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: house

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

A lib to persist blobs by their sha256
10 versions
Latest release: almost 7 years ago
752 downloads last month

Papers Mentioning house 960

10.3382/ps/pez354
Transcriptomic analysis of early B-cell development in the chicken embryo
Cited by: 6
Author(s): Nikhil Nuthalapati, J. D. Evans, Robert L. Taylor, S. L. Branton, Bindu Nanduri, G. T. Pharr
Software Mentions: 3
Published: about 5 years ago
10.1073/pnas.2003724117
Genome mapping of a <i>LYST</i> mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles
Cited by: 28
Author(s): Asier Ullate-Agote, Ingrid Burgelin, Adrien Debry, Carine Langrez, Florent Montange, Rodrigue Peraldi, Jean Daraspe, Henrik Kaessmann, Michel C. Milinkovitch, Athanasia C. Tzika
Software Mentions: 3
Published: about 4 years ago
10.3390/cells9081795
Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles
Cited by: 18
Author(s): Clotilde Garrido, Oliver D. Caspari, Yves Choquet, Francis‐André Wollman, Ingrid Lafontaine
Software Mentions: 3
Published: over 4 years ago
10.1186/s12863-017-0584-5
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)
Cited by: 20
Author(s): Adugna Abdi Woldesemayat, Peter van Heusden, Bongani K. Ndimba, Alan Christoffels
Software Mentions: 3
Published: almost 7 years ago
10.1111/cpr.12832
An approach using<i>Caenorhabditis elegans</i>screening novel targets to suppress tumour cell proliferation
Cited by: 4
Author(s): Yuqin Mao, San-Feng Han, Shilong Zhang, Zhengyan Zhang, Chao‐Yue Kong, Huiling Chen, Zhanming Li, Pei-Ran Cai, Bing Han, Li‐Shun Wang
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1008736
Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step
Cited by: 14
Author(s): Xiaohua Ye, Hang Su, Daniel Wrapp, Daniel C. Freed, Fengsheng Li, Zihao Yuan, Aimin Tang, Leike Li, Zhiqiang Ku, Wei Xiong, Dabbu Kumar Jaijyan, Hua Zhu, Dai Wang, Jason S. McLellan, Ningyan Zhang, Tong-Ming Fu, Zhiqiang An
Software Mentions: 3
Published: over 4 years ago
10.3390/proteomes9020029
Mining Proteome Research Reports: A Bird’s Eye View
Cited by: 1
Author(s): Jagajjit Sahu
Software Mentions: 3
Published: over 3 years ago
10.1038/s41419-020-2381-8
MOB2 suppresses GBM cell migration and invasion via regulation of FAK/Akt and cAMP/PKA signaling
Cited by: 41
Author(s): Ke Jiang, Gang Yao, Lulu Hu, Yumei Yan, Jia Liu, Jingwei Shi, Youwei Chang, Ye Zhang, Dapeng Liang, Dachuan Shen, Guirong Zhang, Meng Shao, Haozhe Piao
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-019-3261-z
Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)
Cited by: 12
Author(s): Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li, Xinchun Lin
Software Mentions: 3
Published: almost 5 years ago
10.1172/jci.insight.149446
Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy
Cited by: 5
Author(s): Katharina E. Meijboom, Viola Volpato, Jimena Monzón‐Sandoval, Joseph M. Hoolachan, Suzan M. Hammond, Frank Abendroth, Olivier G. de Jong, Gareth Hazell, Nina Ahlskog, Matthew J. Wood, Caleb Webber, Mélissa Bowerman
Software Mentions: 3
Published: over 3 years ago
10.3390/jcm8081253
Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines
Cited by: 22
Author(s): Sugandha Bhatia, James Monkman, Tony Blick, Pascal H.G. Duijf, Shivashankar H. Nagaraj, Erik W. Thompson
Software Mentions: 3
Published: over 5 years ago
10.1038/srep25533
The impact of amplification on differential expression analyses by RNA-seq
Cited by: 188
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0129422
Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties
Cited by: 45
Author(s): Nagaraja Reddy Rama Reddy, Rucha Harishbhai Mehta, Palak Harendrabhai Soni, Jayanti Makasana, Narendra Gajbhiye, P. Manivel, Jitendra Kumar
