pypi: bowtie | Projects | Ecosyste.ms: Papers

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

10.1186/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

10.1186/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

10.1080/23802359.2019.1679677

The complete mitochondrial genome of soft coral Sarcophyton trocheliophorum (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

10.1080/23802359.2017.1325343

The complete mitochondrial genome of the Egyptian honey bee, Apis mellifera lamarckii (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 Sinularia maxima 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 (Zanthoxylum simulans)
Cited by: 2
Author(s): Na Hou, Gang Wang, Shi Jing Feng, An Zhi Wei
Software Mentions: 1
Published: almost 9 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

10.1038/srep21602

Smad2 and Smad3 have differential sensitivity in relaying TGFβ signaling and inversely regulate early lineage specification
Cited by: 71
Author(s): Ling Liu, Xu Liu, Xudong Ren, Yuan Tian, Zhenyu Chen, Xiangjie Xu, Yanhua Du, Cizhong Jiang, Yujiang Fang, Zhongliang Liu, Beibei Fan, Quanbin Zhang, Guohua Jin, Xiao Yang, Xiaoqing Zhang
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22687

High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Cited by: 39
Author(s): Xuelin Zhao, Hong Yu, Lingfeng Kong, Shikai Liu, Qi Li
Software Mentions: 1
Published: over 10 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

10.1080/23802359.2017.1318683

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

10.1038/srep28637

DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
Cited by: 27
Author(s): Hao Kang Li, Ru-Tsun Mai, Hsien Da Huang, Chih‐Hung Chou, Yi-Chun Chang, Yao-Wen Chang, Li Ru You, Chun Ming Chen, Yan-Hwa Wu Lee
Software Mentions: 1
Published: over 10 years ago

10.1038/srep32479

Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs
Cited by: 74
Author(s): Weimin Wang, Chong Li, Fadi Li, Xiaojuan Wang, Xiaoxue Zhang, Ting Liu, Fang Nian, Xiangpeng Yue, Fĕi Li, Xiangyu Pan, Yongfu La, Futao Mo, Fangbin Wang, Baosheng Li
Software Mentions: 1
Published: about 10 years ago

10.1038/srep33510

Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets
Cited by: 30
Author(s): Sari Toropainen, Einari A. Niskanen, Marjo Malinen, Päivi Sutinen, Minna U. Kaikkonen, Jorma J. Palvimo
Software Mentions: 1
Published: about 10 years ago

10.1038/srep35873

Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase
Cited by: 25
Author(s): Hugo Mathé-Hubert, Dominique Colinet, Emeline Deleury, Maya Belghazi, Marc Ravallec, Julie Poulain, Carole Dossat, Marylène Poirié, Jean‐Luc Gatti
Software Mentions: 1
Published: about 10 years ago

10.1038/srep38228

MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii
Cited by: 22
Author(s): Xiang Gao, Fengge Zhang, Jinlu Hu, Wenkai Cai, Shengfang Ge, Dongsheng Dai, Kaiyao Huang, Gaohong Wang
Software Mentions: 1
Published: almost 10 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

10.1186/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

10.1038/srep39742

Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis
Cited by: 65
Author(s): Simon Rayner, Sören Bruhn, Helen Vallhov, Ann‐Catrin Andersson, R. Blake Billmyre, Annika Scheynius
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep40503

Genome-wide DNA methylation profile in mungbean
Cited by: 10
Author(s): Yang Jae Kang, Ahra Bae, Sangrea Shim, Taeyoung Lee, Jayern Lee, Dani Satyawan, Moon Young Kim, Suk-Ha Lee
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep40713

Global identification of microRNAs associated with chlorantraniliprole resistance in diamondback moth Plutella xylostella (L.)
Cited by: 26
Author(s): Bin Zhu, Xiuxia Li, Ying Liu, Xiwu Gao, Pei Liang
Software Mentions: 1
Published: almost 10 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

10.3390/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

10.1186/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

10.1590/0074-02760190498

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

DUXAP8, 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

10.1186/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

10.1007/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: almost 14 years ago

10.1038/srep04853

Characterization of limes (Citrus aurantifolia) grown in Bhutan and Indonesia using high-throughput sequencing
Cited by: 22
Author(s): Tshering Penjor, Takashi Mimura, Ryoji Matsumoto, Masashi Yamamoto, Yukio Nagano
Software Mentions: 1
Published: over 12 years ago

10.1038/srep45490

Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea
Cited by: 34
Author(s): Ashish Kumar Srivastava, Gaurav Sablok, Michael Hackenberg, Uday Deshpande, Penna Suprasanna
Software Mentions: 1
Published: over 9 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

