Ecosyste.ms: Papers

10.7554/eLife.10501

Egr-5 is a post-mitotic regulator of planarian epidermal differentiation
Cited by: 92
Author(s): Kimberly C. Tu, Li-Chun Cheng, Hanh Thi-Kim Vu, Jeffrey J. Lange, Sean A. McKinney, Chris Seidel, Alejandro Sánchez Alvarado
Software Mentions: 1
Published: about 9 years ago

10.7717/peerj.11079

Characterization of the first vaginal <i>Lactobacillus crispatus</i> genomes isolated in Brazil
Cited by: 3
Author(s): Marcelle Oliveira de Almeida, Rodrigo Dias de Oliveira Carvalho, Flávia Figueira Aburjaile, Fábio Miranda, Janaína Canário Cerqueira, Bertram Brenig, Preetam Ghosh, Rommel Thiago Jucá Ramos, Rodrigo Bentes Kato, Siomar de Castro Soares, Artur M. S. Silva, Vasco Azevedo, Marcus Vinícius Canário Viana
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.17820

The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains
Cited by: 216
Author(s): Erin G. Conlon, Lei Lü, Aarti Sharma, Takashi Yamazaki, Timothy Tang, Neil A. Shneider, James L. Manley
Software Mentions: 1
Published: about 8 years ago

10.1186/s13756-018-0363-8

Whole genome sequence revealed the fine transmission map of carbapenem-resistant Klebsiella pneumonia isolates within a nosocomial outbreak
Cited by: 23
Author(s): Wenjun Sui, Haijian Zhou, Pengcheng Du, Lijun Wang, Tian Qin, Mei Wang, Hao Ren, Yue Huang, Jing Hou, Chen Chen, Xinxin Lu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12876-020-01460-3

Effects of proton pump inhibitor use on the esophageal microbial community
Cited by: 8
Author(s): Sadia Tasnim, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Richard B. Pyles, Ikenna Okereke
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-12-440

Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes
Cited by: 10
Author(s): Tobias Mourier
Software Mentions: 1
Published: about 13 years ago

10.1530/REP-17-0592

Identification and verification of potential piRNAs from domesticated yak testis
Cited by: 16
Author(s): Jishang Gong, Quanwei Zhang, Qi Wang, Youji Ma, Jiaxiang Du, Yong Zhang, Xingxu Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-15-583

Transcriptional landscape of repetitive elements in normal and cancer human cells
Cited by: 232
Author(s): Steven W. Criscione, Yue Zhang, W. T. Thompson, John M. Sedivy, Nicola Neretti
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms18040723

Dysregulated IER3 Expression is Associated with Enhanced Apoptosis in Titin-Based Dilated Cardiomyopathy
Cited by: 10
Author(s): Qifeng Zhou, Johannes-Martin Hahn, Balram Neupane, Parwez Aidery, Siegfried Labeit, Meinrad Gawaz, Michael Gramlich
Software Mentions: 1
Published: over 7 years ago

10.1098/rsob.190116

Biochemical analysis of nucleosome targeting by Tn5 transposase
Cited by: 9
Author(s): Shoko Sato, Yasuhiro Arimura, Tomoya Kujirai, Akihito Harada, Kazuhira Maehara, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7930

Detection of disease in <i>Cucurbita maxima</i> Duch. ex Lam<i>.</i> caused by a mixed infection of <i>Zucchini yellow mosaic virus</i>, <i>Watermelon mosaic virus</i>, and <i>Cucumber mosaic virus</i> in Southeast China using a novel small RNA sequencing method
Cited by: 2
Author(s): Yi Wang, Ping Zhu, Qin Zhou, Xiaojun Zhou, Zeqing Guo, Linrun Cheng, Liyan Zhu, Xiaochan He, Yidan Zhu, Huanming Yang
Software Mentions: 1
Published: about 5 years ago

10.1155/2021/8845520

Changes in the Small RNA Expression in Endothelial Cells in Response to Inflammatory Stimulation
Cited by: 1
Author(s): Peixi Liu, Lingli Hu, Yuan Shi, Yingjun Liu, Guangrong Yu, Yingjie Zhou, Qingzhu An, Wei Zhu
Software Mentions: 1
Published: over 3 years ago

10.1186/s12862-018-1274-2

Diverse RNA interference strategies in early-branching metazoans
Cited by: 20
Author(s): Andrew Calcino, Selene L. Fernández-Valverde, Ryan J. Taft, Bernard M. Degnan
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.2861

Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia
Cited by: 6
Author(s): Scott William Roy
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13071-015-0656-1

