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: pypi: package

https://packages.ecosyste.ms/registries/pypi.org/packages/package

package is a package to package your package
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Latest release: over 13 years ago
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Papers Mentioning package 1,300

10.1371/journal.pcbi.1000300
Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
Cited by: 55
Author(s): Schraga Schwartz, Nurit Gal-Mark, Nir Kfir, Oren Ram, Eddo Kim, Gil Ast
Software Mentions: 3
Published: over 15 years ago
10.1038/tp.2016.101
Epigenetic differences in monozygotic twins discordant for major depressive disorder
Cited by: 37
Author(s): Karim Malki, Elena Koritskaya, Fraser Harris, Kevin Bryson, Mark Herbster, Maria Grazia Tosto
Software Mentions: 3
Published: over 8 years ago
10.1002/sim.8450
Improving safety of the continual reassessment method via a modified allocation rule
Cited by: 8
Author(s): Pavel Mozgunov, Thomas Jaki
Software Mentions: 3
Published: almost 5 years ago
10.1177/0962280219873005
Simultaneous inference for multiple marginal generalized estimating equation models
Cited by: 8
Author(s): Robin Ristl, Ludwig A. Hothorn, Christian Ritz, Martin Posch
Software Mentions: 3
Published: about 5 years ago
10.1101/2020.08.22.262931
Theoretical basis for stabilizing messenger RNA through secondary structure design
Cited by: 16
Author(s): Hannah K. Wayment-Steele, Do Soon Kim, Christian A. Choe, John J Nicol, Roger Wellington-Oguri, Andrew Watkins, R Andres Parra Sperberg, Po-Ssu Huang, Eterna Participants, Rhiju Das
Software Mentions: 3
Published: about 4 years ago
10.3390/s21072447
A BCI Based Alerting System for Attention Recovery of UAV Operators
Cited by: 8
Author(s): Jong-Hyuk Park, Jonghun Park, Dongmin Shin, Yerim Choi
Software Mentions: 3
Published: over 3 years ago
10.1186/s13148-019-0619-z
Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors
Cited by: 16
Author(s): Songlin Li, Yuan Yuan, He Xiao, Jiajia Dai, Yunfei Ye, Qin Zhang, Zhimin Zhang, Yuhan Jiang, Jia Luo, Jing Hu, Chuan Chen, Ge Wang
Software Mentions: 3
Published: over 5 years ago
10.1038/s42003-018-0176-6
Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent
Cited by: 76
Author(s): Kun Wang, Johannes A. Lenstra, Liang Liu, Quanjun Hu, Tao Ma, Qiang Qiu, Jianquan Liu
Software Mentions: 3
Published: about 6 years ago
10.1186/s13395-020-00236-3
A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations
Cited by: 109
Author(s): Andrea De Micheli, Jason A. Spector, Olivier Elemento, Benjamin D. Cosgrove
Software Mentions: 3
Published: over 4 years ago
10.1002/sim.7628
Targeted maximum likelihood estimation for a binary treatment: A tutorial
Cited by: 70
Author(s): Miguel Ángel Luque-Fernandez, Michael Schomaker, Bernard Rachet, Mireille E. Schnitzer
Software Mentions: 3
Published: over 6 years ago
10.1186/1471-2229-13-122
P-TRAP: a Panicle Trait Phenotyping tool
Cited by: 66
Author(s): Faroq Al-Tam, Hélène Adam, António dos Anjos, Mathias Lorieux, Pierre Larmande, Alain Ghesquière, Stéfan Jouannic, Hamid Reza Shahbazkia
Software Mentions: 3
Published: about 11 years ago
10.3390/ph14010041
Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients
Cited by: 4
Author(s): Hana Votavová, Zuzana Urbanová, David Kundrát, Michaela Dostálová Merkerová, Martin Vostrý, Monika Hruba, Jaroslav Čermák, Monika Beličková
Software Mentions: 3
Published: almost 4 years ago
10.7717/peerj.7366
Asexual reproduction of a few genotypes favored the invasion of the cereal aphid<i>Rhopalosiphum padi</i>in Chile
Cited by: 4
Author(s): María E Rubio-Meléndez, Joceline Barrios-Sanmartín, Felipe E. Pina-Castro, Christian C. Figueroa, C. Ramı́rez
Software Mentions: 3
Published: over 5 years ago
