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: bioconductor: Mfuzz
https://packages.ecosyste.ms/registries/bioconductor.org/packages/Mfuzz
Soft clustering of time series gene expression data
1 version
Latest release: about 1 year ago
4 dependent packages
108,790 downloads total
Papers Mentioning Mfuzz 160
10.1002/pmic.201400392
Visualization of proteomics data using R and BioconductorCited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago
10.12688/f1000research.9973.2
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment testsCited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: about 6 years ago
10.1038/srep42130
Dissecting the brown adipogenic regulatory network using integrative genomicsCited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: over 7 years ago
10.1128/mSystems.00200-20
High-Throughput Stool Metaproteomics: Method and Application to Human SpecimensCited by: 14
Author(s): Carlos Gutiérrez González, Hannah C. Wastyk, Madeline Topf, Christopher D. Gardner, Justin L. Sonnenburg, Joshua E. Elias
Software Mentions: 11
Published: over 4 years ago
10.1186/1756-0500-3-81
Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arraysCited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 14 years ago
10.1038/s41392-021-00753-7
Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patientsCited by: 18
Author(s): Xiang-Na Zhao, Yue You, Xiaoming Cui, Han Gao, Guolin Wang, Shengbo Zhang, Lilin Ye, Lei Duan, Ka-Li Zhu, Yuling Wang, Li Li, Jianhua Lu, Haibin Wang, Jingfang Fan, Huanwei Zheng, Erfu Dai, Luyi Tian, Mai‐Juan Ma
Software Mentions: 11
Published: about 3 years ago
10.1186/s12885-019-5965-x
Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune responseCited by: 32
Author(s): Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo
Software Mentions: 11
Published: about 5 years ago
10.1038/s41598-019-48495-5
Latent-period stool proteomic assay of multiple sclerosis model indicates protective capacity of host-expressed protease inhibitorsCited by: 9
Author(s): Carlos Gutiérrez González, Stephanie Tankou, Laura M. Cox, Ellen P. Casavant, Howard L. Weiner, Joshua E. Elias
Software Mentions: 11
Published: about 5 years ago
10.3389/fcell.2020.00268
Comparative Transcriptome Landscape of Mouse and Human HeartsCited by: 14
Author(s): Tatsuya Anzai, Takanori Yamagata, Hideki Uosaki
Software Mentions: 9
Published: over 4 years ago
10.3390/ijms151221788
Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of PigsCited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: almost 10 years ago
10.7554/eLife.34058
A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscleCited by: 63
Author(s): Maria L. Spletter, Christiane Barz, Assa Yeroslaviz, Xu Zhang, Sandra B. Lemke, Adrien Bonnard, Erich Brunner, Giovanni Cardone, Konrad Basler, Bianca Habermann, Frank Schnorrer
Software Mentions: 9
Published: over 6 years ago
10.1038/s41419-021-03552-8
Transcriptional profiling reveals the transcription factor networks regulating the survival of striatal neuronsCited by: 12
Author(s): Lin Yang, 智慧 蘇, Zi-Wu Wang, Zhenmeiyu Li, Zicong Shang, Heng Du, Shuai Liu, Dashi Qi, Zhengang Yang, Zhejun Xu, Zhuangzhi Zhang
Software Mentions: 8
Published: over 3 years ago
10.1186/s12915-017-0379-1
Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectorsCited by: 55
Author(s): Édouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, T. S. Yunusov, Kévin Floch, Sebastián Schornack
Software Mentions: 8
Published: over 7 years ago
10.1002/ece3.5249
Immune and environment‐driven gene expression during invasion: An eco‐immunological application of RNA‐SeqCited by: 15
Author(s): D. Selechnik, Mark F. Richardson, Richard Shine, Gregory P. Brown, Lee A. Rollins
Software Mentions: 8
Published: over 5 years ago
10.1186/s13040-017-0150-8
RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case studyCited by: 15
Author(s): Bork A. Berghoff, Torgny Karlsson, Thomas Källman, E. Gerhart H. Wagner, Manfred Grabherr
Software Mentions: 7
Published: about 7 years ago
10.1371/journal.pone.0076051
Alterations in miRNA Levels in the Dentate Gyrus in Epileptic RatsCited by: 79
Author(s): Anna Bot, Konrad J. Dębski, Katarzyna Łukasiuk
Software Mentions: 7
Published: about 11 years ago
10.1371/journal.pone.0007225
MicroRNAs Show Mutually Exclusive Expression Patterns in the Brain of Adult Male RatsCited by: 94