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0192253
Transcriptional profiling of liver tissues in chicken embryo at day 16 and 20 using RNA sequencing reveals differential antioxidant enzyme activity
Cited by: 10
Author(s): Shaohua Yang, Lu Lu Wang, Zhaoyuan Shi, Xiaoqian Ou, Wei Wang, Chen Xue, Guoqing Liu
Software Mentions: 3
Published: almost 7 years ago
10.1093/gigascience/giy058
Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization
Cited by: 38
Author(s): Pengju Zhao, Ying Yu, Wen Feng, Huarui Du, Jian Yu, Hao Kang, Xianrui Zheng, Zhiquan Wang, George E. Liu, Catherine W. Ernst, Xueqin Ran, Jiafu Wang, Jianfeng Liu
Software Mentions: 3
Published: over 6 years ago
10.1093/gigascience/giy075
Binning enables efficient host genome reconstruction in cnidarian holobionts
Cited by: 15
Author(s): Juan Sebastián Celis, Daniel Wibberg, Catalina Ramírez‐Portilla, Oliver Rupp, Alexander Sczyrba, Anderson M. Winkler, Jörn Kalinowski, Thomas Wilke
Software Mentions: 3
Published: over 6 years ago
10.1093/gigascience/giz129
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop
Cited by: 65
Author(s): Gláucia Mendes Souza, Marie‐Anne Van Sluys, Carolina Gimiliani Lembke, Hayan Lee, Gabriel Rodrigues Alves Margarido, Carlos Takeshi Hotta, Jonas Weissmann Gaiarsa, Augusto Lima Diniz, Mona N. Oliveira, Sávio Siqueira Ferreira, Milton Yutaka Nishiyama, Felipe Ten Caten, Geovani Tolfo Ragagnin, Pablo de Morais Andrade, Robson Francisco de Souza, Gianlucca Gonçalves Nicastro, Ravi Pandya, Changsoo Kim, Hui Guo, Alan Mitchell Durham, Monalisa Sampaio Carneiro, Jisen Zhang, Xingtan Zhang, Qing Zhang, Ray Ming, Michael C. Schatz, Bob Davidson, Andrew H. Paterson, David Heckerman
Software Mentions: 3
Published: almost 5 years ago
10.1111/1744-7917.12696
Co‐infection of <i>Wolbachia</i> and <i>Spiroplasma</i> in spider mite <i>Tetranychus truncatus</i> increases male fitness
Cited by: 8
Author(s): Kang Xie, Yi‐Jia Lu, Kun Yang, Shi‐Mei Huo, Xiao‐Yue Hong
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0185227
The first transcriptome of Italian wall lizard, a new tool to infer about the Island Syndrome
Cited by: 4
Author(s): Martina Trapanese, Maria Buglione, Valeria Maselli, Simona Petrelli, Serena Aceto, Domenico Fulgione
Software Mentions: 3
Published: about 7 years ago
10.1186/1471-2407-5-86
Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression
Cited by: 63
Author(s): Asa Oudes, Jared C. Roach, Laura S Walashek, Lillian J. Eichner, Lawrence D. True, Robert L. Vessella, Alvin Y. Liu
Software Mentions: 3
Published: over 19 years ago
10.1371/journal.pone.0208171
Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype
Cited by: 75
Author(s): Pamela Vernocchi, Federica Del Chierico, Alessandra Russo, Fabio Majo, Martina Rossitto, Mariacristina Valerio, Luca Casadei, Antonietta La Storia, Francesca De Filippis, Cristiano Rizzo, Cesare Manetti, Paola Paci, Federico Marini, Ersilia Fiscarelli, Bruno Dallapiccola, Vincenzina Lucidi, Alfredo Miccheli, Lorenza Putignani
Software Mentions: 3
Published: almost 6 years ago
10.15252/emmm.202011987
Combined targeting of G protein‐coupled receptor and <scp>EGF</scp> receptor signaling overcomes resistance to <scp>PI</scp> 3K pathway inhibitors in <scp>PTEN</scp> ‐null triple negative breast cancer
Cited by: 17
Author(s): Davide Zecchin, Christopher Moore, Fanourios Michailidis, Stuart Horswell, Sareena Rana, Michael Howell, Julian Downward
Software Mentions: 3
Published: over 4 years ago
10.1186/s12864-020-07055-2
Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows
Cited by: 10
Author(s): Huiyan Hu, Qiong Jia, Jianzhong Xi, Bo Zhou, Zhiqiang Li
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0147950
Differential Gene Expression Patterns in Chicken Cardiomyocytes during Hydrogen Peroxide-Induced Apoptosis