10.7717/peerj.6115
The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog,<i>Hyalinobatrachium fleischmanni</i>(Anura: Centrolenidae)
Cited by: 19
Author(s): Ángela María Mendoza, Wilmar Bolívar-García, Ella Vázquez‐Domínguez, Roberto Ibáñez, Gabriela Parra Olea
Software Mentions: 3
Published: almost 6 years ago
10.3389/fgene.2014.00250
Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index
Cited by: 60
Author(s): Robert M. Cronin, Julie R. Field, Yuki Bradford, Christian M. Shaffer, Robert J. Carroll, Jonathan D. Mosley, Lisa Bastarache, Todd L. Edwards, Scott J. Hebbring, Simon Lin, Lucia A. Hindorff, Paul K. Crane, Sarah A. Pendergrass, Marylyn D. Ritchie, Dana C. Crawford, Jyotishman Pathak, Suzette J. Bielinski, David Carrell, David R. Crosslin, David H. Ledbetter, David J. Carey, Gerard Tromp, Marc S. Williams, Eric B. Larson, Gail P. Jarvik, Peggy L. Peissig, Murray H. Brilliant, Catherine A. McCarty, Christopher G. Chute, Iftikhar J. Kullo, Erwin Böttinger, Rex L. Chisholm, Maureen E. Smith, Dan M. Roden, Joshua C. Denny
Software Mentions: 3
Published: over 10 years ago
10.7717/peerj.8683
Patterns of change in α and β taxonomic and phylogenetic diversity in the secondary succession of semi-natural grasslands in the Northern Apennines
Cited by: 6
Author(s): Lorenzo Lazzaro, Lorenzo Lastrucci, Daniele Viciani, Renato Benesperi, Vincenzo Gonnelli, Andrea Coppi
Software Mentions: 3
Published: over 4 years ago
10.3390/cells9010165
In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells
Cited by: 4
Author(s): L. Francisco Lorenzo‐Martín, Xosé R. Bustelo
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41598-021-85850-x
On the use of envelope following responses to estimate peripheral level compression in the auditory system
Cited by: 5
Author(s): Gerard Encina-Llamas, Torsten Dau, Bastian Epp
Software Mentions: 3
Published: over 3 years ago
10.3389/fcvm.2020.622236
Characteristics of Blood Metabolic Profile in Coronary Heart Disease, Dilated Cardiomyopathy and Valvular Heart Disease Induced Heart Failure
Cited by: 9
Author(s): Chang Liu, Ruihua Li, Yang Liu, Zhenguo Li, Yanan Sun, Peiyuan Yin, Rihong Huang
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-020-72735-8
Genome-wide association mapping for wheat blast resistance in CIMMYT’s international screening nurseries evaluated in Bolivia and Bangladesh
Cited by: 26
Author(s): Philomin Juliana, Xinyao He, Muhammad Rezaul Kabir, Krishna Kanta Roy, Md. Babul Anwar, Félix Marza, Jesse Poland, Sandesh Shrestha, Ravi P. Singh, Pawan Kumar Singh
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-020-73748-z
Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae)
Cited by: 1
Author(s): Yi Chiang Hsieh, Chih-Hsiung Chang, Jeng Der Chung, Shih Ying Hwang
Software Mentions: 3
Published: about 4 years ago
10.3758/s13414-015-0860-2
The long and the short of priming in visual search
Cited by: 24
Author(s): Wouter Kruijne, Martijn Meeter
Software Mentions: 3
Published: over 9 years ago
10.1186/1756-3305-6-359
Bayesian geostatistical modelling of soil-transmitted helminth survey data in the People’s Republic of China
Cited by: 49
Author(s): Ying-Si Lai, Xiao‐Nong Zhou, Jürg Utzinger, Penelope Vounatsou
Software Mentions: 3
Published: almost 11 years ago
10.1038/s41598-020-65115-9
Dichotomy between the transcriptomic landscape of naturally versus accelerated aged murine hearts
Cited by: 0
Author(s): Federica De Majo, Jana-Charlotte Hegenbarth, Frank Rühle, Christian Bär, Thomas Thum, Martine de Boer, Dirk J. Duncker, Blanche Schroen, Anne-Sophie Armand, Monika Stoll, León J. De Windt
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0141830
Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna
Cited by: 5