10.1038/srep46578

Influenza C in Lancaster, UK, in the winter of 2014–2015
Cited by: 10
Author(s): Kate V. Atkinson, L.A. Bishop, Glenn Rhodes, Nicolas Salez, Neil R. 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 9 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

10.1155/2014/948408

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

10.1186/1471-2164-15-690

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

10.1038/s41598-017-02752-7

Chronic low-dose exposure to a mixture of environmental endocrine disruptors induces microRNAs/isomiRs deregulation in mouse concomitant with intratesticular estradiol reduction
Cited by: 27
Author(s): Julio Buñay, Eduardo Larriba, Ricardo D. Moreno, Jesús del Mazo
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-06255-3

Dynamic transcriptomic analysis of the early response of female flowers of Populus alba × P. glandulosa to pollination
Cited by: 4
Author(s): Pian Rao, Zhong Chen, Xiaoyu Yang, Kai Gao, Xiong Yang, Tianyun Zhao, Siyan Li, Bo Wu, Xinmin An
Software Mentions: 1
Published: over 9 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/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

10.3390/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

10.3390/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

10.1038/s41598-017-11752-6

Generation of a new mouse model of glaucoma characterized by reduced expression of the AP-2β and AP-2δ proteins
Cited by: 7
Author(s): Maria Monica Barzago, Mami Kurosaki, Maddalena Fratelli, Marco Bolis, Chiara Giudice, Laura Nordio, Elisa Cerri, Luciano Domenici, Mineko Terao, Enrico Garattini
Software Mentions: 1
Published: about 9 years ago

10.3390/biology9110358

Cloning of Thalassiosira pseudonana’s Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli
Cited by: 3
Author(s): Ryan R. Cochrane, Stephanie L. Brumwell, Arina Shrestha, Daniel J. Giguere, Samir Hamadache, Gregory B. Gloor, David R. Edgell, Bogumil J. Karas
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-14676-3

Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues
Cited by: 20
Author(s): Shinichi Hashimoto, Yuta Tabuchi, Hideaki Yurino, Yoshihiko Hirohashi, Shungo Deshimaru, Takuya Asano, Tasuku Mariya, Kenshiro Oshima, Yuzuru Takamura, Yoshiaki Ukita, Akio Ametani, Naoto Kondo, Norikazu Monma, Tomomi Takeda, Sadahiko Misu, Toshitugu Okayama, Kazuho Ikeo, Tsuyoshi Saito, Shuya Kaneko, Yutaka Suzuki, Masahira Hattori, Kouji Matsushima, Toshihiko Torigoe
Software Mentions: 1
Published: about 9 years ago

10.1093/bioinformatics/bts452

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
Cited by: 172
Author(s): Michaël Ryan, James Cleland, RyangGuk Kim, Wing Chung Wong, John N. Weinstein
Software Mentions: 1
Published: over 14 years ago

10.1093/bioinformatics/btv199

Cellular phenotype database: a repository for systems microscopy data
Cited by: 10
Author(s): Catherine Kirsanova, Alvis Brāzma, Gabriella Rustici, Ugis Sarkans
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-017-16546-4

STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array
Cited by: 73
Author(s): Hannah Hochgerner, Peter Lönnerberg, Rebecca D. Hodge, Jaromír Mikes, Abeer Heskol, Hermann Hubschle, Philip Lin, Simone Picelli, Gioele La Manno, Michael Ratz, Jude Dunne, Syed Akhtar Husain, Ed Lein, Maithreyan Srinivasan, Amit Zeisel, Sten Linnarsson
Software Mentions: 1
Published: almost 9 years ago

10.1186/1752-0509-6-S2-S14

MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues
Cited by: 35
Author(s): Sung‐Chou Li, Kuo‐Wang Tsai, Hung‐Wei Pan, Yung‐Ming Jeng, Meng‐Ru Ho, Wen-Hsiung Li
Software Mentions: 1
Published: almost 15 years ago

10.1186/1756-0500-2-257

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
Cited by: 5
Author(s): Nicolas Buisine, Laurent M. Sachs
Software Mentions: 1
Published: almost 18 years ago

10.1038/s41598-017-17852-7

Inferring evolutionary responses of Anolis carolinensis introduced into the Ogasawara archipelago using whole genome sequence data
Cited by: 6
Author(s): Satoshi Tamate, Watal M. Iwasaki, Kenneth L. Krysko, Brian J. Camposano, Hideaki Mori, Ryo Funayama, Keiko Nakayama, Takashi Makino, Masakado Kawata
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-18672-5

Respiratory Syncytial Virus Infection Changes Cargo Composition of Exosome Released from Airway Epithelial Cells
Cited by: 82
Author(s): Harendra Singh Chahar, Tiziana Corsello, Andrzej Kudlicki, Narayana Komaravelli, Antonella Casola
Software Mentions: 1
Published: almost 9 years ago