Cited by: 8
Author(s): Chunyun Wan, Jinmei Xiang, Youwen Li, Deliang Guo
Software Mentions: 3
Published: almost 9 years ago
10.1016/j.cell.2012.04.011
Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development
Cited by: 389
Author(s): Martin A.M. Reijns, Björn Rabe, Rachel E. Rigby, Pleasantine Mill, Katy R. Astell, Laura A. Lettice, Shelagh Boyle, Andrea Leitch, Margaret Keighren, Fiona Kilanowski, Paul S. Devenney, David Sexton, Graeme R. Grimes, Ian Holt, Robert E. Hill, Martin S. Taylor, Kirstie A. Lawson, Julia R. Dorin, Andrew P. Jackson
Software Mentions: 3
Published: over 12 years ago
10.7554/eLife.41927
Nuclear genetic regulation of the human mitochondrial transcriptome
Cited by: 50
Author(s): Ali At, Lena Boehme, Guillermo Carbajosa, Vlad C. Seitan, Kerrin S. Small, Alan Hodgkinson
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0212514
Comparative transcriptomic analysis reveals genes regulating the germination of morphophysiologically dormant Paris polyphylla seeds during a warm stratification
Cited by: 11
Author(s): Dengqun Liao, Juan Zhu, Zhang Menghuan, Peng Sun, Jianhe Wei, Jianjun Qi
Software Mentions: 3
Published: over 5 years ago
10.1186/s13072-019-0312-7
Folate deficiency induced H2A ubiquitination to lead to downregulated expression of genes involved in neural tube defects
Cited by: 16
Author(s): Pei Pei, Xiyue Cheng, Jianhua Yu, Jinying Shen, Xue Li, Jianxin Wu, Shan Wang, Ting Zhang
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pone.0243085
Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions
Cited by: 7
Author(s): Jin-Hyun Kim, Joo-Seok Park, Chang Kyu Lee, Min‐Gyun Jeong, Jiu Liang Xu, Yong-Soo Choi, Han‐Sung Jung, Hyunju Choi
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13072-015-0028-2
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates
Cited by: 16
Author(s): Parameswaran Ramachandran, Gareth Palidwor, Theodore J. Perkins
Software Mentions: 3
Published: about 9 years ago
10.1007/s00429-019-01893-x
Mapping the structural connectivity between the periaqueductal gray and the cerebellum in humans
Cited by: 29
Author(s): Alberto Cacciola, Salvatore Bertino, Gianpaolo Antonio Basile, Debora Di Mauro, Alessandro Calamuneri, Gaetana Chillemi, Antonio Duca, Daniele Bruschetta, Paolo Flace, Angelo Favaloro, Rocco Salvatore Calabrò, Giuseppe Anastasi, Demetrio Milardi
Software Mentions: 3
Published: over 5 years ago
10.1038/srep26942
Hyperlipidemia-associated gene variations and expression patterns revealed by whole-genome and transcriptome sequencing of rabbit models
Cited by: 23
Author(s): Zhen Wang, Jifeng Zhang, Hong Li, Junyi Li, Manabu Niimi, Guohui Ding, Haifeng Chen, Jie Xu, Hongjiu Zhang, Ze Xu, Yulin Dai, Tuantuan Gui, Shengdi Li, Zhi Li, Sujuan Wu, Mushui Cao, Lu Zhou, Xingyu Lu, Junxia Wang, Jing Yang, Yunhe Fu, Dongshan Yang, Jun Song, Tianqing Zhu, Ли Шен, Bo Niu, Ziyun Wang, Tomonari Koike, Masashi Shiomi, Enqi Liu, Luonan Chen, Jianglin Fan, Y. Eugene Chen, Yixue Li
Software Mentions: 3
Published: over 8 years ago
10.3390/genes10070503
Landscape of Overlapping Gene Expression in the Equine Placenta
Cited by: 8
Author(s): Pouya Dini, Jamie K. Norris, Hesham A. Ali, Shavahn C. Loux, Mariano Carossino, A. Esteller-Vico, Ernest Bailey, Theodore S. Kalbfleisch, Peter Daels, Barry A. Ball
Software Mentions: 3
Published: over 5 years ago
10.3390/genes11030261
Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection
Cited by: 24
Author(s): Silvia Laura Toffolatti, Gabriella De Lorenzis, Matteo Brilli, Mirko Moser, Vahid Shariati, Elahe Tavakol, Giuliana Maddalena, Alessandro Passera, P. Casati, Massimo Pindo, Alessandro Cestaro, D. Maghradze, O. Failla, P.A. Bianco, F. Quaglino
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0202471