Author(s): Natacha Nikolic, Stéphanie Duthoy, Antoine Destombes, Nathalie Bodin, Wendy West, Alexis Puech, Jérôme Bourjea
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0245685
Brain organoid formation on decellularized porcine brain ECM hydrogels
Cited by: 44
Author(s): Robin Simsa, Theresa S.P. Rothenbücher, Hakan Gürbüz, Nidal Ghosheh, Jenny Emnéus, Lachmi Jenndahl, David L. Kaplan, Niklas Bergh, Alberto Martínez Serrano, Per Fogelstrand
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0008320
Applied Climate-Change Analysis: The Climate Wizard Tool
Cited by: 158
Author(s): Evan H. Girvetz, Chris Zganȷar, George T. Raber, Edwin P. Maurer, Peter Kareiva, Joshua J. Lawler
Software Mentions: 3
Published: almost 15 years ago
10.1038/s41598-020-61178-w
Radiomics prognostication model in glioblastoma using diffusion- and perfusion-weighted MRI
Cited by: 41
Author(s): Ji Eun Park, Ho Sung Kim, Youngheun Jo, Roh Eul Yoo, Seung Hong Choi, Soo Jung Nam
Software Mentions: 3
Published: over 4 years ago
10.3390/v10040192
Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot-and-Mouth Disease Virus in Africa
Cited by: 22
Author(s): Lidia Lasecka-Dykes, Caroline F. Wright, Antonello Di Nardo, Greg Logan, Valérie Mioulet, Terry Jackson, Tobias J. Tuthill, Nick J. Knowles, Donald P. King
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-018-36300-8
Robust in-silico identification of Cancer Cell Lines based on RNA and targeted DNA sequencing data
Cited by: 1
Author(s): Raik Otto, Jan-Niklas Rössler, Christine Sers, Soulafa Mamlouk, Ulf Leser
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-018-33693-4
RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways
Cited by: 17
Author(s): Adil Lateef, Sudheesh K. Prabhudas, Purushothaman Natarajan
Software Mentions: 3
Published: about 6 years ago
10.1186/s12985-019-1253-2
HPV viral load in self-collected vaginal fluid samples as predictor for presence of cervical intraepithelial neoplasia
Cited by: 10
Author(s): Malin Berggrund, Inger Gustavsson, Riina Aarnio, Julia Hedlund-Lindberg, Karin Sanner, Ingrid Wikström, Stefan Enroth, Matts Olovsson, Ulf Gyllensten
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0095347
Identification of Gene Expression Changes from Colitis to CRC in the Mouse CAC Model
Cited by: 14
Author(s): Xin Li, Yuyan Gao, Ming Yang, Qi Zhao, Guangyu Wang, Yan Yang, Yue Yang, Hui Liu, Yanqiao Zhang
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0084573
A DNA Methylation Network Interaction Measure, and Detection of Network Oncomarkers
Cited by: 28
Author(s): Thomas E. Bartlett, Sofia C. Olhede, Alexey Zaikin
Software Mentions: 3
Published: almost 11 years ago
10.1038/s41598-018-32514-y
Agricultural landscapes and the Loire River influence the genetic structure of the marbled newt in Western France
Cited by: 5
Author(s): Jean‐Marc Costanzi, Pascal Mège, Alexandre Boissinot, Françis Isselin-Nondedeu, Sarah M. Guérin, Olivier Lourdais, Audrey Trochet, Quentin Le Petitcorps, Agathe Legrand, François Varenne, Pierre Antoine Grillet, Sophie Morin-Pinaud, Damien Picard
Software Mentions: 3
Published: about 6 years ago
10.1186/1755-8794-6-28
Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma
Cited by: 24
Author(s): Zhilin Qu, Jun Zhang, Hong Jin, Sitong Sheng
Software Mentions: 3
Published: about 11 years ago
10.1038/s41598-018-24508-7
Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment
Cited by: 72
Author(s): Geon Goo Han, Jun-Yeong Lee, Gwi-Deuk Jin, Jongbin Park, Yo Han Choi, Seoung-Hun Kang, B. J. Chae, Eun Bae Kim, Yun‐Jaie Choi
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-018-27474-2
A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions
Cited by: 7
Author(s): Abigail N. Leistra, Grant Gelderman, Steven W. Sowa, Alex Moon-Walker, Howard M. Salis, Lydia M. Contreras