Extracellular Onchocerca-derived small RNAs in host nodules and blood
Cited by: 98
Author(s): Juan F. Quintana, Benjamin L. Makepeace, Simon A. Babayan, Alasdair Ivens, Kenneth Pfarr, Mark Blaxter, Alexander Yaw Debrah, Samuel Wanji, Henrietta F. Ngangyung, Germanus S. Bah, Vincent N. Tanya, David W. Taylor, Achim Hoerauf, Amy H. Buck
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-016-2493-9

Clam focal and systemic immune responses to QPX infection revealed by RNA-seq technology
Cited by: 20
Author(s): Kailai Wang, Carmelo S. del Castillo, Matthieu Le Corre, Emmanuelle Pales Espinosa, Bassem Allam
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-017-3598-5

Transposable Element Bm1645 is a Source of BmAGO2-associated Small RNAs that affect its expression in Bombyx mori
Cited by: 1
Author(s): Hongqiang Si, Yunjie Cao, Honglin Zhu, Dan Li, Zhengbing Lv, Qing Sheng, Zhou Nie
Software Mentions: 1
Published: over 7 years ago

10.1186/s12915-018-0571-y

The piRNA pathway responds to environmental signals to establish intergenerational adaptation to stress
Cited by: 41
Author(s): Tony Bélicard, Pree Jareosettasin, Peter Sarkies
Software Mentions: 1
Published: about 6 years ago

10.1186/s13287-021-02452-0

LINGO-1 regulates Wnt5a signaling during neural stem and progenitor cell differentiation by modulating miR-15b-3p levels
Cited by: 4
Author(s): Chenguang Zhao, Jie Qin, Jia Li, Shan Jiang, Fengkui Ju, Wei Sun, Zhen Ren, Yibing Ji, Rui Wang, Xiaolong Sun, Xiang Mou, Hua Yuan
Software Mentions: 1
Published: over 3 years ago

10.1186/s13071-015-0863-9

Small mosquitoes, large implications: crowding and starvation affects gene expression and nutrient accumulation in Aedes aegypti
Cited by: 54
Author(s): David Price, Faye Schilkey, Alexander Ulanov, Immo A. Hansen
Software Mentions: 1
Published: over 9 years ago

10.7150/thno.36639

Glyoxalase 1 Prevents Chronic Hyperglycemia Induced Heart-Explant Derived Cell Dysfunction
Cited by: 10
Author(s): Melanie Villanueva, Connor Michie, Sandrine Parent, Georges N. Kanaan, Ghazaleh Rafatian, Pushpinder Kanda, Bin Ye, Wenbin Liang, Mary‐Ellen Harper, Darryl R. Davis
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-017-1801-y

Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
Cited by: 5
Author(s): Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan Rath, Aaron R. Cox, Siva Dharman Naidu
Software Mentions: 1
Published: about 7 years ago

10.7150/thno.47845

Elevated IgE promotes cardiac fibrosis by suppressing miR-486a-5p
Cited by: 12
Author(s): Hongmei Zhao, Hongqin Yang, Chi Geng, Yang Chen, Yaqin Tang, Zhiwei Li, Junling Pang, Ting Shu, Yu Nie, Yongshuo Liu, Jia Ke, Jing Wang
Software Mentions: 1
Published: almost 4 years ago

10.3390/toxins10030096

True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra subspinipes
Cited by: 39
Author(s): Jennifer J. Smith, Eivind A. B. Undheim
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-020-07206-5

Sperm miRNAs— potential mediators of bull age and early embryo development
Cited by: 22
Author(s): Chongyang Wu, Patrick Blondin, Christian Vigneault, Rémi Labrecque, Marc‐André Sirard
Software Mentions: 1
Published: about 4 years ago

10.3390/v8050120

Characterization of a Novel Polerovirus Infecting Maize in China
Cited by: 62
Author(s): Sha Chen, Guangzhuang Jiang, Ji Wu, Yong Liu, Yajuan Qian, Xueping Zhou
Software Mentions: 1
Published: over 8 years ago

10.1007/s11248-020-00196-w

CRISPR/Cas9-mediated targeted mutagenesis of TAS4 and MYBA7 loci in grapevine rootstock 101-14
Cited by: 29
Author(s): Sukumaran Sunitha, Christopher D. Rock
Software Mentions: 1
Published: over 4 years ago

10.1080/21505594.2020.1856560

The novel outer membrane protein from OprD/Occ family is associated with hypervirulence of carbapenem resistant Acinetobacter baumannii ST2/KL22
Cited by: 6
Author(s): Mingxi Hua, Jingyuan Liu, Pengcheng Du, Xinzhe Liu, Min Li, Huizhu Wang, Chen Chen, Xinmin Xu, Jiang Yu, Yajie Wang, Hui Zeng, Ang Li
Software Mentions: 1
Published: almost 4 years ago

