10.1038/s41598-020-77381-8

MicroRNA retrocopies generated via L1-mediated retrotransposition in placental mammals help to reveal how their parental genes were transcribed
Cited by: 3
Author(s): Pan Cheng, Yi-Chung Lin
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-78260-y

Algorithms for ribosome traffic engineering and their potential in improving host cells' titer and growth rate
Cited by: 14
Author(s): Hadas Zur, Rachel Cohen-Kupiec, Sophie Vinokour, Tamir Tuller
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-79698-w

Reference standards for accurate validation and optimization of assays that determine integrated lentiviral vector copy number in transduced cells
Cited by: 10
Author(s): Barbara S. Paugh, Lajos Baranyi, Amélie Roy, Hua‐Jun He, Lindsay Harris, Kenneth D. Cole, Moria Artlip, Caroline Raimund, Patricia S. Langan, Swapan Kumar Jana, Rimas J. Orentas, Sheng Lin‐Gibson, Winfried Krueger, Boro Dropulić
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pbio.2006459

A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
Cited by: 80
Author(s): William J. Fitzsimmons, Robert J. Woods, John McCrone, Andrew Woodman, Jamie J. Arnold, Madhumita Yennawar, Richard P. Evans, Craig Ε. Cameron, Adam S. Lauring
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.3000289

Resolving noise–control conflict by gene duplication
Cited by: 47
Author(s): Michal Chapal, Sefi Mintzer, Sagie Brodsky, Miri Carmi, Naama Barkai
Software Mentions: 1
Published: almost 7 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 12 years ago

10.1371/journal.pbio.2004526

Zbtb7a is a transducer for the control of promoter accessibility by NF-kappa B and multiple other transcription factors
Cited by: 35
Author(s): José M. Ramos Pittol, Agata Oruba, Gerhard Mittler, Simona Saccani, Dominic van Essen
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.1000523

Control of Transcription by Cell Size
Cited by: 108
Author(s): Chia-Yung Wu, P. Alexander Rolfe, David K. Gifford, Gerald R. Fink
Software Mentions: 1
Published: about 16 years ago

10.3390/plants9030362

AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis
Cited by: 6
Author(s): Yan Liu, Wenrui Gao, Shizhou Wu, Lu Lu, Yaqiu Chen, Jinxin Guo, Shuzhen Men, Xiaoming Zhang
Software Mentions: 1
Published: over 6 years ago

10.1007/s11103-017-0679-4

Structure, target-specificity and expression of PN_LNC_N13, a long non-coding RNA differentially expressed in apomictic and sexual Paspalum notatum
Cited by: 13
Author(s): Ana Claudia Ochogavía, Giulio Galla, Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Claudia Pessino
Software Mentions: 1
Published: about 9 years ago

10.1111/pbi.13049

Impact of differential<scp>DNA</scp>methylation on transgene expression in cotton<i>(Gossypium hirsutum L.)</i>events generated by targeted sequence insertion
Cited by: 3
Author(s): Aurine Verkest, Stephane Bourout, Jurgen Debaveye, Kristine Reynaert, Bernadette Saey, Ilse van den Brande, Kathleen D’Halluin
Software Mentions: 1
Published: almost 8 years ago

10.1111/pbi.12701

Spearmint R2R3‐<scp>MYB</scp> transcription factor Ms<scp>MYB</scp> negatively regulates monoterpene production and suppresses the expression of geranyl diphosphate synthase large subunit (<i>Ms<scp>GPPS</scp></i>.<i><scp>LSU</scp></i>)
Cited by: 83
Author(s): Vaishnavi Amarr Reddy, Qian Wang, Niha Dhar, Nitin Kumar, Prasanna Nori Venkatesh, Chakravarthy Rajan, Deepa Panicker, Vishweshwaran Sridhar, Hui-Zhu Mao, Rajani Sarojam
Software Mentions: 1
Published: over 9 years ago

10.1098/rstb.2018.0319

A gossypol biosynthetic intermediate disturbs plant defence response
Cited by: 13
Author(s): Xiu Tian, Xin Fang, Jin-Quan Huang, Ling-Jian Wang, Ying‐Bo Mao, Xiao‐Ya Chen
Software Mentions: 1
Published: almost 8 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 9 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 7 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 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 7 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 5 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 10 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 8 years ago

10.1038/s41598-021-96425-1

Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean
Cited by: 9
Author(s): Dipak Kumar Sahoo, Anindya Bijoy Das, Xiaoqiu Huang, Silvia R. Cianzio, Madan K. Bhattacharyya
Software Mentions: 1
Published: about 5 years ago

10.1038/s41392-020-00238-z

Novel insights into stress-induced susceptibility to influenza: corticosterone impacts interferon-β responses by Mfn2-mediated ubiquitin degradation of MAVS
Cited by: 14
Author(s): Zhi-Pu Luo, Lifang Liu, Yingnan Jiang, Lu-Ping Tang, Wen Li, Shu-Hua Ouyang, Long-Fang Tu, Yanping Wu, Haibiao Gong, Chang-Yu Yan, Shan Jiang, Yuhui Lu, Tongzheng Liu, Zhuhua Jiang, Hiroshi Kojima, Yang Yu, Xin‐Sheng Yao, Yi-Fang Li, Rong‐Rong He
Software Mentions: 1
Published: about 6 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 12 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 10 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 9 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 8 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 5 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 11 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 8 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 9 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 6 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 8 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: almost 6 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 10 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 6 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 6 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 8 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 5 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 7 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 9 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 6 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 8 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 9 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 6 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 10 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 14 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: about 7 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 9 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 9 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 10 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 8 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 7 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 16 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 5 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: about 12 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 9 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 10 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 9 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 11 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 9 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 10 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 5 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 11 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 7 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 7 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 7 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 12 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 10 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 7 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 9 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 6 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 6 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: over 9 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 5 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 10 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 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 11 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 8 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 8 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 5 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 14 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 7 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 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 7 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 11 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 12 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 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 14 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 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: about 6 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 8 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 13 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 10 years ago

10.1155/2013/270805

A Guide RNA Sequence Design Platform for the CRISPR/Cas9 System for Model Organism Genomes
Cited by: 57
Author(s): Ming Ma, Adam Yongxin Ye, Weiguo Zheng, Lei Kong
Software Mentions: 1
Published: almost 14 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 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 14 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 11 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: over 6 years ago

10.3390/biology10090896

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements
Cited by: 2
Author(s): Ilektra-Chara Giassa, Panagiotis Alexiou
Software Mentions: 1
Published: about 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 10 years ago