Biomarkers for classification and class prediction of stress in a murine model of chronic subordination stress
Cited by: 10
Author(s): Dominik Langgartner, Andrea M. Füchsl, Lisa Kaiser, Tatjana Meier, Sandra Foertsch, Christian Buske, Stefan O. Reber, Medhanie Mulaw
Software Mentions: 3
Published: about 6 years ago
10.1186/s12864-015-1959-5
Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0135215
Transcriptome Analysis of Thermal Parthenogenesis of the Domesticated Silkworm
Cited by: 11
Author(s): Peigang Liu, Yongqiang Wang, Xin Du, Lusong Yao, Fengbo Li, Zhiqi Meng
Software Mentions: 3
Published: over 9 years ago
10.1007/s41109-016-0007-y
Comparison method for community detection on brain networks from neuroimaging data
Cited by: 18
Author(s): Fumihiko Taya, Joshua de Souza, Nitish V. Thakor, Anastasios Bezerianos
Software Mentions: 3
Published: over 8 years ago
10.3390/genes9080373
Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat
Cited by: 12
Author(s): Hanna Sigeman, Suvi Ponnikas, Elin Videvall, Hongkai Zhang, Pallavi Chauhan, Sara Naurin, Bengt Hansson
Software Mentions: 3
Published: over 6 years ago
10.1016/j.bpj.2018.09.002
Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR
Cited by: 3
Author(s): Graham M. Saunders, Hannah E. Bruce Macdonald, Jonathan W. Essex, Syma Khalid
Software Mentions: 3
Published: about 6 years ago
10.1186/1471-2164-15-446
Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea
Cited by: 14
Author(s): Facundo Giorello, Matías Feijoo, Guillermo D’Elı́a, Lourdes Valdez, Juan C. Opazo, Valeria Varas, Daniel E. Naya, Enrique P. Lessa
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0199021
Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG
Cited by: 28
Author(s): Kejin Zhuang, Yujun Jiang, Xiaohan Feng, Li Li, Fangfang Dang, Wei Zhang, Chaoxin Man
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0176739
Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system
Cited by: 21
Author(s): Eija Nissilä, François P. Douillard, Jarmo Ritari, Lars Paulín, Hanna Järvinen, Pia Rasinkangas, Karita Haapasalo, Seppo Meri, Hanna Jarva, Willem M. de Vos
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0248371
Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
Cited by: 30
Author(s): Massab Umair, Aamer Ikram, Muhammad Salman, Adnan Khurshid, Masroor Alam, Nazish Badar, R. Suleman, Faheem Tahir, Salman Sharif, Joel M. Montgomery, Shannon Whitmer, John D. Klena
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2021.720800
Disruption of Photomorphogenesis Leads to Abnormal Chloroplast Development and Leaf Variegation in Camellia sinensis
Cited by: 7
Author(s): Xizhi Gao, Chenyu Zhang, Cui Lu, Minghan Wang, Nianci Xie, Jianjiao Chen, Yunfei Li, Jiahao Chen, Chengwen Shen
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pcbi.1008939
How multisite phosphorylation impacts the conformations of intrinsically disordered proteins
Cited by: 22
Author(s): Fan Jin, Frauke Gräter
Software Mentions: 3
Published: over 3 years ago
10.3389/fvets.2021.644474
Identification of Photoperiod-Induced LncRNAs and mRNAs in Pituitary Pars Tuberalis of Sheep
Cited by: 10
Author(s): Qing Xia, Mingxing Chu, Xiaoyun He, Qiuyue Liu, Xiaosheng Zhang, Jinlong Zhang, Xiaofei Guo, Ran Di
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0183975
Biophysical analysis of the effect of chemical modification by 4-oxononenal on the structure, stability, and function of binding immunoglobulin protein (BiP)
Cited by: 4
Author(s): Dinen D. Shah, Surinder Singh, Monika Dzieciątkowska, Krishna Mallela
Software Mentions: 3
Published: about 7 years ago
10.3389/fnins.2017.00709
Multi-modal Brain MRI in Subjects with PD and iRBD
Cited by: 12