Author(s): Line Olsen, Mikkel Klausen, Lone Helboe, Finn Cilius Nielsen, Thomas Werge
Software Mentions: 7
Published: about 15 years ago
10.1186/s12870-020-02808-3
Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel OrangeCited by: 18
Author(s): Haipeng Zhang, Jiajing Chen, Zhaoxin Peng, Meiyan Shi, Xiao Liu, Wen Huang, Youwu Jiang, Yunjiang Cheng, Juan Xu, Hongyan Zhang
Software Mentions: 7
Published: almost 4 years ago
10.3389/fncel.2020.612560
Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro DifferentiationCited by: 19
Author(s): Jakub Červenka, Jiřina Tylečková, Helena Kupcová Skalníková, Kateřina Vodičková Kepková, Ievgeniia Poliakh, Ivona Valeková, Lucie Pfeiferová, Michal Kolář, Michaela Vaškovičová, Tereza Pánková, Petr Vodička
Software Mentions: 7
Published: almost 4 years ago
10.1186/s13059-021-02372-5
Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1Cited by: 11
Author(s): Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Francesca Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf, Juan Valcárcel
Software Mentions: 7
Published: over 3 years ago
10.1242/dev.199561
Global proteomic analyses of human cytotrophoblast differentiation/invasionCited by: 4
Author(s): Hao Chen, Katherine E. Williams, Elaine Kwan, Mirhan Kapidzic, Kenisha A. Puckett, Rayyan Aburajab, Joshua F. Robinson, Susan J. Fisher
Software Mentions: 7
Published: over 3 years ago
10.1038/s42003-021-02217-8
LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading framesCited by: 6
Author(s): Martin Blythe, Ayhan Kocer, Alejandro Rubio-Roldán, Tom Giles, Abdulkadir Abakir, Côme Ialy-Radio, Lee M. Wheldon, Oxana Bereshchenko, Stefano Bruscoli, Alexander Kondrashov, Joël R. Drevet, Richard D. Emes, Andrew D. Johnson, John R. McCarrey, Daniel Gackowski, Julie Cocquet, José L. García‐Pérez, Alexey Ruzov
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-020-6767-x
Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goatsCited by: 11
Author(s): Dongdong Bo, Xunping Jiang, Guiqiong Liu, Feng Xu, Ronggui Hu, Teketay Wassie, Yuqing Chong, S. Sohail Ahmed, Chenhui Liu, Shishay Girmay
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-019-41336-5
Female novelty and male status dynamically modulate ejaculate expenditure and seminal fluid proteome over successive matings in red junglefowlCited by: 9
Author(s): Aitor Álvarez-Fernández, Kirill Borziak, Grant C. McDonald, Steve Dorus, Tommaso Pizzari
Software Mentions: 6
Published: over 5 years ago
10.3390/plants10061039
Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in PepperCited by: 2
Author(s): Yeon Mi Lee, Geun Young Chae, Min Kyung Kim, Seungill Kim
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-017-19059-2
Consensus Clustering of temporal profiles for the identification of metabolic markers of pre-diabetes in childhood (EarlyBird 73)Cited by: 4
Author(s): Mario Lauria, Maria Persico, N. Ðorđević, Ornella Cominetti, Alice Matone, Joanne Hosking, Alison Jeffery, Jonathan Pinkney, Laeticia Da Silva, Corrado Priami, Ivan Montoliu, François‐Pierre J. Martin
Software Mentions: 6
Published: almost 7 years ago
10.1186/s13072-018-0250-9
Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infectionCited by: 29
Author(s): José Luis Ruiz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Jean-Bosco Ouédraogo, Victor G. Corcés, Elena Gómez-Díaz
Software Mentions: 6
Published: almost 6 years ago
10.1371/journal.pone.0066826
A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic DevelopmentCited by: 31
Author(s): Alicia N. Schep, Boris Adryan
Software Mentions: 6
Published: over 11 years ago
10.1534/g3.113.006742
The Developmental Transcriptome of the Mosquito <i>Aedes aegypti</i>, an Invasive Species and Major Arbovirus VectorCited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: about 11 years ago
10.1186/1741-7007-8-26
Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in DrosophilaCited by: 22
Author(s): Carlo G. Artieri, Rama S. Singh
Software Mentions: 5
Published: over 14 years ago
10.3389/fpls.2018.01309
A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative GenomicsCited by: 17
Author(s): Chuanmei Zhu, Jiani Yang, Mathew S. Box, Elizabeth A. Kellogg, Andrea L. Eveland
Software Mentions: 5
Published: about 6 years ago
10.3389/fcell.2021.641987
