Korf, Danielle G. Lemay
Software Mentions: 2
Published: over 6 years ago
10.1111/zsc.12110
Form, function and phylogeny: comparative morphometrics of Lake Tanganyika's cichlid tribe Tropheini
Cited by: 23
Author(s): Katrin A. Wanek, Christian Sturmbauer
Software Mentions: 2
Published: over 9 years ago
10.3390/cancers13040751
Prognostic Effect of Inflammatory Genes on Stage I–III Colorectal Cancer—Integrative Analysis of TCGA Data
Cited by: 6
Author(s): Eun Kyung Choe, Sang‐Woo Lee, So Yeon Kim, Manu Shivakumar, Kyu Joo Park, Young Jun Chai, Dokyoon Kim
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-019-2959-2
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction
Cited by: 9
Author(s): Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Marco Notaro, Alessandro Petrini, Elena Casiraghi, Giuliano Grossi, Jessica Gliozzo, Giorgio Valentini
Software Mentions: 2
Published: about 5 years ago
10.1016/j.csbj.2020.05.002
Coarse-grained (hybrid) integrative modeling of biomolecular interactions
Cited by: 17
Author(s): Jorge Roel‐Touris, Alexandre Bonvin
Software Mentions: 2
Published: almost 5 years ago
10.1007/s00439-019-01987-w
How to increase our belief in discovered statistical interactions via large-scale association studies?
Cited by: 12
Author(s): Kristel Van Steen, Jason H. Moore
Software Mentions: 2
Published: over 5 years ago
10.3390/ijerph16224556
Decreased Vertical Trunk Inclination Angle and Pelvic Inclination as the Result of Mid-High-Heeled Footwear on Static Posture Parameters in Asymptomatic Young Adult Women
Cited by: 6
Author(s): Jakub Michoński, Marcin Witkowski, Bożena Glinkowska, Robert Sitnik, Wojciech Glinkowski
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.csbj.2015.08.005
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Cited by: 22
Author(s): Xiaojun Xu, Yan Cheng, Robert M. Wohlhueter, Ivaylo Ivanov
Software Mentions: 2
Published: almost 10 years ago
10.7554/eLife.31097
Prediction of enzymatic pathways by integrative pathway mapping
Cited by: 26
Author(s): Sara Calhoun, Magdalena Korczynska, D. Wichelecki, Brian San Francisco, Suwen Zhao, Dmitry A. Rodionov, M.W. Vetting, Nawar Al-Obaidi, Henry J. Lin, Matthew J. O’Meara, David A. Scott, John H. Morris, Daniel Russel, Steven C. Almo, Andrei L. Osterman, J.A. Gerlt, Matthew P. Jacobson, Brian K. Shoichet, Andrej Šali
Software Mentions: 2
Published: almost 7 years ago
10.7554/eLife.46302
Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding
Cited by: 23
Author(s): J. Lauer, Sandra Segeletz, Alice Cezanne, Giambattista Guaitoli, Francesco Raimondi, Marc Gentzel, Vikram Alva, Michael Habeck, Yannis Kalaidzidis, Marius Ueffing, Andrei N. Lupas, Christian Johannes Gloeckner, Marino Zerial
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-020-3474-1
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces
Cited by: 3
Author(s): Felippe C. Queiroz, Adriana Maria Patarroyo Vargas, M. G. A. Oliveira, Giovanni Comarela, Simonton Andrade Silveira
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms22115914
Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential
Cited by: 1
Author(s): mengsheng zha, Nan Wang, Chaoyang Zhang, Zheng Wang
Software Mentions: 2
Published: over 3 years ago
10.1186/s13063-016-1252-1
Comparing systemic therapy and cognitive behavioral therapy for social anxiety disorders: study protocol for a randomized controlled pilot trial