Author(s): Silvia Mangia, Alena Svátková, Daniele Mascali, Mikko J. Nissi, Philip Burton, Petr Bednařík, Edward J. Auerbach, Federico Giove, Lynn E. Eberly, Michael J. Howell, Igor Nestrašil, Paul Tuite, Shalom Michaeli
Software Mentions: 3
Published: almost 7 years ago
10.3389/fphar.2018.00912
Investigating the Molecular Mechanism of Aqueous Extract of Cyclocarya paliurus on Ameliorating Diabetes by Transcriptome Profiling
Cited by: 7
Author(s): Jing Li, Mei Luo, Minghua Hu, An‐Yuan Guo, Xiangliang Yang, Qiong Zhang, Yanhong Zhu
Software Mentions: 3
Published: over 6 years ago
10.1534/g3.120.401728
High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster<i>Crassostrea gigas</i>
Cited by: 10
Author(s): Xiaoshen Yin, Alberto Arias‐Pérez, Tevfik Hamdi Kitapci, Dennis Hedgecock
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pcbi.1007293
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
Cited by: 20
Author(s): Fábio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark Gerstein
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0094270
Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs
Cited by: 27
Author(s): Nicholas J. Schurch, Christian Callebaut, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G. Storey, Whi McLean, Sara J. Brown, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0041389
Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux
Cited by: 42
Author(s): Erin Lynch, Morgan G. I. Langille, Aaron E. Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen, Marc T. Facciotti
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pone.0043554
A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata
Cited by: 17
Author(s): Erica Lasek‐Nesselquist
Software Mentions: 3
Published: about 12 years ago
10.3389/fmicb.2016.01342
Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios
Cited by: 55
Author(s): Samantha M. Gromek, Andrea M. Suria, Matthew S. Fullmer, Jillian L. Garcia, J. Peter Gogarten, Spencer V. Nyholm, Marcy J. Balunas
Software Mentions: 3
Published: about 8 years ago
10.3389/fmicb.2017.01009
Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes
Cited by: 8
Author(s): Tam Tran, Sophie Mangenot, Ghislaine Magdelenat, Emilie Payen, Zoé Rouy, Hassiba Belahbib, Barry M. Grail, D. Barrie Johnson, Violaine Bonnefoy, Emmanuel Talla
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0082989
Genome-Wide Methylation and Gene Expression Changes in Newborn Rats following Maternal Protein Restriction and Reversal by Folic Acid
Cited by: 55
Author(s): Gioia Altobelli, Irina Bogdarina, Elia Stupka, Adrian Clark, Simon C. Langley‐Evans
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pbio.3001026
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
Cited by: 66
Author(s): Alexander Kloosterman, Peter Cimermančič, E. A. Aboutabl, Congcong Du, Michalis Hadjithomas, Mohamed S. Donia, Michael A. Fischbach, Gilles P. van Wezel, Marnix H. Medema
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pbio.2003769
Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
Cited by: 88
Author(s): Eleni Gentekaki, Bruce A. Curtis, Courtney W. Stairs, Vladimír Klimeš, Marek Eliáš, Dayana E. Salas‐Leiva, Emily K. Herman, Laura Eme, María Cecilia Arias, Bernard Henrissat, Frédérique Hilliou, Mary J. Klute, Hiroshi Suga, Shehre-Banoo Malik, Arthur W. Pightling, Martin Kolísko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger
Software Mentions: 3
Published: about 7 years ago
10.1186/1471-2105-14-315
A novel strategy for classifying the output from an in silicovaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms
Cited by: 32
Author(s): Stephen J. Goodswen, Paul J. Kennedy, John Ellis
Software Mentions: 3
Published: about 11 years ago
10.1186/s12864-017-4016-8
Characterization of mechanisms underlying degradation of sclerotia of Sclerotinia sclerotiorum by Aspergillus aculeatus Asp-4 using a combined qRT-PCR and proteomic approach