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0165823
Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem
Cited by: 37
Author(s): Bilal A. Padder, Kelvin Kamfwa, Halima E. Awale
Software Mentions: 3
Published: about 8 years ago
10.1038/s41598-019-46492-2
Global impact of diet and temperature over aquaculture of Octopus vulgaris paralarvae from a transcriptomic approach
Cited by: 24
Author(s): Pablo García-Fernández, María Prado-Álvarez, Manuel Nande, Daniel García de la serrana, C. Perales-Raya, E. Almansa, Inmaculada Varó, Camino Gestal
Software Mentions: 3
Published: over 5 years ago
10.1002/1878-0261.12903
REST promotes ETS1‐dependent vascular growth in medulloblastoma
Cited by: 9
Author(s): Shavali Shaik, Satoru Maegawa, Amanda R. Haltom, Feng Wang, Xue Xiao, Tara Dobson, Ajay Sharma, Yanwen Yang, Jyothishmathi Swaminathan, Vikas Kundra, Xiao Nan Li, Keri Schadler, Arif Harmanci, Lin Xu, Vidya Gopalakrishnan
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41597-020-00702-z
LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants
Cited by: 47
Author(s): Martin Freiberg, Marten Winter, Alessandro Gentile, Alexander Zizka, Alexandra N. Muellner‐Riehl, Alexandra Weigelt, Christian Wirth
Software Mentions: 3
Published: almost 4 years ago
10.1002/pmic.201700388
Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib‐Resistant Non‐Small Cell Lung Cancer Cells
Cited by: 19
Author(s): Wang Li, Heyong Wang, Yan Yang, Tian Zhao, Zhixiong Zhang, Ye Tian, Zhaomie Shi, Xiaojun Peng, Fēi Li, Yonghong Feng, Lei Zhang, Gening Jiang, Fan Zhang
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0113567
Movement Pattern Variability in Stone Knapping: Implications for the Development of Percussive Traditions
Cited by: 25
Author(s): Robert Rein, Tomomi Nonaka, Blandine Bril
Software Mentions: 3
Published: almost 10 years ago
10.1155/2020/5314187
To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations
Cited by: 6
Author(s): Holli-Joi Sullivan, Xiaoyan Wang, Shaina Nogle, Susan Liao, Chun Wu
Software Mentions: 3
Published: over 4 years ago
10.1002/jcp.29046
Identification of methylation‐driven genes related to prognosis in clear‐cell renal cell carcinoma
Cited by: 11
Author(s): Jia Wang, Qiujing Zhang, Qingqing Zhu, Chengxiang Li, Xueli Nan, Fuxia Wang, Lihua Fang, Jie Liu, Chao Xie, Shuai Fu, Bao-Liang Song
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0126859
Increased Expression of Angiogenic and Inflammatory Proteins in the Vitreous of Patients with Ischemic Central Retinal Vein Occlusion
Cited by: 42
Author(s): Christoph Ehlken, Bastian Grundel, Daniel de Sousa Michels, Bernd Junker, Andreas Stahl, Günther Schlunck, Lutz L. Hansen, Nicolas Feltgen, Gottfried Martin, Hansjürgen Agostini, Amelie Pielen
Software Mentions: 3
Published: over 9 years ago
10.1016/j.ajhg.2020.08.016
Unsupervised Clustering of Missense Variants in HNF1A Using Multidimensional Functional Data Aids Clinical Interpretation
Cited by: 23
Author(s): Sara Althari, Laeya Abdoli Najmi, Amanda J. Bennett, Ingvild Aukrust, Jana K. Rundle, Kevin Colclough, Janne Molnes, Alba Kaci, Sameena Nawaz, Timme van der Lugt, Neelam Hassanali, Anubha Mahajan, Anders Molven, Sian Ellard, Mark McCarthy, Lise Bjørkhaug, Pål Rasmus Njølstad, Anna L. Gloyn
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0161135
Advanced Online Survival Analysis Tool for Predictive Modelling in Clinical Data Science
Cited by: 1
Author(s): Julio Montes-Torres, José Luis Subirats, Nuria Ribelles, Daniel Urda, Leonardo Franco, Emilio Alba, José M. Jerez
Software Mentions: 3
Published: over 8 years ago
10.1002/prot.25094
FF12MC: A revised AMBER forcefield and new protein simulation protocol
Cited by: 34
Author(s): Yuan Ping Pang
Software Mentions: 3
Published: over 8 years ago