10.1080/21505594.2018.1475797

Eicosanoid biosynthesis influences the virulence of <i>Candida parapsilosis</i>
Cited by: 16
Author(s): T. Chakraborty, Ernst Thuer, Marieke Heijink, Renáta Tóth, László Bodai, Csaba Vágvölgyi, Martin Giera, Toni Gabaldón, Attila Gácser
Software Mentions: 1
Published: over 6 years ago

10.3906/biy-2103-3

Transcriptome profiling of Stevia rebaudiana MS007 revealed genes involved in flower development
Cited by: 2
Author(s): Nurul Hidayah Samsulrizal, Khairul Shahyidi Khadzran, Tamil Chelvan Meenakshi Sundram, Zarina Zainuddin, Siti Hajar Nor Shaarani, Nur Sabrina Ahmad Azmi, Sarahani Harun
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms20071754

The miRNA-Mediated Post-Transcriptional Regulation of Maize in Response to High Temperature
Cited by: 35
Author(s): Moubiao Zhang, Panpan An, Hongping Li, Xiuling Wang, Jinlong Zhou, Pengfei Dong, Yali Zhao, Qun Wang, LI Chao-hai
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.00897-17

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
Cited by: 47
Author(s): Sukrit Silas, Kira S. Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R. Krishnamurthy, Becky Xu Hua Fu, Larry G. Hansen, David Wang, Matthew B. Sullivan, Andrew Millard, Martha R. J. Clokie, Devaki Bhaya, Alan M. Lambowitz, Nikos C. Kyrpides, Eugene V. Koonin, Andrew Fire
Software Mentions: 1
Published: about 7 years ago

10.1186/s12985-021-01500-8

Role of human Pegivirus infections in whole Plasmodium falciparum sporozoite vaccination and controlled human malaria infection in African volunteers
Cited by: 3
Author(s): Anneth-Mwasi Tumbo, Tobias Schindler, Jean-Pierre Dangy, Nina Orlova-Fink, Jose Raso Bieri, Maximillian Mpina, Florence A. Milando, Omar Juma, Ally Hamad, Elizabeth Nyakarungu, Mwajuma Chemba, Ali Mtoro, Kamaka Ramadhan, Ally Olotu, Damas Makweba, Stephen Mgaya, Kenneth Stuart, Matthieu Perreau, Jack T. Stapleton, Said Jongo, Stephen L. Hoffman, Marcel Tanner, Salim Abdulla, Claudia Daubenberger
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12985-018-1014-7

NS3 Protein from Rice stripe virus affects the expression of endogenous genes in Nicotiana benthamiana
Cited by: 8
Author(s): Gentu Wu, Guixian Zheng, Qiao Hu, Mingge Ma, Mingjun Li, Xihuan Sun, Fei Yan, Ling Qing
Software Mentions: 1
Published: over 6 years ago

10.1186/s12985-017-0803-8

The effects of potato virus Y-derived virus small interfering RNAs of three biologically distinct strains on potato (Solanum tuberosum) transcriptome
Cited by: 14
Author(s): Lindani Moyo, S. V. Ramesh, Madhu Kappagantu, Neena Mitter, Vidyasagar Sathuvalli, H. R. Pappu
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00201-20

Virulence as a Side Effect of Interspecies Interaction in <i>Vibrio</i> Coral Pathogens
Cited by: 18
Author(s): Esther Rubio-Portillo, Ana Belén Martín‐Cuadrado, Andrés Mauricio Caraballo‐Rodríguez, Forest Rohwer, Pieter C. Dorrestein, Josefa Antón
Software Mentions: 1
Published: about 4 years ago

10.1186/s12985-016-0663-7

RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis
Cited by: 22
Author(s): Feng Sun, Fang Peng, Juan Li, Linlin Du, Ying Lan, Tong Zhou, Yanting Fan, Wenbiao Shen, Yijun Zhou
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-14-31

Estimation of data-specific constitutive exons with RNA-Seq data
Cited by: 6
Author(s): Ellis Patrick, Michael Buckley, Jean Yee Hwa Yang
Software Mentions: 1
Published: almost 12 years ago

10.3390/ijms20164058

Comparative Analysis of miRNA Abundance Revealed the Function of Vvi-miR828 in Fruit Coloring in Root Restriction Cultivation Grapevine (Vitis vinifera L.)
Cited by: 16
Author(s): Qiuju Chen, Bohan Deng, Jie Gao, Zhongyang Zhao, Zili Chen, Shiren Song, Lei Wang, Liping Zhao, Wenping Xu, Caixi Zhang, Shiping Wang, Chao Ma
Software Mentions: 1
Published: over 5 years ago