Timing Does Matter: Nerve-Mediated HDAC1 Paces the Temporal Expression of Morphogenic Genes During Axolotl Limb RegenerationCited by: 3
Author(s): Mu-Hui Wang, Chih‐Cheng Hsu, Cheng‐Hsun Wu, Ling-Ling Chiou, Yi-Tzang Tsai, Hsuan-Shu Lee, Shau-Ping Lin
Software Mentions: 5
Published: over 3 years ago
10.1016/j.celrep.2019.11.066
Molecular Basis for Autosomal-Dominant Renal Fanconi Syndrome Caused by HNF4ACited by: 28
Author(s): Valentina Marchesin, Albert Pérez-Martí, G. Le Meur, Roman Pichler, Kelli Grand, Enriko Klootwijk, Anne Kesselheim, Robert Kleta, Soeren S. Lienkamp, Matias Simons
Software Mentions: 5
Published: almost 5 years ago
10.7554/eLife.41556
Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phaseCited by: 40
Author(s): Sven Schenk, Stephanie Bannister, Fritz J. Sedlazeck, Dorothea Anrather, Bùi Quang Minh, Andrea Bileck, Markus Hartl, Arndt von Haeseler, Christopher Gerner, Florian Raible, Kristin Tessmar-Raible
Software Mentions: 5
Published: over 5 years ago
10.1186/s12915-020-00769-5
Multiple links between 5-methylcytosine content of mRNA and translationCited by: 71
Author(s): Ulrike Schümann, He-Na Zhang, Tennille Sibbritt, Anyu Pan, Attila Horváth, Simon Gross, Susan J. Clark, Li Yang, Thomas Preiß
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-020-66759-3
The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifoliaCited by: 6
Author(s): Ximena Gómez‐Maqueo, Diana Soriano, Noé Velázquez-Rosas, Sandra Alvarado-López, Karina Jiménez‐Durán, María Del Mar Garciadiego, Alicia Gamboa‐deBuen
Software Mentions: 5
Published: over 4 years ago
10.1155/2018/7691794
Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in MouseCited by: 6
Author(s): Minjung Kim, Yi Yin Yu, Ji-Hoi Moon, Insong Koh, Jae Hyung Lee
Software Mentions: 5
Published: almost 7 years ago
10.1186/s12864-019-5560-1
Transcriptomic analysis of different tissue layers in antler growth Center in Sika Deer (Cervus nippon)Cited by: 26
Author(s): Hengxing Ba, Datao Wang, Tung On Yau, Ying Shang, Chunyi Li
Software Mentions: 5
Published: over 5 years ago
10.1534/g3.119.401006
The Developmental Transcriptome of <i>Aedes albopictus</i>, a Major Worldwide Human Disease VectorCited by: 25
Author(s): Stephanie Gamez, Igor Antoshechkin, Stelia C. Méndez‐Sánchez, Omar S. Akbari
Software Mentions: 5
Published: over 4 years ago
10.1002/pld3.142
Tomato locule number and fruit size controlled by natural alleles of <i>lc</i> and <i>fas</i>Cited by: 61
Author(s): Yi Hsuan Chu, Jyan Chyun Jang, Zejun Huang, Esther van der Knaap
Software Mentions: 5
Published: over 5 years ago
10.3389/fcell.2021.648331
Fibrillarin-GFP Facilitates the Identification of Meiotic Competent OocytesCited by: 6
Author(s): Ting Wang, Jie Na
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-021-07646-7
Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzziiCited by: 18
Author(s): Victoria A. Ingham, Faye Brown, Hilary Ranson
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2021.628192
KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan PigsCited by: 7
Author(s): Tao Wang, Yuanyuan Guo, Shengwei Liu, Chaoxin Zhang, Tongyan Cui, Kun Ding, Peng Wang, Xibiao Wang, Zhipeng Wang
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2020.608325
Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial AdaptationCited by: 1
Author(s): Xiaoli Ma, Mei Shang, Baofeng Su, Anne A. Wiley, Max R. Bangs, Veronica Alston, Rhoda Mae C. Simora, Mai Thi Thanh Nguyen, Nathan J. C. Backenstose, Anthony G. Moss, Dương Thúy Yên, Xiaozhu Wang, Rex A. Dunham
Software Mentions: 4
Published: almost 4 years ago
10.3390/genes11091066
Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadenseCited by: 6
Author(s): Gongmin Cheng, Longyan Zhang, Hengling Wei, Hantao Wang, Jianhua Lü, Shuxun Yu
Software Mentions: 4
Published: about 4 years ago
10.3389/fimmu.2021.691142
Dynamic Network Biomarker of Pre-Exhausted CD8+ T Cells Contributed to T Cell Exhaustion in Colorectal CancerCited by: 16
Author(s): Jiaqi Hu, Chongyin Han, Jiayuan Zhong, Huisheng Liu, Rui Li, Wei Luo, Pei Chen, Fei Ling
Software Mentions: 4
Published: about 3 years ago
10.18632/aging.203046
Aging-related markers in rat urine revealed by dynamic metabolic profiling using machine learningCited by: 4
Author(s): Dan Shi, Qilong Tan, Jingqi Ruan, Zhen Tian, Xinyue Wang, Jinxiao Liu, Xin Liu, Zhipeng Liu, Yuntao Zhang, Chongde Sun, Yucun Niu