10.1038/srep24180
Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years
Cited by: 21
Author(s): Xiaotao Jiang, Feng Guo, Tong Zhang
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0172141
Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation
Cited by: 11
Author(s): Kelvin Kamfwa, Dongyan Zhao, James D. Kelly, Karen A. Cichy
Software Mentions: 3
Published: almost 8 years ago
10.1111/joa.13437
Cortical and trabecular bone structure of the hominoid capitate
Cited by: 12
Author(s): Emma E. Bird, Tracy L. Kivell, Matthew M. Skinner
Software Mentions: 3
Published: over 3 years ago
10.18632/aging.202775
Male-specific age estimation based on Y-chromosomal DNA methylation
Cited by: 11
Author(s): Athina Vidaki, Diego Montiel González, Benjamin Planterose Jiménez, Manfred Kayser
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0192775
Functional characterization and genomic studies of a novel murine submandibular gland epithelial cell line
Cited by: 6
Author(s): Sang‐Won Min, Eun-Ah Christine Song, Akinsola Oyelakin, Christian Gluck, Kirsten Smalley, Rose‐Anne Romano
Software Mentions: 3
Published: almost 7 years ago
10.3390/microorganisms9081734
Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata)
Cited by: 1
Author(s): Carolina Osuna‐Mascaró, Jorge Doña, Kevin P. Johnson, Manuel de Rojas
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-021-83274-1
Preservation of epoxyeicosatrienoic acid bioavailability prevents renal allograft dysfunction and cardiovascular alterations in kidney transplant recipients
Cited by: 4
Author(s): Thomas Duflot, Charlotte Laurent, Anne Soudey, Xavier Fonrose, M. Hamzaoui, Michèle Iacob, Dominique Bertrand, Julie Favre, Isabelle Étienne, Colette Roche, David Coquerel, M. Le Besnerais, Safa Louhichi, Tracy Tarlet, Dongyang Li, V. Brunel, Christophe Morisseau, Vincent Richard, Robinson Joannidès, Françoise Stanke‐Labesque, Fabien Lamoureux, Dominique Guerrot, J. Bellien
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0117439
Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae)
Cited by: 65
Author(s): Matteo Montagna, Bessem Chouaia, Giuseppe Mazza, Erica M. Prosdocimi, Elena Crotti, Valeria Mereghetti, Violetta Vacchini, Annamaria Giorgi, Alessio De Biase, S. Longo, Rita Cervo, G.C. Lozzia, Alberto Alma, Claudio Bandi, Daniele Daffonchio
Software Mentions: 3
Published: almost 10 years ago
10.1186/1471-2105-6-129
Considerations when using the significance analysis of microarrays (SAM) algorithm
Cited by: 110
Author(s): Ola Larsson, Claes Wahlestedt, James A. Timmons
Software Mentions: 3
Published: over 19 years ago
10.3390/antiox9121190
Differential Sex-Dependent Regulation of the Alveolar Macrophage miRNome of SP-A2 and co-ex (SP-A1/SP-A2) and Sex Differences Attenuation after 18 h of Ozone Exposure
Cited by: 7
Author(s): Nithyananda Thorenoor, David S. Phelps, Joanna Floros
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0251827
Multiple spatial reference frames underpin perceptual recalibration to audio-visual discrepancies
Cited by: 8
Author(s): David Watson, Michael A. Akeroyd, Neil W. Roach, Ben S. Webb
Software Mentions: 3
Published: over 3 years ago
10.1093/gbe/evw077
“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
Cited by: 80
Author(s): Marco Fondi, Antti Karkman, Manu Tamminen, Emanuele Bosi, Marko Virta, Renato Fani, Eric J. Alm, James O. McInerney
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0143436
Analysis of Stage-Specific Gene Expression Profiles in the Uterine Endometrium during Pregnancy in Pigs
Cited by: 17
Author(s): Mingoo Kim, Heewon Seo, Yohan Choi, Inkyu Yoo, Minseok Seo, Chang Kyu Lee, Heebal Kim, Hakhyun Ka
Software Mentions: 3
Published: about 9 years ago
10.1186/s13059-019-1923-9
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