10.1111/acel.12621

Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape
Cited by: 38
Author(s): Zhaoyi Chen, Wing Y. Chang, Alton Etheridge, Hilmar Strickfaden, Zhigang Jin, Gareth Palidwor, Ji-Hoon Cho, Kai Wang, Sarah Y. Kwon, Carole Doré, Angela Raymond, Akitsu Hotta, James Ellis, Rita A. Kandel, F. Jeffrey Dilworth, Theodore J. Perkins, Michael J. Hendzel, David J. Galas, William L. Stanford
Software Mentions: 1
Published: over 7 years ago

10.15252/msb.20167028

Metabolic constraints on the evolution of antibiotic resistance
Cited by: 125
Author(s): Mattia Zampieri, Tim N. Enke, Victor Chubukov, Vito Ricci, Laura J. V. Piddock, Uwe Sauer
Software Mentions: 1
Published: over 7 years ago

10.1002/mgg3.251

hg19K: addressing a significant lacuna in hg19-based variant calling
Cited by: 4
Author(s): Savita Karthikeyan, Pushpinder Bawa, Subhashini Srinivasan
Software Mentions: 1
Published: about 8 years ago

10.3390/molecules23071604

Transcriptomic Analysis of the Candidate Genes Related to Aroma Formation in Osmanthus fragrans
Cited by: 22
Author(s): Xia Yang, Haiyan Li, Yuanzheng Yue, Wenjie Ding, Chen Xu, Tingting Shi, Gongwei Chen
Software Mentions: 1
Published: over 6 years ago

10.1128/mSystems.00459-19

Global Screening of Genomic and Transcriptomic Factors Associated with Phenotype Differences between Multidrug-Resistant and -Susceptible Candida haemulonii Strains
Cited by: 8
Author(s): Hao Zhang, Y. Niu, Jingwen Tan, Weixia Liu, Miao‐Kun Sun, Ence Yang, Qian Wang, Ruoyu Li, Yejun Wang, Wei Liu
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-12-S3-S8

Perfect Hamming code with a hash table for faster genome mapping
Cited by: 4
Author(s): Yasuhiro Takenaka, Shigeto Seno, Hideo Matsuda
Software Mentions: 1
Published: almost 14 years ago

10.1093/molbev/msab188

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication
Cited by: 8
Author(s): Oscar Alejandro Pérez‐Escobar, Sidonie Bellot, Natalia A. S. Przelomska, Jonathan M. Flowers, Mark Nesbitt, Philippa Ryan, Rafał M. Gutaker, Muriel Gros-Balthazard, Tom Wells, Benedikt G. Kuhnhäuser, Rowan J. Schley, Diego Bogarín, Steven Dodsworth, Rudy Diaz, Manuela Lehmann, Peter Petoe, Wolf L. Eiserhardt, Michaela Preick, Michael Hofreiter, Irka Hajdas, Michael D. Purugganan, Alexandre Antonelli, Barbara Gravendeel, Ilia J. Leitch, María Fernanda Torres Jiménez, Alexander S. T. Papadopulos, Guillaume Chomicki, Susanne S. Renner, William J. Baker
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-15-690

Temporal transcriptome analysis of the chicken embryo yolk sac
Cited by: 56
Author(s): Liran Yadgary, Eric A. Wong, Zehava Uni
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-4265-6

Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology
Cited by: 6
Author(s): Daragh Matthews, M.G. Diskin, David A. Kenny, Christopher J. Creevey, Kate Keogh, Sinéad M. Waters
Software Mentions: 1
Published: about 7 years ago

10.1007/s00439-016-1654-x

Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression
Cited by: 41
Author(s): Marco Cavalli, Gang Pan, Helena Nord, Ola Wallerman, Emelie Wallén Arzt, Olof Berggren, Ingegerd Elvers, Maija‐Leena Eloranta, Lars Rönnblom, Kerstin Lindblad Toh, Claes Wadelius
Software Mentions: 1
Published: over 8 years ago

10.1186/s40246-017-0105-7

Identification of novel genes associated with HIV-1 latency by analysis of histone modifications
Cited by: 4
Author(s): Kyung-Chang Kim, Sun Young Lee, Junseock Son, YoungHyun Shin, Choon Sik Yoon, Chun Kang, Byeong‐Sun Choi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-015-1572-7

Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)
Cited by: 64
Author(s): Yang Yao, Robert Sebra, Benjamin Pullman, Wanqiong Qiao, Inga Peter, Robert J. Desnick, C. Ronald Geyer, John F. DeCoteau, Stuart A. Scott
Software Mentions: 1
Published: over 9 years ago

10.1093/molbev/msx175

Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment
Cited by: 14
Author(s): Oliver Smith, Sarah Palmer, A. R. Clapham, Pamela Rose, Yuan Liu, Jun Wang, Robin G. Allaby
Software Mentions: 1
Published: over 7 years ago