Software Mentions: 4
Published: over 3 years ago
10.18632/aging.102754
The whole transcriptome regulation as a function of mitochondrial polymorphisms and aging in Caenorhabditis elegansCited by: 9
Author(s): Yuanjian Song, Yuechen Wang, Ying Liu, Liang Wang, WenDa Zhang, Jing Cheng, Yushan Zhu, Haoyu Zhang, Qiang Zhang, Haichen Niu, Yingwei Zheng, Mengyu Liang, Mengqiong Deng, Hao Shi, Hao Wang, Fang Zhang
Software Mentions: 4
Published: almost 5 years ago
10.1007/s12035-020-02128-5
Molecular Regulatory Mechanism and Toxicology of Neurodegenerative Processes in MPTP/Probenecid-Induced Progressive Parkinson’s Disease Mice Model Revealed by TranscriptomeCited by: 12
Author(s): Weiwei Yang, Wenwen Hao, Zhen Meng, Shuizi Ding, Xiaodi Li, Tao Zhang, Weixiao Huang, Liang Xu, Yu Zhang, Jian Yang, Xiaosong Gu
Software Mentions: 4
Published: about 4 years ago
10.3390/ijms22157939
Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture ConditionsCited by: 5
Author(s): Byung Chul Kim, Kyu Hwan Kwack, Jeewan Chun, Jae Hyung Lee
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-017-07100-3
Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcriptionCited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: over 7 years ago
10.1111/tpj.14205
Identification and characterization of a core set of ROS wave‐associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess lightCited by: 84
Author(s): Sara I. Zandalinas, Soham Sengupta, David J. Burks, Rajeev K. Azad, Ron Mittler
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-021-07416-5
Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencingCited by: 20
Author(s): Wei Wang, Lei Wang, Ling Wang, Mingqian Tan, Collins Ogutu, Ziyan Yin, Jian Zhou, Jiaomei Wang, Lijun Wang, Xin Yan
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-021-07731-x
Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of miceCited by: 16
Author(s): Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiaowei Chi, Tongzuo Zhang
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.ppat.1006391
Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoesCited by: 114
Author(s): Faye H. Rodgers, Mathilde Gendrin, Claudia A. S. Wyer, George K. Christophides
Software Mentions: 4
Published: over 7 years ago
10.1186/s40635-021-00373-z
Longitudinal multi-omics transition associated with fatality in critically ill COVID-19 patientsCited by: 8
Author(s): Chaoyang Sun, Yuzhe Sun, Ping Wu, Wencheng Ding, Shiyou Wang, Jiafeng Li, Langchao Liang, Chaochao Chai, Yu Fu, Zhiming Li, Linnan Zhu, Jia Ju, Xin Liao, Xiaoyuan Huang, Feng Li, Ding Ma, Liang He, Dongsheng Chen, Gang Chen, Xin Jin, Peng Wu
Software Mentions: 4
Published: over 3 years ago
10.1186/s13568-020-01119-y
Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry systemCited by: 23
Author(s): Shenzheng Zeng, Sukontorn Khoruamkid, Warinphorn Kongpakdee, Dongdong Wei, Lingfei Yu, Hao Wang, Zhao‐Peng Deng, Shaoping Weng, Zhijian Huang, Jianguo He, Kriengkrai Satapornvanit
Software Mentions: 4
Published: about 4 years ago
10.1002/emmm.201201974
Alteration of the micro <scp>RNA</scp> network during the progression of Alzheimer's diseaseCited by: 393
Author(s): Pierre Lau, Koen Bossers, Rekin’s Janky, Evgenia Salta, Carlo Sala Frigerio, Shahar Barbash, Roy Rothman, Annerieke Sierksma, Amantha Thathiah, David Greenberg, Aikaterini S. Papadopoulou, Tilmann Achsel, Torik Ayoubi, Hermona Soreq, Joost Verhaagen, Dick F. Swaab, Stein Aerts, Bart De Strooper
Software Mentions: 4
Published: about 11 years ago
10.1016/j.omtn.2018.04.018
Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated HeartCited by: 10
Author(s): Davood Sabour, Rui S. R. Machado, José Pinto, Susan Rohani, Raja Ghazanfar Ali Sahito, Jürgen Hescheler, Matthias E. Futschik, Agapios Sachinidis
Software Mentions: 3
Published: about 6 years ago
10.1074/mcp.RA120.002102
Changes in the Oligodendrocyte Progenitor Cell Proteome with AgeingCited by: 46
Author(s): Alerie Guzman de la Fuente, Rayner M L Queiroz, Tanay Ghosh, Christopher E McMurran, Juan F. Cubillos, Dwight E. Bergles, Denise Fitzgerald, Clare A. Jones, Kathryn S. Lilley, Colin P. Glover, R. J. M. Franklin
Software Mentions: 3
Published: over 4 years ago
10.1186/s13068-020-01677-0
Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungusCited by: 25
Author(s): Hans Kristian Mattila, Mari Mäkinen, Taina Lundell