Cited by: 15
Author(s): Xiaojia Hu, Lü Qin, Daniel P. Roberts, Dilip K. Lakshman, Yiqin Gong, Jude E. Maul, Lin Xie, Chang Yeon Yu, Yinshui Li, Lei Hu, Liao Xiang-sheng, Lixin Xing
Software Mentions: 3
Published: about 7 years ago
10.3389/fmicb.2019.02411
A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein
Cited by: 12
Author(s): Zhanming Fan, Shangxin Song, Yafang Ma, Xinglian Xu
Software Mentions: 3
Published: about 5 years ago
10.3389/fmicb.2019.00060
Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors
Cited by: 5
Author(s): Ricardo Ulloa, Ana Moya-Beltrán, Camila Rojas-Villalobos, Harold Núñez, P. Chiacchiarini, Edgardo R. Donati, Alejandra Giaveno, Raquel Quatrini
Software Mentions: 3
Published: almost 6 years ago
10.34133/2019/5809404
Development of Optimized Phenomic Predictors for Efficient Plant Breeding Decisions Using Phenomic-Assisted Selection in Soybean
Cited by: 45
Author(s): Kyle A. Parmley, Koushik Nagasubramanian, Soumik Sarkar, Baskar Ganapathysubramanian, Asheesh K. Singh
Software Mentions: 3
Published: almost 6 years ago
10.3389/fgene.2018.00332
A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen
Cited by: 17
Author(s): Stephen J. Goodswen, Paul J. Kennedy, John Ellis
Software Mentions: 3
Published: over 6 years ago
10.3389/fnhum.2014.00625
A single session of exercise increases connectivity in sensorimotor-related brain networks: a resting-state fMRI study in young healthy adults
Cited by: 63
Author(s): A. Saeed Rajab, David Crane, Laura Middleton, Andrew D. Robertson, Michelle Hampson, Bradley J. MacIntosh
Software Mentions: 3
Published: over 10 years ago
10.1111/pbi.12940
Chromosome‐based survey sequencing reveals the genome organization of wild wheat progenitor <i>Triticum dicoccoides</i>
Cited by: 27
Author(s): Bala Anı Akpınar, Sezgi Biyiklioglu, Burcu Alptekin, M. Havránková, Jan Vrána, Jaroslav Doležel, Assaf Distelfeld, Pilar Hernández, Hikmet Budak
Software Mentions: 3
Published: over 6 years ago
10.1186/1471-2164-14-837
Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1
Cited by: 81
Author(s): Nikolai V. Ravin, Michael A. Eldarov, Vitaly V. Kadnikov, Alexey V. Beletsky, Jessica Schneider, Eugenia S. Mardanova, Elena M. Smekalova, Maria I. Zvereva, О. А. Донцова, Andrey V. Mardanov, K. G. Skryabin
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pgen.1009686
A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing
Cited by: 11
Author(s): Akihiro Nita, Akinobu Matsumoto, Ronghao Tang, Chisa Shiraishi, Kazuya Ichihara, Daisuke Saito, Mikita Suyama, Tomoharu Yasuda, Gaku Tsuji, Masutaka Furue, Bunpei Katayama, Toshiyuki Ozawa, Takaho Murata, Teruki Dainichi, Kenji Kabashima, Atsushi Hatano, Masaki Matsumoto, Keiichi I. Nakayama
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pgen.1006382
Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin
Cited by: 18
Author(s): Ryosuke Kita, Hunter B. Fraser
Software Mentions: 3
Published: about 8 years ago
10.3389/fgene.2019.01040
Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat
Cited by: 10
Author(s): Yinghui Ling, Qi Zheng, Yunsheng Li, Menghua Sui, Hao Wu, Yunhai Zhang, Mingxing Chu, Yuehui Ma, Fugui Fang, Lei Xu
Software Mentions: 3
Published: about 5 years ago
10.1186/s12870-020-02483-4
Transcriptome and metabolite analysis reveal the drought tolerance of foxtail millet significantly correlated with phenylpropanoids-related pathways during germination process under PEG stress
Cited by: 32
Author(s): Ai‐Nong Yu, Jinfeng Zhao, Zhenhua Wang, Kai Chen, Peng Zhang, Gang Tian, Xin Liu, Erhu Guo, Yan-Wei Du, Yuwen Wang
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2019.00659
Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements
Cited by: 8
Author(s): Iliyas Rashid, Ajey Kumar Pathak, Ravindra Kumar, Prachi Srivastava, Mahender Singh, S. Murali, Basdeo Kushwaha
Software Mentions: 3
Published: over 5 years ago
10.3389/fgene.2014.00150
Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing—the FRAGMENT approach
Cited by: 8
Author(s): Chang Sun, Thomas McAndrew, Benjamin Smith, Zigui Chen, Marina Frimer, Robert D. Burk
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0079402
Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity
Cited by: 1
Author(s): Sara B. Linker, Dale J. Hedges
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pbio.3000421
Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy
Cited by: 44
Author(s): Reshef Tal, Shafiq Shaikh, Pallavi Pallavi, Aya Tal, Francesc López-Giráldez, Fang Lyu, Yuanyuan Fang, Shruti Chinchanikar, Ying Liu, Harvey J. Kliman, Myles H. Alderman, Nicola Pluchino, Jehanzeb Kayani, Ramanaiah Mamillapalli, Diane S. Krause, Hugh S. Taylor
Software Mentions: 3
Published: about 5 years ago
10.1186/s12859-015-0833-4
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Cited by: 33
Author(s): Guillaume Rivière, Christophe Klopp, Ibouniyamine Nabihoudine, Arnaud Huvet, Pierre Boudry, Pascal Favrel
Software Mentions: 3
Published: almost 9 years ago
10.3389/fgene.2020.00652
Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes
Cited by: 25
Author(s): Bin Zeng, Ting Chen, Junyi Luo, Mei-Ying Xie, Limin Wei, Qianyun Xi, Jiajie Sun, Yongliang Zhang
Software Mentions: 3
Published: over 4 years ago
10.3389/fmicb.2021.714920
Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems
Cited by: 2
Author(s): Michael Hoffert, Rika E. Anderson, Julie Réveillaud, Leslie G. Murphy, Ramunas Stepanauskas, J. A. Huber
Software Mentions: 3
Published: over 3 years ago
10.3389/fmolb.2020.00040
Computational Investigation of Voltage-Gated Sodium Channel β3 Subunit Dynamics
Cited by: 4
Author(s): William G. Glass, Anna L. Duncan, Philip C. Biggin
Software Mentions: 3
Published: over 4 years ago
10.1038/srep36789
Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China
Cited by: 18
Author(s): Yang Xiao, Xuanjin Cheng, Jun Liu, Chuang Li, Wenyan Nong, Yinbing Bian, Man Kit Cheung, Hoi Shan Kwan
Software Mentions: 3
Published: about 8 years ago
10.3390/pathogens9121078
Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble
Cited by: 13
Author(s): Albert Ros-Lucas, Florencia Correa‐Fiz, Laia Bosch-Camós, Fernando Rodrı́guez, Julio Alonso-Padilla
Software Mentions: 2
Published: almost 4 years ago
10.1186/1756-3305-7-151
Identification and characterization of alternative splicing in parasitic nematode transcriptomes
Cited by: 6
Author(s): Sahar Abubucker, Samantha N. McNulty, Bruce A. Rosa, Makedonka Mitreva
Software Mentions: 2
Published: over 10 years ago
10.3389/fbioe.2021.644216
Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates
Cited by: 3
Author(s): Tania Chroumpi, Mao Peng, Lye Meng Markillie, Hugh D. Mitchell, Carrie Nicora, Chelsea Hutchinson, Vanessa Paurus, Nikola Tolić, Chaevien S. Clendinen, Galya Orr, Scott E. Baker, Miia Mäkelä, Ronald P. de Vries
Software Mentions: 2
Published: over 3 years ago
10.3390/v12111270
Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes
Cited by: 12
Author(s): Léo Blanca, Eugène Christo-Foroux, Sofia Rigou, Matthieu Legendre
Software Mentions: 2
Published: about 4 years ago
10.1186/s12870-021-03024-3
Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)
Cited by: 18
Author(s): Chunmeng Wang, Bobo Song, Yuqin Dai, Shaoling Zhang, Xiaosan Huang
Software Mentions: 2
Published: over 3 years ago
10.1002/2211-5463.12925
Cracking of jujube fruits is associated with differential expression of metabolic genes
Cited by: 5
Author(s): Yaling Liu, Peng-Fei Zhang, Yaping Geng, Xinglong Xie, Pengfei Wen