10.1093/humrep/dew056

Depolarization of sperm membrane potential is a common feature of men with subfertility and is associated with low fertilization rate at IVF
Cited by: 46
Author(s): Sean G. Brown, Stephen J. Publicover, Steven A. Mansell, Polina V. Lishko, Hannah Williams, Mythili Ramalingam, Stuart M. Wilson, Christopher L.R. Barratt, Keith A. Sutton, Sarah Martins da Silva
Software Mentions: 1
Published: over 8 years ago

10.1093/molbev/msab133

Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses
Cited by: 8
Author(s): Minkyu Park, Pascal‐Antoine Christin, Jeffrey L. Bennetzen
Software Mentions: 1
Published: over 3 years ago

10.1186/s13229-015-0040-1

Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex
Cited by: 82
Author(s): Michal Mor, Stefano Nardone, Dev Sharan Sams, Evan Elliott
Software Mentions: 1
Published: over 9 years ago

10.1080/23802359.2019.1679677

The complete mitochondrial genome of soft coral <i>Sarcophyton trocheliophorum</i> (Cnidaria: Anthozoa) using next-generation sequencing
Cited by: 4
Author(s): Chengji Shen, Ya-Ting Dan, Alireza Asem, Pei-Zheng Wang, Wei Xue, Xiao-Bo Tong, Weidong Li
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21041228

A Post-Processing Algorithm for miRNA Microarray Data
Cited by: 15
Author(s): Stepan Nersisyan, M. Yu. Shkurnikov, А. А. Полозников, Andrey Turchinovich, Barbara Burwinkel, Никита Анисимов, Alexander G. Tonevitsky
Software Mentions: 1
Published: almost 5 years ago

10.7150/ijms.50248

MicroRNA expression profile of Lacrimal Glands in rabbit autoimmune dacryoadenitis model
Cited by: 2
Author(s): Bo Liu, Lu Zhao, Yankai Wei, Sisi Chen, Lingzhai Bian, Di Guo, Min Gao, Hong Nian
Software Mentions: 1
Published: almost 5 years ago

10.3892/ijmm.2014.1973

Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method
Cited by: 6
Author(s): Xinmei Wang, Mingyue Li, Yingchun Yin, Liang Li, Youshan Tao, Dengguo Chen, Jianzhao Li, Hongmei Han, Zhenbo Hou, Baohua Zhang, Yu Ding, Haiyan Cui, Hengming Zhang
Software Mentions: 1
Published: about 10 years ago

10.3389/fcell.2021.679325

Meis2 Is Required for Inner Ear Formation and Proper Morphogenesis of the Cochlea
Cited by: 6
Author(s): María Beatriz Durán Alonso, Victor Vendrell, Iris López‐Hernández, Donna M. Martin, Fernando Giráldez, Laura Carramolino, Giovanna Giovinazzo, Enrique Vázquez, Miguel Torres, Thomas Schimmang
Software Mentions: 1
Published: over 3 years ago

10.1080/23802359.2017.1325343

The complete mitochondrial genome of the Egyptian honey bee, <i>Apis mellifera lamarckii</i> (Insecta: Hymenoptera: Apidae)
Cited by: 17
Author(s): Amin Eimanifar, Rebecca T. Kimball, Edward L. Braun, Dahi M. Moustafa, Nizar Haddad, Stefan Fuchs, Bernd Grünewald, Jamie Ellis
Software Mentions: 1
Published: almost 8 years ago

10.1080/23802359.2019.1674740

The complete mitochondrial genome of <i>Sinularia maxima</i> Verseveldt, 1971 (Octocorallia: Alcyonacea) using next-generation sequencing
Cited by: 3
Author(s): You Chen, Ya-Ting Dan, Hao Lu, Pei-Zheng Wang, Alireza Asem, Weidong Li
Software Mentions: 1
Published: over 5 years ago

10.1080/23802359.2017.1419082

The complete chloroplast genome of an aromatic Chinese pepper (<i>Zanthoxylum simulans</i>)
Cited by: 2
Author(s): Na Hou, Gang Wang, Shi Jing Feng, An Zhi Wei
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms21072309

The Encystment-Related MicroRNAs and Its Regulation Molecular Mechanism in Pseudourostyla cristata Revealed by High Throughput Small RNA Sequencing
Cited by: 3
Author(s): Nan Pan, Muhammad Zeeshan Bhatti, Haiyang Zhang, Bing Ni, Xinpeng Fan, Jiwu Chen
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms21082666