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pgen.1000311
Developmental Constraints on Vertebrate Genome EvolutionCited by: 104
Author(s): Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 3
Published: almost 16 years ago
10.1186/s13227-018-0091-4
Mouse Obox and Crxos modulate preimplantation transcriptional profiles revealing similarity between paralogous mouse and human homeobox genesCited by: 12
Author(s): Amy H. Royall, Ignacio Maeso, Thomas L. Dunwell, Peter W.H. Holland
Software Mentions: 3
Published: almost 7 years ago
10.1186/s13068-017-0700-9
Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatmentsCited by: 17
Author(s): Paul Daly, Jolanda M. van Munster, Martin Blythe, Roger Ibbett, Matthew Kokolski, Sanyasi Gaddipati, Erika Lindquist, Vasanth Singan, Kerrie Barry, Anna Lipzen, Chew Yee Ngan, Young-Mo Kim, Leanne Jade G. Chan, Steven T. Pullan, Stéphane Delmas, Paul Ravi Waldron, Igor V. Grigoriev, Gregory A. Tucker, Blake A. Simmons, David B. Archer
Software Mentions: 3
Published: over 7 years ago
10.3389/fonc.2021.621462
Gene Expression Profile of the Human Colorectal Carcinoma LoVo Cells Treated With Sporamin and ThapsigarginCited by: 3
Author(s): Chun Yang, Si-Jia Chen, Bowen Chen, Kai-Wen Zhang, Jingjie Zhang, Rong Xiao, Peng-Gao Li
Software Mentions: 3
Published: over 3 years ago
10.3390/ijms21114074
Quantitative Phosphoproteomics Reveals Cell Alignment and Mitochondrial Length Change under Cyclic Stretching in Lung CellsCited by: 4
Author(s): Wei Hsuan Wang, Chia‐Lang Hsu, Hsuan‐Cheng Huang, Hsueh‐Fen Juan
Software Mentions: 3
Published: over 4 years ago
10.3390/ijms20112735
Transcription Profiles Reveal the Regulatory Synthesis of Phenols during the Development of Lotus Rhizome (Nelumbo nucifera Gaertn)Cited by: 13
Author(s): Ting Min, Yinqiu Bao, Baixue Zhou, Yang Yi, Limei Wang, Wenfu Hou, Youwei Ai, Hongxun Wang
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0143436
Analysis of Stage-Specific Gene Expression Profiles in the Uterine Endometrium during Pregnancy in PigsCited 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: almost 9 years ago
10.1038/s41438-021-00632-w
High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancyCited by: 30
Author(s): Yuhao Gao, Qinsong Yang, Xue Yan, Xinyue Wu, Feng Yang, Jianzhao Li, Jia Wei, Junbei Ni, Mudassar Ahmad, Songling Bai, Yuanwen Teng
Software Mentions: 3
Published: about 3 years ago
10.1534/g3.114.013870
Whole-Genome Expression Analysis in the Third Instar Larval Midgut of <i>Drosophila melanogaster</i>Cited by: 25
Author(s): Thomas W. R. Harrop, Stephen L. Pearce, Phillip J. Daborn, Philip Batterham
Software Mentions: 3
Published: about 10 years ago
10.3389/fvets.2021.666512
Tandem Mass Tag-Based Quantitative Proteomic Analysis of Chicken Bursa of Fabricius Infected With Reticuloendotheliosis VirusCited by: 3
Author(s): Dahan Yang, Xiaoping Lv, Shujun Zhang, Shangen Zheng
Software Mentions: 3
Published: over 3 years ago
10.1186/s12870-015-0511-8
Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)Cited by: 276
Author(s): Zhenshan Liu, Mingming Xin, Jinxia Qin, Huiru Peng, Zhongfu Ni, Yingyin Yao, Qixin Sun
Software Mentions: 3
Published: over 9 years ago
10.1534/g3.119.400340
Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of<i>Tribolium castaneum</i>Cited by: 8
Author(s): Sher Afzal Khan, Heather Eggleston, K.M. Myles, Zach N. Adelman
Software Mentions: 3
Published: over 5 years ago
10.1111/j.1525-142X.2010.00400.x
Molecular signaling in zebrafish development and the vertebrate phylotypic periodCited by: 37
Author(s): Aurélie Comte, Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 3
Published: over 14 years ago
10.7717/peerj.2834
Transcriptome analysis of the oriental melon (<i>Cucumis melo</i>L. var.<i>makuwa</i>) during fruit developmentCited by: 26
Author(s): Ah-Young Shin, Yongmin Kim, Namjin Koo, Su‐Min Lee, Seok-Hyeon Nahm, Suk‐Yoon Kwon
Software Mentions: 3
Published: almost 8 years ago
10.1038/s41598-018-32792-6
Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomicsCited by: 16
Author(s): Martin Jacobsen, Robert J. Beynon, Lee A. Gethings, Amy J. Claydon, James Langridge, Johannes P.C. Vissers, Alistair J. P. Brown, Dean E. Hammond
Software Mentions: 3
Published: about 6 years ago
10.7717/peerj.8185