Cited by: 52
Author(s): Serena Manara, Francesco Asnicar, Francesco Beghini, Davide Bazzani, Fabio Cumbo, Moreno Zolfo, Eleonora Nigro, Nicolai Karcher, Paolo Manghi, Marisa Isabell Metzger, Edoardo Pasolli, Nicola Segata
Software Mentions: 3
Published: almost 5 years ago
10.1186/s13059-014-0414-2
Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes
Cited by: 67
Author(s): Antony M. Chettoor, Scott A. Givan, Rex A. Cole, Clayton T Coker, Erica Unger-Wallace, Zuzana Vejlupkova, Erik Vollbrecht, John E. Fowler, Evans Mulenga
Software Mentions: 3
Published: over 10 years ago
10.1099/mgen.0.000154
Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells
Cited by: 16
Author(s): Tonya Watkins, Hong Liu, Matthew Chung, Tracy H. Hazen, Julie C. Dunning Hotopp, Scott G. Filler, Vincent M. Bruno
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0070017
Genes Dysregulated to Different Extent or Oppositely in Estrogen Receptor-Positive and Estrogen Receptor-Negative Breast Cancers
Cited by: 12
Author(s): Xianxiao Zhou, Tao Shi, Bailiang Li, Yuannv Zhang, Xiaopei Shen, Hongdong Li, Hong Guan, Chunyang Liu, Zheng Guo
Software Mentions: 3
Published: over 11 years ago
10.1186/gb-2014-15-5-r71
A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions
Cited by: 28
Author(s): Alayne Brunner, Jun Li, Xiangqian Guo, Robert T. Sweeney, Sushama Varma, Shirley Zhu, Rui Li, Robert Tibshirani, Robert B. West
Software Mentions: 3
Published: almost 11 years ago
10.1186/s12864-021-08016-z
Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemaker
Cited by: 13
Author(s): Rashid Minhas, Henry Loeffler‐Wirth, Yusra Siddiqui, Tomasz Obrębski, Shikha Vashisht, Karim Abu Nahia, Aleksandra Paterek, Angelika Brzozowska, Łukasz Bugajski, Katarzyna Piwocka, Vladimir Korzh, Hans Binder, Cecilia Lanny Winata
Software Mentions: 3
Published: about 3 years ago
10.1186/s13059-014-0412-4
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Cited by: 55
Author(s): Rebecca Worsley Hunt, Wyeth W. Wasserman
Software Mentions: 3
Published: over 10 years ago
10.1186/s12859-020-03622-2
Conditional permutation importance revisited
Cited by: 55
Author(s): Dries Debeer, Carolin Strobl
Software Mentions: 3
Published: over 4 years ago
10.1111/2041-210X.12246
Effects of phylogenetic reconstruction method on the robustness of species delimitation using single‐locus data
Cited by: 169
Author(s): Cuong Q. Tang, Aelys M. Humphreys, Diego Fontaneto, Timothy G. Barraclough
Software Mentions: 3
Published: about 10 years ago
10.1186/s12859-016-0975-z
CoeViz: a web-based tool for coevolution analysis of protein residues
Cited by: 39
Author(s): Frazier N. Baker, Aleksey Porollo
Software Mentions: 3
Published: over 8 years ago
10.1016/j.cub.2020.10.025
The Proteomic Landscape of Centromeric Chromatin Reveals an Essential Role for the Ctf19CCAN Complex in Meiotic Kinetochore Assembly
Cited by: 11
Author(s): Weronika E. Borek, Nadine Vincenten, Eris Duro, Vasso Makrantoni, Christos Spanos, Krishna K. Sarangapani, Flávia de Lima Alves, David A. Kelly, Charles L. Asbury, Juri Rappsilber, Adèle L. Marston
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13059-014-0567-z
The draft genome of Primula veris yields insights into the molecular basis of heterostyly
Cited by: 90
Author(s): Michael Nowak, Giancarlo Russo, Ralph Schlapbach, Cuong Nguyen Huu, Michael Lenhard, Elena Conti
Software Mentions: 3
Published: almost 10 years ago
10.1186/1472-6785-12-19
Contrasting habitat associations of imperilled endemic stream fishes from a global biodiversity hot spot
Cited by: 18
Author(s): Albert Chakona, Ernst R. Swartz
Software Mentions: 3
Published: almost 13 years ago
10.1371/journal.pone.0166586
Cohesion and Coalition Formation in the European Parliament: Roll-Call Votes and Twitter Activities