Transcriptional Profiling of the Probiotic Escherichia coli Nissle 1917 Strain under Simulated Microgravity
Cited by: 19
Author(s): Jaewoo Yim, Sung Won Cho, Beomhee Kim, Sungwoo Park, Yong Han, Sang Woo Seo
Software Mentions: 1
Published: over 4 years ago

10.18632/oncotarget.15517

Identification and characterization of L1-specific endo-siRNAs essential for early embryonic development in pig
Cited by: 10
Author(s): Heng Zhang, Ji‐Long Liu, Yurong Tai, Xiaolei Zhang, Jiaming Zhang, Shichao Liu, Jiawei Lv, Qingran Kong
Software Mentions: 1
Published: almost 8 years ago

10.1080/23802359.2017.1318683

The complete mitochondrial genome and phylogenetic placement of Apis nigrocincta Smith (Insecta: Hymenoptera: Apidae), an Asian, cavity-nesting honey bee
Cited by: 9
Author(s): Amin Eimanifar, Rebecca T. Kimball, Edward L. Braun, Stefan Fuchs, Bernd Grünewald, Jamie Ellis
Software Mentions: 1
Published: almost 8 years ago

10.3389/fendo.2019.00485

Growth Hormone Promotes in vitro Maturation of Human Oocytes
Cited by: 29
Author(s): Yue Li, Hui Liu, Qingqing Yu, Hongbin Liu, Tao Huang, Shigang Zhao, Jinlong Ma, Han Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/s40168-015-0100-y

In silico analyses of metagenomes from human atherosclerotic plaque samples
Cited by: 76
Author(s): Suparna Mitra, Daniela I. Drautz–Moses, Morten Alhede, Myat Thiri Maw, Yang Liu, Rikky W. Purbojati, Zhei Hwee Yap, Kavita K. Kushwaha, Alexandra Gheorghe, Thomas Bjarnsholt, Georg Nørgaard Hansen, Henrik Sillesen, Hans Petter Hougen, Peter Riis Hansen, Liang Yang, Tim Tolker‐Nielsen, Stephan C. Schuster, Michael Givskov
Software Mentions: 1
Published: about 9 years ago

10.3389/fcell.2021.670435

PERK Signaling Controls Myoblast Differentiation by Regulating MicroRNA Networks
Cited by: 9
Author(s): Ying Tan, Yin Zhang, Bin Li, Yangwen Ou, Shu‐Juan Xie, Peipei Chen, Shi-Qiang Mei, Qiao-Juan Huang, Ling‐Ling Zheng, Liang‐Hu Qu
Software Mentions: 1
Published: over 3 years ago

10.3389/fbioe.2015.00007

Computational Prediction of miRNA Genes from Small RNA Sequencing Data
Cited by: 33
Author(s): Wenjing Kang, Marc R. Friedländer
Software Mentions: 1
Published: almost 10 years ago

10.1128/MRA.00835-18

Sequence Variation in Multidrug-Resistant Plasmid pLUH01, Isolated from Human Nasopharyngeal Swabs
Cited by: 0
Author(s): Kate V. Atkinson, L.A. Bishop, Glenn Rhodes, Nicolas Salez, Neil McEwan, Matthew J. Hegarty, Julie Robey, Nicola Harding, Simon Wetherell, Robert M. Lauder, Roger W. Pickup, Mark Wilkinson, Derek Gatherer
Software Mentions: 1
Published: over 6 years ago

10.1186/s12934-018-1050-4

Functional analysis of the role of CcpA in Lactobacillus plantarum grown on fructooligosaccharides or glucose: a transcriptomic perspective
Cited by: 18
Author(s): Yan-qing Lu, Sichao Song, Huaixiang Tian, Haiyan Yu, Jianxin Zhao, Chen Chen
Software Mentions: 1
Published: almost 6 years ago

10.3389/fgene.2020.00947

MicroRNA Expression Profiling of Bone Marrow–Derived Proangiogenic Cells (PACs) in a Mouse Model of Hindlimb Ischemia: Modulation by Classical Cardiovascular Risk Factors
Cited by: 3
Author(s): Michel Desjarlais, Sylvie Dussault, José Carlos Rivera, Sylvain Chemtob, Alain Rivard
Software Mentions: 1
Published: over 4 years ago

10.1002/2211-5463.13139

CRISPR‐based knock‐in mutagenesis of the pioneer transcription factor FOXA1: optimization of strategies for multi‐allelic proteins in cancer cells
Cited by: 4
Author(s): Li Shen, Joseph P. Garay, Colby A. Tubbs, Hector L. Franco
Software Mentions: 1
Published: over 3 years ago

10.1186/s12934-021-01594-3

In-situ muconic acid extraction reveals sugar consumption bottleneck in a xylose-utilizing Saccharomyces cerevisiae strain
Cited by: 5
Author(s): Thomas Nicolaï, Quinten Deparis, María R. Foulquié-Moreno, Johan M. Thevelein
Software Mentions: 1
Published: over 3 years ago