Global transcriptome analysis of different stages of preimplantation embryo development in river buffaloCited by: 2
Author(s): Chaoyou Pang, Mingzhou Bai, Chi Zhang, Junhui Chen, Xingrong Lu, Tingxian Deng, Xiaoya Ma, Anqin Duan, Shasha Liang, Yun-Qi Huang, Zhihui Xiu, Xianwei Liang
Software Mentions: 3
Published: almost 5 years ago
10.7717/peerj.6626
The transcriptomic response to a short day to long day shift in leaves of the reference legume <i>Medicago truncatula</i>Cited by: 15
Author(s): Geoffrey Thomson, James Taylor, Joanna Putterill
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-021-07457-w
Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infectionCited by: 27
Author(s): Roger de Pedro Jové, Marina Puigvert, Pau Sebastià, Alberto P. Macho, Jhonatas Sirino Monteiro, Núria S. Coll, João Carlos Setúbal, Marc Valls
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2020.01278
Combined Proteome and Transcriptome Analysis of Heat-Primed Azalea Reveals New Insights Into Plant Heat Acclimation MemoryCited by: 14
Author(s): Xiuyun Wang, Li Zheng, Bing Liu, Hong Zhou, Mohamed S. Elmongy, Yiping Xia
Software Mentions: 3
Published: about 4 years ago
10.1186/s13619-021-00076-6
Canonical and early lineage-specific stem cell types identified in planarian SirNeoblastsCited by: 5
Author(s): Kaimeng Niu, Hao Xu, Yuanyi Zhou Xiong, Yun Zhao, Chong Gao, Chris Seidel, Xue Pan, Yuqing Ying, Kai Y. Lei
Software Mentions: 3
Published: over 3 years ago
10.1186/s12862-021-01866-x
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularisCited by: 5
Author(s): Amélie Vernale, Maria Mandela Prünster, Fabio Marchianò, Henry Debost, Nicolas Brouilly, Caroline Rocher, Dominique Massey-Harroche, Emmanuelle Renard, André Le Bivic, Bianca Habermann, Carole Borchiellini
Software Mentions: 3
Published: about 3 years ago
10.3389/fonc.2021.704531
Transcriptomic Analyses of the Adenoma-Carcinoma Sequence Identify Hallmarks Associated With the Onset of Colorectal CancerCited by: 10
Author(s): Hong Qin, Bing Li, Xiumei Cai, Zheng‐tao Lv, Shi‐Lun Cai, Yun‐Shi Zhong, Bo Wen
Software Mentions: 3
Published: about 3 years ago
10.1111/imcb.12371
Time‐resolved mRNA and miRNA expression profiling reveals crucial coregulation of molecular pathways involved in epithelial–pneumococcal interactionsCited by: 3
Author(s): Haiyan Li, Li Lin, Chong Lei, Shu-Ge Gu, Shunhang Wen, Gang Yu, Xin Hu, Lin Dong, Hailin Zhang, Changchong Li
Software Mentions: 2
Published: over 4 years ago
10.18632/aging.102667
Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarctionCited by: 6
Author(s): Hang Shi, Haoran Sun, Jiayao Li, Ziyi Bai, Jie Wu, Xiuhong Li, Yingli Lv, Guangde Zhang
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13223-017-0192-y
Canadian Society of Allergy and Clinical Immunology annual scientific meeting 2016Cited by: 5
Author(s): Mohammad A. Alsayegh, Hanan Alshamali, Mousa Khadada, A Ciccolini, Anne K. Ellis, Diana Quint, William Powley, Laurie Lee, Yahya Fiteih, Shairaz Baksh, Harissios Vliagoftis, Sebastien K. Gerega, Brad Millson, Katia Charland, Stéphane Barakat, Xichun Sun, Ricardo Jiménez, Susan Waserman, Mark FitzGerald, Jacques Hébert, Josiane Cognet-Sicé, Kevin E. Renahan, S. Huq, Rishma Chooniedass, Scott Sawyer, Hans Pasterkamp, Allan B. Becker, Steven G. Smith, Shiyuan Zhang, Kavisha Jayasundara, Claire E. Tacon, Alex Simidchiev, Gilbert Nadeau, Necdet Gunsoy, Hana Müllerová, Frank Albers, Young Woong Kim, Casey P. Shannon, Amrit Singh, Helen Neighbour, Mark Larché, Scott J. Tebbutt, Annika Klopp, Lorena Vehling, Allan B. Becker, Padmaja Subbarao, Piushkumar J. Mandhane, Stuart E. Turvey, Malcolm R. Sears, Meghan B. Azad, Keely Loewen, Barret A. Monchka, Salaheddin M. Mahmud, Geert ’t Jong, Cristina Longo, Gillian Bartlett, Francine M Ducharme, Tibor Schuster, Brenda MacGibbon, Tracie A. Barnett, Michelle L. North, Jeff Brook, Elizabeth Lee, Vanessa Omana, Jenny Thiele, Lisa M. Steacy, Greg J. Evans, Miriam L. Diamond, Gordon Sussman, Yann Amistani, Kathy Abiteboul, Mark W. Tenn, Chenxi Yang, Christopher Carlsten, Edward M. Conway, Douglas G. Mack, Rofina Yasmin Othman, Colin Barber, Chrystyna Kalicinsky, Andrea E. Burke, Mary Messieh, Parameswaran Nair, Thomas H. Chun, Lindsay Douglas, Joel Liem, Lucy Duan, Charlotte E. Miller, Pascale Dupuis, Lori Connors, Michael Fein, Joseph Shuster, Hani Hadi, Brooke I. Polk, Nikita Raje, Roxane