Cited by: 32
Author(s): Darko Cherepnalkoski, Andreas Karpf, Igor Mozetič, Miha Grčar
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0230865
Guano morphology has the potential to inform conservation strategies in British bats
Cited by: 4
Author(s): Roselyn Ware, Benjamin Garrod, Hannah Macdonald, Robin G. Allaby
Software Mentions: 3
Published: over 4 years ago
10.1186/s12711-021-00633-2
Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
Cited by: 21
Author(s): Beatriz Batista Trigo, Adam Taiti Harth Utsunomiya, Alvaro A. A. D. Fortunato, Marco Milanesi, Rafaela Beatriz Pintor Torrecilha, Harrison J. Lamb, Loan Nguyen, Elizabeth M. Ross, Ben J. Hayes, Romulo Cláudio Morozini Padula, Thayla Souza Sussai, Ludmilla Balbo Zavarez, Rafael Silva Cipriano, Maria Margareth Theodoro Caminhas, Flávia L. Lopes, Cassiano Pelle, Tosso Leeb, Danika L. Bannasch, Derek M. Bickhart, Timothy P. L. Smith, Tad S. Sonstegard, José Fernando Garcia, Yuri Tani Utsunomiya
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0080540
Association Testing Strategy for Data from Dense Marker Panels
Cited by: 1
Author(s): Donghyung Lee, Silviu‐Alin Bacanu
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pone.0059927
Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment
Cited by: 39
Author(s): Joseph P. Peacock, Jesse Cole, Senthil K. Murugapiran, Jeremy A. Dodsworth, James S. Fisher, Duane P. Moser, Brian P. Hedlund
Software Mentions: 3
Published: over 11 years ago
10.1186/s12859-020-3500-3
circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs
Cited by: 16
Author(s): Simona Aufiero, Yolan J. Reckman, Anke J. Tijsen, Yigal M. Pinto, Esther E. Creemers
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0038347
Inhibition of Specific NF-κB Activity Contributes to the Tumor Suppressor Function of 14-3-3σ in Breast Cancer
Cited by: 25
Author(s): Julia Inglés‐Esteve, M.L González Morales, Alba Dalmases, Ricard Garcia-Carbonell, Alba Jené-Sanz, Núria López‐Bigas, Mar Iglesias, Cristina Ruiz-Herguido, Ana Rovira, Federico Rojo, Joan Albanell, Roger R. Gomis, Anna Bigas, Lluís Espinosa
Software Mentions: 3
Published: over 12 years ago
10.1186/gb-2004-5-11-r94
Cited by: 131
Author(s): Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel Martin, Christine A. Orengo, Xiaohui Liu, Paul Kellam
Software Mentions: 3
Published: almost 21 years ago
10.1371/journal.pone.0193301
Association of whole blood n-6 fatty acids with stunting in 2-to-6-year-old Northern Ghanaian children: A cross-sectional study
Cited by: 17
Author(s): Mary Adjepong, C. Austin Pickens, Raghav Jain, William S. Harris, Reginald Adjetey Annan, Jenifer I. Fenton
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0114047
Statistical Modeling of the Abundance of Vectors of West African Rift Valley Fever in Barkédji, Senegal
Cited by: 19
Author(s): Cheikh Talla, Diawo Diallo, Ibrahima Dia, Yamar Bâ, Jacques André Ndione, Amadou Alpha Sall, Andrew P. Morse, Aliou Diop, Mawlouth Diallo
Software Mentions: 3
Published: almost 10 years ago
10.1186/1471-2105-12-S1-S36
Integrated metabolome and transcriptome analysis of the NCI60 dataset
Cited by: 37
Author(s): Gang Su, Charles F. Burant, Christopher W.W. Beecher, Brian D. Athey, Fan Meng
Software Mentions: 3
Published: almost 14 years ago
10.1186/s12933-021-01299-2
Metabolic syndrome and the plasma proteome: from association to causation
Cited by: 16
Author(s): Mohamed A. Elhadad, Rory Wilson, Shaza B. Zaghlool, Cornelia Huth, Christian Gieger, Harald Grallert, Johannes Graumann, Wolfgang Rathmann, Wolfgang Köenig, Moritz F. Sinner, Kristian Hveem, Karsten Suhre, Barbara Thorand, Christian Jonasson, Mélanie Waldenberger, Annette Peters
Software Mentions: 3
Published: over 3 years ago