Cited by: 6
Author(s): Christina Hunger, Rebecca Hilzinger, Theresa Koch, Johannes Mander, Anja Sander, Hinrich Bents, Jochen Schweitzer
Software Mentions: 1
Published: over 8 years ago
10.1186/s13063-017-2290-z
Improving readiness for recruitment through simulated trial activation: the Adjuvant Steroids in Adults with Pandemic influenza (ASAP) trial
Cited by: 3
Author(s): Wei Shen Lim, Garry Meakin, Clare Brittain, Thomas Bewick, Lelia Duley
Software Mentions: 1
Published: almost 7 years ago
10.1186/s13063-018-3050-4
Dexamethasone for adult patients with a symptomatic chronic subdural haematoma (Dex-CSDH) trial: study protocol for a randomised controlled trial
Cited by: 36
Author(s): Angelos G. Kolias, Ellie Edlmann, Eric Peter Thelin, Diederik Bulters, Patrick Holton, Nigel Suttner, Kevin Agyemang, Yahia Al‐Tamimi, Daniel Gatt, Simon Thomson, Ian Anderson, Oliver C. Richards, Peter Whitfield, Monica Gherle, Karen Caldwell, Carol Davis-Wilkie, Silvia Tarantino, Garry Barton, Hani J. Marcus, Ajai Chari, Paul M. Brennan, Antonio Belli, Simon Bond, Carole Turner, Lynne Whitehead, Ian B. Wilkinson, Peter J. Hutchinson
Software Mentions: 1
Published: almost 6 years ago
10.3390/ijerph14091046
A Multivariate Dynamic Spatial Factor Model for Speciated Pollutants and Adverse Birth Outcomes
Cited by: 0
Author(s): Kimberly Kaufeld, Montse Fuentes, Brian J. Reich, Amy H. Herring, Gary M. Shaw, Maria A. Terres
Software Mentions: 1
Published: about 7 years ago
10.3390/ijerph18189653
Oxidative Stress Parameters in Goitrogen-Exposed Crested Newt Larvae (Triturus spp.): Arrested Metamorphosis
Cited by: 3
Author(s): Jelena P. Gavrić, Svetlana G. Despotović, Branka R. Gavrilović, Tijana B. Radovanović, Tamara G. Petrović, Maja Ajduković, Tijana Vučić, Milena Cvijanović, Caterina Faggio, Marko D. Prokić
Software Mentions: 1
Published: about 3 years ago
10.1673/031.012.5301
Morphometric and Genetic Differentiation of Two Sibling Gossamer-Wing Damselflies,<i>Euphaea formosa</i>and<i>E. yayeyamana</i>, and Adaptive Trait Divergence in Subtropical East Asian Islands
Cited by: 13
Author(s): Yat Hung Lee, Chung Ping Lin
Software Mentions: 1
Published: over 12 years ago
10.7554/eLife.54558
Identifying the immune interactions underlying HLA class I disease associations
Cited by: 12
Author(s): Bisrat J. Debebe, Lies Boelen, James C. Lee, Iavi Protocol C Investigators, Eduard J. Sanders, Omu Anzala, Anatoli Kamali, Pontiano Kaleebu, Etienne Karita, William Kilembe, Mubiana Inambao, Shabir Lakhi, Susan Allen, Eric Hunter, Vinodh Edward, Pat Fast, Matt A. Price, Jill Gilmour, Jianming Tang, Chloe L. Thio, Jacquie Astemborski, Gregory D. Kirk, Salim I. Khakoo, Sharyne Donfield, James J. Goedert, Becca Asquith
Software Mentions: 1
Published: over 4 years ago
10.2196/24839
Effectiveness of Internet-Based Cognitive Behavior Therapy (Fatigue in Teenagers on the Internet) for Adolescents With Chronic Fatigue Syndrome in Routine Clinical Care: Observational Study
Cited by: 2
Author(s): Eline Albers, Linde N Nijhof, Emma E Berkelbach van der Sprenkel, Elise M. van de Putte, Sanne L. Nijhof, Hans Knoop
Software Mentions: 1
Published: about 3 years ago
10.1186/1866-1955-6-1
Associations of HLA alleles with specific language impairment
Cited by: 34