Labrosse, Philippe Bégin, Louis Paradis, Anne Des Roches, Jonathan Lacombe-Barrios, Sanju Mishra, Gina Lacuesta, Meredith Chiasson, Babar Haroon, Kara Robertson, Thomas B. Issekutz, Desmond Leddin, Stephen Couban, Lori Connors, Adrienne M. Roos, Amin Kanani, Edmond S. Chan, R. Robert Schellenberg, Lana Rosenfield, Anna Cvetkovic, K. N. Woodward, Jaclyn Quirt, Wade Watson, Edson Castilho, Jennifer Sullivan, Beverley Temple, Donna Martin, Victoria E. Cook, Christopher Mills, Elodie Portales‐Casamar, Lisa Fu, Alexander Ho, Jeffrey S. Zaltzman, Lucy Chen, Peter Vadas, Sofianne Gabrielli, Ann E. Clarke, Harley Eisman, Judy Morris, Lawrence Joseph, Sebastien LaVieille, Moshe Ben‐Shoshan, François Graham, Charles S. Barnes, Jay M. Portnoy, Vincent Stagg, Elinor Simons, Diana L. Lefebvre, David Dai, Piushkumar J. Mandhane, Malcolm R. Sears, Herman Tam, F. Estelle R. Simons, Dhaifallah S Alotaibi, Bassel Dawod, Matthew Tunis, Jean S. Marshall, Marylin Desjardins, Marianne Béland, Duncan Lejtenyi, Jean-Phillipe Drolet, Martine Lemire, Christos Tsoukas, Francisco Noya, Reza Alizadehfar, Christine McCusker, Bruce Mazer, Danay Maestre‐Batlle, Evelyn Gunawan, Christopher F. Rider, Anette Kocbach Bølling, Olga M. Pena, Daniel Suez, Isaac Melamed, Iftikhar Hussaın, Mark R. Stein, Sudhir Gupta, Kenneth Paris, Sandor Fritsch, Christelle Bourgeois, Heinz Leibl, Barbara McCoy, Martin Noël, Leman Yel, Ori Scott, Brenda Reid, Adelle Atkinson, Vy Hong-Diep Kim, Chaim M. Roifman, Eyal Grunebaum, Eiman Al-Selahi, Fernando Alemán, Amber Oberle, Mike Trus, Gordon Sussman, Amin Kanani, Olivier Chambenoi, Sima Chiva-Razavi, Savannah Grodecki, Nikhil Joshi, Peter Menikefs, David W. Holt, Teresa Pun, Damian Tworek, Raphael Hanna, Delia Heroux, Elli Rosenberg, Leah T. Stiemsma, Stuart E. Turvey, Judah A. Denburg, Christopher Mill, Timothy Teoh, Preeti Zimmer, Vishal Avinashi, Mihaela Paina, Ahmed A. Darwish Hassan, John Paul Oliveria, Chris Olesovsky, Gail M. Gauvreau, Linda Pedder, Paul K. Keith, Greg Plunkett, Michelle L. Bolner, Persia Pourshahnazari, Donald Stark, Kateryna Vostretsova, Andrew Moses, A. Maurice Wakeman, Alexander Singer, Thomas Gerstner, Elissa M. Abrams, Sara F. Johnson, Roberta L. Woodgate
Software Mentions: 2
Published: over 7 years ago
10.1186/s13223-016-0164-7
AllerGen’s 8th research conferenceCited by: 0
Author(s): Marie‐Claire Arrieta, Andrea Arevalos, Leah T. Stiemsma, Marta E. Chico, Carlos Sandoval, Minglian Jin, Jens Walter, Philip J. Cooper, B. Brett Finlay, Émilie Bernatchez, Matthew Gold, Anick Langlois, Pascale Blais-Lecours, Caroline Duchaine, David Marsolais, Kelly M. McNagny, Marie‐Renée Blanchet, Jordan Brubacher, Bimal Chhetri, Kelly Sabaliauskas, Kate Bassil, Jeff Kwong, Frances Coates, Tim K. Takaro, Angela Chow, Gregory E. Miller, Eric Chen, Piushkumar J. Mandhane, Stuart E. Turvey, Susan J. Elliott, Allan B. Becker, Padmaja Subbarao, Malcolm R. Sears, Anita L. Kozyrskyj, Aimée Dubeau, Zihang Lu, Susan Balkovec, Krzysztof Kowalik, Per Gustafsson, Félix Ratjen, Rachel D. Edgar, Nicole R. Bush, Julie L. MacIssac, Lisa M. McEwen, Thomas Boyce, Michael S. Kobor, Melanie Emmerson, Bingqing Shen, Theo J. Moraes, Sofianne Gabrielli, Ann E. Clarke, Harley Eisman, Judy Morris, Lawrence Joseph, Sebastien LaVieille, Moshe Ben‐Shoshan, Shofiq Islam, Christof Brückmann, Vanessa Nieratschker, Kyla C. Jamieson, David Proud, Cynthia Kanagaratham, Pierre Camateros, František Kopřiva, Jennifer Henri, Marián Hajdúch, Danuta Radzioch, Liane J. Kang, Petya Koleva, Catherine J. Field, Tedd Konya, James A. Scott, Theodore Konya, Meghan B. Azad, Jeff Brook, David S. Guttman, Manjeet Kumari, Sarah L. Bridgman, Mon Hnin Tun, Rupasri Mandal, David S. Wishart, Ahwon Lee, Jeff Xia, Erin E Gill, Bob Hancock, Danay Maestre, Darren Sutherland, Jeremy A. Hirota, Olga M. Pena, Christopher Carlsten, Meaghan J. Jones, Julia L. MacIsaac, William H. Dow, Luis Rosero-Bixby, David H. Rehkopf, Takeshi Morimoto, Steven G. Smith, John-Paul Oliveria, Suzanne Beaudin, Abbey Schlatman, Karen Howie, Caitlin Obminski, Graeme Nusca, Roma Sehmi, Gail M. Gauvreau, Paul M. O’Byrne, Michelle L. North, Cheng Peng, Marco Sánchez-Guerra, Hyang-Min Byun, Anne K. Ellis, Andrea A. Baccarelli, Joseph O. Okeme, Suman Dhal, Aman Saini, Miriam L. Diamond, Christopher J. Olesovsky, Brittany Salter, Michael Wang, Paige