Software Mentions: 2
Published: over 4 years ago
10.3389/fnagi.2020.599112
Altered Weibull Degree Distribution in Resting-State Functional Brain Networks Is Associated With Cognitive Decline in Mild Cognitive Impairment
Cited by: 1
Author(s): Yifei Zhang, Xiaodan Chen, Xinyuan Liang, Zhijiang Wang, Tian Xie, Xiao Wang, Yuhu Shi, Weiming Zeng, Huali Wang
Software Mentions: 2
Published: almost 4 years ago
10.1080/21505594.2018.1511677
Genomic analysis of the original Elberg <i>Brucella melitensis</i> Rev.1 vaccine strain reveals insights into virulence attenuation
Cited by: 9
Author(s): Mali Salmon‐Divon, Adva Yeheskel, Jonathan D. Kornspan
Software Mentions: 2
Published: about 6 years ago
10.1111/febs.14175
An engineered photoswitchable mammalian pyruvate kinase
Cited by: 26
Author(s): Stefanie Gehrig, Jamie A. Macpherson, Paul C. Driscoll, Alastair Symon, Stephen R. Martin, James I. MacRae, Jens Kleinjung, Franca Fraternali, Dimitrios Anastasiou
Software Mentions: 2
Published: over 7 years ago
10.1002/2211-5463.13245
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains
Cited by: 0
Author(s): Gon Carmi, Alessandro Gorohovski, Milana Frenkel‐Morgenstern
Software Mentions: 2
Published: over 3 years ago
10.3389/fnagi.2021.657221
Effective Connectivity During Rest and Music Listening: An EEG Study on Parkinson’s Disease
Cited by: 5
Author(s): Emanuela Maggioni, Federica Arienti, Stella Minella, Francesca Mameli, Linda Borellini, Martina Nigro, F. Cogiamanian, Anna Maria Bianchi, S. Cerutti, S. Barbieri, Paolo Brambilla, Gianluca Ardolino
Software Mentions: 2
Published: over 3 years ago
10.3389/fendo.2019.00293
The Effect of Wnt Pathway Modulators on Human iPSC-Derived Pancreatic Beta Cell Maturation
Cited by: 29
Author(s): Heidrun Vethe, Luiza Ghila, Magnus Berle, Laurence Hoareau, Øystein Ariansen Haaland, Hanne Scholz, João A. Paulo, Simona Chera, Helge Ræder
Software Mentions: 2
Published: over 5 years ago
10.3390/vaccines9060658
Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis
Cited by: 28
Author(s): Abdur Rehman, Sajjad Ahmad, Farah Shahid, Aqel Albutti, Ameen S. S. Alwashmi, Mohammad Aljasir, Naif Alhumeed, Muhammad Qasim, Usman Ali Ashfaq, Muhammad Tahir ul Qamar
Software Mentions: 2
Published: over 3 years ago
10.3390/vaccines9050432
Conformational and Immunogenicity Studies of the Shigella flexneri Serogroup 6 O-Antigen: The Effect of O-Acetylation
Cited by: 9
Author(s): Nicole I Richardson, Neil Ravenscroft, Vanessa Arato, Davide Oldrini, Francesca Micoli, Michelle M. Kuttel
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-15-682
Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing
Cited by: 30
Author(s): Christopher Cowled, Cameron R. Stewart, Vladimir A Likić, Marc R. Friedländer, Mary Tachedjian, Kristie A. Jenkins, Mark Tizard, Pauline Cottee, Glenn A. Marsh, Peng Zhou, Michelle L. Baker, Andrew G.D. Bean, Lin‐Fa Wang
Software Mentions: 2
Published: almost 11 years ago
10.15252/msb.20209584
<scp>P</scp> recision design of stable genetic circuits carried in highly‐insulated <i>E. coli</i> genomic landing pads
Cited by: 31
Author(s): Yong‐Jin Park, Amin Espah Borujeni, Thomas E. Gorochowski, Jinwoo Shin, Christopher A. Voigt
Software Mentions: 2
Published: over 4 years ago
10.1186/s12859-021-03995-y
FiNGS: high quality somatic mutations using filters for next generation sequencing
Cited by: 6
Author(s): Christopher P. Wardell, Cody Ashby, Michael Bauer
Software Mentions: 2
Published: almost 4 years ago
10.1186/1472-6831-11-33
Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis
Cited by: 100
Author(s): Shi Huang, Fang Yang, Xiaowei Zeng, Jie Chen, Rui Li, Ting Wen, Chun Li, Wei Wei, Jiquan Liu, Lan Chen, Catherine Davis, Jian Xu
Software Mentions: 2
Published: almost 13 years ago