10.12688/f1000research.15931.2

FastQ Screen: A tool for multi-genome mapping and quality control
Cited by: 682
Author(s): Steven Wingett, Simon Andrews
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-13-S6-S4

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments
Cited by: 7
Author(s): Ekaterina E. Khrameeva, Mikhail S. Gelfand
Software Mentions: 1
Published: over 12 years ago

10.1111/eva.12412

Genomic signatures among <i>Oncorhynchus nerka</i> ecotypes to inform conservation and management of endangered Sockeye Salmon
Cited by: 44
Author(s): Krista M. Nichols, Christine C. Kozfkay, Shawn R. Narum
Software Mentions: 1
Published: about 8 years ago

10.3389/fgene.2013.00150

The detection of microRNA associated with Alzheimer's disease in biological fluids using next-generation sequencing technologies
Cited by: 104
Author(s): Lesley Cheng, Camelia Quek, Xin Sun, Shayne A. Bellingham, Andrew F. Hill
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13072-018-0210-4

Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline
Cited by: 31
Author(s): Elizaveta Radion, Valeriya Morgunova, Sergei Ryazansky, Natalia Akulenko, Sergey Lavrov, Yuri Abramov, Pavel A Komarov, Sergey I. Glukhov, Ivan Olovnikov, Alla Kalmykova
Software Mentions: 1
Published: over 6 years ago

10.1186/s13072-015-0012-x

Divergence of transcriptional landscape occurs early in B cell activation
Cited by: 23
Author(s): Trent Fowler, Alexander S. Garruss, Amalendu Ghosh, Supriyo De, Kevin G. Becker, William H. Wood, Matthew T. Weirauch, Stephen T. Smale, Bruce J. Aronow, Ranjan Sen, Ananda L. Roy
Software Mentions: 1
Published: over 9 years ago

10.1590/0074-02760190498

Deep sequencing of small RNAs reveals the repertoire of miRNAs and piRNAs in Biomphalaria glabrata
Cited by: 5
Author(s): Fábio Ribeiro Queiroz, Laysa Gomes Portilho, Wander de Jesus Jeremias, Elio H. Baba, Laurence Rodrigues do Amaral, Luciana Maria Silva, Paulo Marcos Zech Coelho, Roberta Lima Caldeira, Matheus de Souza Gomes
Software Mentions: 1
Published: almost 5 years ago

10.15252/embr.201948925

Transfer of extracellular vesicle‐micro <scp>RNA</scp> controls germinal center reaction and antibody production
Cited by: 41
Author(s): Lola Fernández-Messina, Ana Rodríguez-Galán, Virginia G. de Yébenes, Cristina Gutiérrez-Vázquez, Sandra Tenreiro, Miguel C. Seabra, Almudena R. Ramiro, Francisco Sánchez-Madrid
Software Mentions: 1
Published: almost 5 years ago

10.15252/emmm.201606523

Sequence variation in <i> <scp>PPP</scp> 1R13L </i> results in a novel form of cardio‐cutaneous syndrome
Cited by: 17
Author(s): Tzipora C. Falik‐Zaccai, Yiftah Barsheshet, Hanna Mandel, Meital Segev, Avraham Lorber, Shachaf Gelberg, Limor Kalfon, Shani Ben Haroush, Adel Shalata, Liat Gelernter‐Yaniv, Sarah Chaim, Dorith Raviv Shay, Morad Khayat, Michal Werbner, Itzhak Levi, Yishay Shoval, Galit Tal, Stavit A. Shalev, Eli Reuveni, Emily Avitan‐Hersh, Eugene Vlodavsky, Liat Appl‐Sarid, Dorit Goldsher, Reuven Bergman, Zvi Segal, Ora Bitterman‐Deutsch, Orly Avni
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2012.00226

Lack of miRNA Misregulation at Early Pathological Stages in Drosophila Neurodegenerative Disease Models
Cited by: 20
Author(s): Anita Reinhardt, Sébastien Feuillette, Marlène Cassar, Céline Callens, Hélène Thomassin, Serge Birman, Magalie Lecourtois, Christophe Antoniewski, Hervé Tricoire
Software Mentions: 1
Published: almost 13 years ago

10.15252/embj.2020105280

Intrinsically disordered protein PID‐2 modulates Z granules and is required for heritable piRNA‐induced silencing in the <i>Caenorhabditis elegans</i> embryo
Cited by: 11
Author(s): Maria Placentino, António Miguel de Jesus Domingues, Jan Schreier, Sabrina Dietz, Svenja Hellmann, Bruno F.M. de Albuquerque, Falk Butter, René F. Ketting
Software Mentions: 1
Published: almost 4 years ago