Lacy, Michael J. O’Sullivan, Chan Y. Park, Jeffrey J. Fredberg, Anne-Marie Lauzon, James G. Martin, Min Hyung Ryu, Neeloffer Mookherjee, Elinor Simons, Diana L. Lefebvre, David Dai, Amrit Singh, Casey P. Shannon, Young Woong Kim, Chen Xi Yang, J. Mark FitzGerald, Louis‐Philippe Boulet, Scott J. Tebbutt, Gurpreet K. Singhera, S. JasemineYang, Delbert R. Dorscheid, Hasantha Sinnock, Susan Goruk, Hamid Tavakoli, Larry D. Lynd, Mark W. Tenn, Jenny Thiele, Daniel E. Adams, Lisa M. Steacy, Bahar Torabi, Sarah De Schryver, Duncan Lejtenyi, Ingrid Baerg, Edmond S. Chan, Bruce Mazer, Maxwell Tran, Wei Dai, Wendy Lou, Radha Chari, Edward M. Conway, Helen Neighbour, Mark Larché
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12915-021-01100-6
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomicsCited by: 18
Author(s): Alexandra Menna, Susanne Dora, Gloria Sáncho-Andrés, Anurag Kashyap, Mukesh Kumar Meena, Kamil Sklodowski, Debora Gasperini, Núria S. Coll, Clara Sánchez‐Rodríguez
Software Mentions: 2
Published: about 3 years ago
10.1186/s12915-016-0267-0
Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammalsCited by: 33
Author(s): Ignacio Maeso, Thomas L. Dunwell, Christopher D R Wyatt, Ferdinand Marlétaz, Borbála Vető, Juan A. Bernal, Shan Quah, Manuel Irimia, Peter W.H. Holland
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2164-14-516
Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profileCited by: 19
Author(s): Jenna Oberstaller, Sandeep J. Joseph, Jessica C. Kissinger
Software Mentions: 2
Published: over 11 years ago
10.1186/s12864-017-4205-5
Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmonCited by: 35
Author(s): Kai Ove Skaftnesmo, Rolf B. Edvardsen, Tomasz Furmanek, Diego Crespo, Eva Andersson, Lene Kleppe, Geir Lasse Taranger, Jan Bogerd, Rüdiger Schulz, Anna Wargelius
Software Mentions: 2
Published: about 7 years ago
10.1186/s12864-018-4657-2
Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injuryCited by: 4
Author(s): Zhihua Li, Rodney Rouse
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-021-07677-0
Dynamic transcriptome and histomorphology analysis of developmental traits of hindlimb thigh muscle from Odorrana tormota and its adaptability to different life history stagesCited by: 1
Author(s): Yilin Shu, Jun He, Huijuan Zhang, Guangxuan Liu, Shikun Li, Shuaitao Deng, Hailong Wu
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-021-07763-3
Transcriptome analysis reveals Vernalization is independent of cold acclimation in ArabidopsisCited by: 12
Author(s): Fēi Li, Qian Hu, Fadi Chen, Jingle Jiang
Software Mentions: 2
Published: over 3 years ago
10.1186/s40659-019-0213-z
Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysisCited by: 6
Author(s): Hongtao Yin, Yan Yu
Software Mentions: 2
Published: almost 6 years ago
10.3390/microorganisms9050991
Global Changes in Asexual Epichloë Transcriptomes during the Early Stages, from Seed to Seedling, of Symbiotum EstablishmentCited by: 6
Author(s): Inoka K Hettiarachchige, Christy J. Vander Jagt, Ross Mann, Tim Sawbridge, Germán Spangenberg, Kathryn M. Guthridge
Software Mentions: 2
Published: over 3 years ago
10.3390/v13040674
Transcriptional Landscape of Vero E6 Cells during Early Swine Acute Diarrhea Syndrome Coronavirus InfectionCited by: 6
Author(s): Sha Zeng, Ouyang Peng, Ruipu Sun, Qiuping Xu, Fangyu Hu, Yan Zhao, Chunyi Xue, Yongchang Cao, Hao Zhang
Software Mentions: 2
Published: over 3 years ago
10.7717/peerj.9936
Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in <i>Gossypium hirsutum</i> L.Cited by: 7
Author(s): Jingjing Wang, Zhaohai Du, Xuehan Huo, Juan Zhou, Chunmei Yu, Jingxia Zhang, Ao Pan, Xiaoyang Wang, Furong Wang, Jun Zhang
Software Mentions: 2
Published: about 4 years ago
10.1111/pbi.12697
An advanced reference genome of<i>Trifolium subterraneum</i>L. reveals genes related to agronomic performanceCited by: 26
Author(s): Parwinder Kaur, Philipp E. Bayer, Zbyněk Milec, Jan Vrána, Yuxuan Yuan, R. Appels, David Edwards, Jacqueline Batley, Phillip Nichols, William Erskine, Jaroslav Doležel
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pbio.1002435
How Many Parameters Does It Take to Describe Disease Tolerance?Cited by: 72
Author(s): Alan K. Louie, Kyung Han Song, Alejandra Guzmán Hotson, Ann T. Tate, David Schneider
Software Mentions: 2
Published: over 8 years ago