10.1186/s12263-020-00680-2
DNA methylation during human adipogenesis and the impact of fructose
Cited by: 7
Author(s): Giulia Tini, Vijayalakshmi Varma, Rosario Lombardo, Greg T. Nolen, Grégory Lefebvre, Patrick Descombes, Sylviane Métairon, Corrado Priami, Jim Kaput, Marie Pier Scott-Boyer
Software Mentions: 3
Published: almost 4 years ago
10.1186/2049-3002-2-18
Metabolic reprogramming induced by ketone bodies diminishes pancreatic cancer cachexia
Cited by: 179
Author(s): Surendra K. Shukla, Teklab Gebregiworgis, Vinee Purohit, Nina V. Chaika, Venugopal Gunda, Prakash Radhakrishnan, Kamiya Mehla, Iraklis I. Pipinos, Robert Powers, Fang Yu, Pankaj K. Singh
Software Mentions: 3
Published: about 10 years ago
10.1371/journal.pone.0182533
A survey of the mycobiota associated with larvae of the black soldier fly (Hermetia illucens) reared for feed production
Cited by: 73
Author(s): Ilaria Varotto-Boccazzi, M. Ottoboni, Elena Martín, Francesco Comandatore, L. Vallone, Thomas Spranghers, Mia Eeckhout, Valeria Mereghetti, L. Pinotti, Sara Epis
Software Mentions: 3
Published: over 7 years ago
10.1002/cam4.1107
Comparative proteomic profiling of the serum differentiates pancreatic cancer from chronic pancreatitis
Cited by: 34
Author(s): Mayank Saraswat, Sakari Joenväärä, Hanna Seppänen, Harri Mustonen, Caj Haglund, Risto Renkonen
Software Mentions: 3
Published: over 7 years ago
10.1002/cam4.961
Nonpromoter methylation of the CDKN2A gene with active transcription is associated with improved locoregional control in laryngeal squamous cell carcinoma
Cited by: 12
Author(s): Miriam M. Ben-Dayan, Thomas J. Ow, Thomas J. Belbin, Joshua Wetzler, Richard V. Smith, Geoffrey Childs, Brenda Diergaarde, D. Neil Hayes, Jennifer R. Grandis, Michael B. Prystowsky, Nicolas F. Schlecht
Software Mentions: 3
Published: almost 8 years ago
10.3390/genes11060696
Comparative Pathway Integrator: A Framework of Meta-Analytic Integration of Multiple Transcriptomic Studies for Consensual and Differential Pathway Analysis
Cited by: 7
Author(s): Xiangrui Zeng, Wei Zong, Chien‐Wei Lin, Zhou Fang, Tianzhou Ma, David A. Lewis, John F. Enwright, George C. Tseng
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0254359
Anatomy into the battle of supporting or opposing reopening amid the COVID-19 pandemic on Twitter: A temporal and spatial analysis
Cited by: 12
Author(s): Lingyao Li, Abdolmajid Erfani, Yu Wang, Qingbin Cui
Software Mentions: 3
Published: over 3 years ago
10.1186/s12859-020-03592-5
Methylation data imputation performances under different representations and missingness patterns
Cited by: 11
Author(s): Pietro Di Lena, Claudia Sala, Andrea Prodi, Christine Nardini
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0073056
Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle
Cited by: 96
Author(s): Elizabeth M. Ross, Peter J. Moate, L. C. Marett, Ben Cocks, Ben J. Hayes
Software Mentions: 3
Published: about 11 years ago
10.3390/genes11070817
SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks
Cited by: 5
Author(s): Maria Nikoghosyan, Maria Schmidt, K. Margaryan, Henry Loeffler‐Wirth, Arsen Arakelyan, Hans Binder
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0131075
Regional Variation in Parasite Species Richness and Abundance in the Introduced Range of the Invasive Lionfish, Pterois volitans
Cited by: 29
Author(s): Andrew J. Sellers, Gregory M. Ruiz, Brian Leung, Mark E. Torchin
Software Mentions: 3
Published: over 9 years ago
10.3390/genes11010046
Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation
Cited by: 14
Author(s): Md. Asaduzzaman, Yoji Igarashi, Abdul Wahab, Md. Nahiduzzaman, Jalilur Rahman, Michael J. Phillips, Songqian Huang, Shuichi Asakawa, Moshiur Rahman, Li Lian Wong
Software Mentions: 3
Published: almost 5 years ago