10.3389/fgene.2021.675027

Rapid Evolution of Autosomal Binding Sites of the Dosage Compensation Complex in Drosophila melanogaster and Its Association With Transcription Divergence
Cited by: 1
Author(s): Aimei Dai, Yushuai Wang, Anthony J. Greenberg, Zhongqi Liufu, Tian Tang
Software Mentions: 1
Published: over 3 years ago

10.1186/s40880-018-0333-9

<i>DUXAP8</i>, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2
Cited by: 55
Author(s): Yifan Lian, Jiebin Yang, Yikai Lian, Chuangxing Xiao, Xuezhen Hu, Hui Xu
Software Mentions: 1
Published: about 6 years ago

10.1186/s13058-015-0593-0

MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene
Cited by: 41
Author(s): Yu Wei Phua, Akira Nguyen, Daniel Roden, Benjamin Elsworth, Niantao Deng, Iva Nikolić, Jessica Yang, Andrea McFarland, Roslin Russell, Warren Kaplan, Mark J. Cowley, Radhika Nair, Elena Zotenko, Sandra A. O’Toole, Shi‐Xiong Tan, David E. James, Susan J. Clark, Hosein Kouros-Mehr, Alexander Swarbrick
Software Mentions: 1
Published: over 9 years ago

10.1242/dmm.024455

Histone lysine-crotonylation in acute kidney injury
Cited by: 78
Author(s): Olga Ruiz‐Andrés, María Dolores Sanchez-Niño, Pablo Cannata‐Ortiz, Marta Ruíz-Ortega, Jesús Egido, Ana B. Sanz
Software Mentions: 1
Published: almost 9 years ago

10.3389/fgene.2019.00222

Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms
Cited by: 13
Author(s): José Henrique Galdino, María Eguiluz, Frank Guzmán, Rogério Margis
Software Mentions: 1
Published: over 5 years ago

10.1007/s00429-012-0474-6

Postnatal isoform switch and protein localization of LEF1 and TCF7L2 transcription factors in cortical, thalamic, and mesencephalic regions of the adult mouse brain
Cited by: 31
Author(s): Andrzej Nagalski, Manuel Irimia, Łukasz Mateusz Szewczyk, José Luis Ferrán, Katarzyna Misztal, Jacek Kuźnicki, M. Wisniewska
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-020-07275-6

Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control
Cited by: 6
Author(s): Hanbang Zhang, Gretchen Ehrenkaufer, Neil Hall, Upinder Singh
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.devcel.2012.06.011

Smchd1-Dependent and -Independent Pathways Determine Developmental Dynamics of CpG Island Methylation on the Inactive X Chromosome
Cited by: 153
Author(s): Anne-Valérie Gendrel, Anwyn Apedaile, Heather Coker, Ausma Termanis, Ilona Zvetkova, Jonathan Godwin, Y. Amy Tang, Derek Huntley, Giovanni Montana, Steven L. Taylor, Eleni Giannoulatou, Edith Heard, Irina Stancheva, Neil Brockdorff
Software Mentions: 1
Published: over 12 years ago

10.1093/database/bau110

piRBase: a web resource assisting piRNA functional study
Cited by: 122
Author(s): Peng Zhang, Xiaohui Si, Geir Skogerbø, Jiajia Wang, Dongya Cui, Yongxing Li, Xubin Sun, Li Liu, Bao‐Fa Sun, Runsheng Chen, Shunmin He, Dawei Huang
Software Mentions: 1
Published: almost 11 years ago

10.1093/database/baz134

SGID: a comprehensive and interactive database of the silkworm
Cited by: 10
Author(s): Zhenglin Zhu, Zhufen Guan, Gexin Liu, Yawang Wang, Ze Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1155/2014/948408

Exploring the miRNA-mRNA Regulatory Network in Clear Cell Renal Cell Carcinomas by Next-Generation Sequencing Expression Profiles
Cited by: 36
Author(s): Sören Müller, Katharina Nowak
Software Mentions: 1
Published: almost 11 years ago

10.1093/database/baab025

Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans
Cited by: 16
Author(s): Tzu-Hsien Yang, Chung‐Yu Wang, Hsiu-Chun Tsai, Cheng-Tse Liu
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.dib.2016.11.022

Dataset for a Dugesia japonica de novo transcriptome assembly, utilized for defining the voltage-gated like ion channel superfamily
Cited by: 12
Author(s): John D. Chan, Dan Zhang, Xiaolong Liu, Magdalena Zarowiecki, Matthew Berriman, Jonathan S. Marchant
Software Mentions: 1
Published: almost 8 years ago