Author(s): Ron Nudel, Nuala H. Simpson, Gillian Baird, Anne O’Hare, Gina Conti‐Ramsden, Patrick Bolton, Elizabeth R Hennessy, Anthony P. Monaco, Julian C. Knight, Bruce Winney, Simon E. Fisher, Dianne F. Newbury
Software Mentions: 1
Published: almost 11 years ago
10.1186/1749-799X-3-44
Assessment of the primary rotational stability of uncemented hip stems using an analytical model: Comparison with finite element analyses
Cited by: 2
Author(s): M Zeman, Nicolas Sauwen, Luc Labey, Michiel Mulier, Georges Van der Perre, Siegfried Jaecques
Software Mentions: 1
Published: about 16 years ago
10.18632/oncotarget.23703
MicroRNA-340 inhibits the proliferation and promotes the apoptosis of colon cancer cells by modulating REV3L
Cited by: 16
Author(s): Roshini Arivazhagan, Jaesuk Lee, Delger Bayarsaikhan, Peter Kwak, Myeongjoo Son, Kyunghee Byun, Ghasem Hosseini Salekdeh, Bong-Hee Lee
Software Mentions: 1
Published: almost 7 years ago
10.1007/s10992-017-9445-y
On Sahlqvist Formulas in Relevant Logic
Cited by: 5
Author(s): Guillermo Badía
Software Mentions: 1
Published: about 7 years ago
10.1111/j.1469-7998.2010.00729.x
Disentangling true shape differences and experimenter bias: are dextral and sinistral snail shells exact mirror images?
Cited by: 26
Author(s): Menno Schilthuizen, Martín Haase
Software Mentions: 1
Published: over 14 years ago
10.3390/ani10040603
The Effect of Shelter on Oxidative Stress and Aggressive Behavior in Crested Newt Larvae (Triturus spp.)
Cited by: 11
Author(s): Tamara G. Petrović, Tijana Vučić, Slobodan Nikolić, Jelena P. Gavrić, Svetlana G. Despotović, Branka R. Gavrilović, Tijana B. Radovanović, Caterina Faggio, Marko D. Prokić
Software Mentions: 1
Published: over 4 years ago
10.1007/s12149-018-1282-8
A new non-invasive graphical method for quantification of cerebral blood flow with[ $$^{123}\hbox {I}$$ 123 I ] IMP
Cited by: 5
Author(s): Masashi Kameyama, Kiyotaka Watanabe
Software Mentions: 1
Published: over 6 years ago
10.3390/antibiotics3030285
Evolution of Metallo-β-lactamases: Trends Revealed by Natural Diversity and in vitro Evolution
Cited by: 69
Author(s): María Rocío Meini, Leticia I. Llarrull, Alejandro J. Vila
Software Mentions: 1
Published: over 10 years ago
10.1186/1471-2105-9-S5-S2
Gene Ontology annotations: what they mean and where they come from
Cited by: 132
Author(s): David P. Hill, Barry Smith, Monica McAndrews-Hill, Judith A. Blake
Software Mentions: 1
Published: over 16 years ago
10.1186/s12859-016-1283-3
Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking
Cited by: 33
Author(s): Long Pei, Min Xu, Zachary Frazier, Frank Alber
Software Mentions: 1
Published: about 8 years ago
10.1186/1471-213X-10-18
Micro-computed tomography-based phenotypic approaches in embryology: procedural artifacts on assessments of embryonic craniofacial growth and development
Cited by: 45
Author(s): Edward M. Schmidt, Trish E. Parsons, Heather A. Jamniczky, Julian Gitelman, Cvett Trpkov, Julia C. Boughner, Cairine Logan, Christoph Wilhelm Sensen, Benedikt Hallgrímsson
Software Mentions: 1
Published: over 14 years ago
10.1186/1471-2148-10-289
The blue lizard spandrel and the island syndrome
Cited by: 84
Author(s): Pasquale Raia, Fabio Maria Guarino, Mimmo Turano, Gianluca Polese, Daniela Rippa, Francesco Carotenuto, Daria Maria Monti, Manuela Cardi, Domenico Fulgione
Software Mentions: 1
Published: about 14 years ago