10.3390/cells10071757

FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes
Cited by: 7
Author(s): Miriam Pagin, Mattias Pernebrink, Mattia Pitasi, Federica Malighetti, Chew-Yee Ngan, Sergio Ottolenghi, Giulio Pavesi, Claudio Cantù, Silvia K. Nicolis
Software Mentions: 1
Published: over 5 years ago

10.1039/d0sc03509b

Single-nucleotide resolution of N6-adenine methylation sites in DNA and RNA by nitrite sequencing
Cited by: 21
Author(s): Yasaman Mahdavi‐Amiri, Kimberley Chung, Ryan Hili
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.stem.2017.09.004

Distinct Cell-Cycle Control in Two Different States of Mouse Pluripotency
Cited by: 61
Author(s): Menno ter Huurne, James Chappell, Stephen Dalton, Hendrik G. Stunnenberg
Software Mentions: 1
Published: about 9 years ago

10.1016/j.celrep.2014.11.033

Rfx6 Maintains the Functional Identity of Adult Pancreatic β Cells
Cited by: 106
Author(s): Julie Piccand, Perrine Strasser, David J. Hodson, A. Meunier, Tao Ye, Céline Keime, Marie‐Christine Birling, Guy A. Rutter, Gérard Gradwohl
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41419-021-03636-5

A family harboring an MLKL loss of function variant implicates impaired necroptosis in diabetes
Cited by: 21
Author(s): Joanne M Hildebrand, Bernice Lo, Sara Tomei, Valentina Di Mattei, Samuel N. Young, Cheree Fitzgibbon, James M. Murphy, Abeer A. Fadda
Software Mentions: 1
Published: over 5 years ago

10.1186/s13148-021-01134-1

Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus
Cited by: 5
Author(s): E Slot, Ruben Boers, Joachim Boers, Wilfred F. J. van IJcken, Dick Tibboel, Joost Gribnau, Robbert J. Rottier, Annelies de Klein
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-019-1964-8

Stromal cells downregulate miR-23a-5p to activate protective autophagy in acute myeloid leukemia
Cited by: 28
Author(s): Saravanan Ganesan, Hamenth Kumar Palani, Vairavan Lakshmanan, Nithya Balasundaram, Ansu Abu Alex, Sachin David, Arvind Venkatraman, Anu Korula, Biju George, Poonkuzhali Balasubramanian, Dasaradhi Palakodeti, Neha Vyas, Vikram Mathews
Software Mentions: 1
Published: about 7 years ago

10.1016/j.cell.2012.06.018

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans
Cited by: 663
Author(s): Alyson Ashe, Alexandra Sapetschnig, Eva-Maria Weick, Jacinth Mitchell, Marloes P. Bagijn, Amy Cording, Anna-Lisa Doebley, Leonard D. Goldstein, Nicolas J Lehrbach, Jérémie Le Pen, Greta Pintacuda, Aisa Sakaguchi, Peter Sarkies, Shawn Ahmed, Eric A. Miska
Software Mentions: 1
Published: over 14 years ago

10.3390/cancers11020209

Metformin Treatment Suppresses Melanoma Cell Growth and Motility Through Modulation of microRNA Expression
Cited by: 49
Author(s): Hui‐Wen Tseng, Sung‐Chou Li, Kuo‐Wang Tsai
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0172721

Identification of the ER-resident E3 ubiquitin ligase RNF145 as a novel LXR-regulated gene
Cited by: 20
Author(s): Emma C. L. Cook, Jessica K. Nelson, Vincenzo Sorrentino, Duco S. Koenis, Martina Moeton, Saskia Scheij, Roelof Ottenhoff, Boris Bleijlevens, Anke Loregger, Noam Zelcer
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0088462

De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
Cited by: 108
Author(s): Cláudio Benício Cardoso-Silva, Everardo Andrade da Costa, Melina Cristina Mancini, Thiago Willian Almeida Balsalobre, Lucas Eduardo Costa Canesin, Luciana Rossini Pinto, Monalisa Sampaio Carneiro, Antônio Augusto Franco Garcia, Anete Pereira de Souza, Renato Vicentini
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0169242

Generation of a Stable Transgenic Swine Model Expressing a Porcine Histone 2B-eGFP Fusion Protein for Cell Tracking and Chromosome Dynamics Studies
Cited by: 12
Author(s): Renan Sper, Sehwon Koh, Xia Zhang, Sean Simpson, Bruce Collins, Jeff Sommer, Robert M. Petters, Ignacio Caballero, Jeffrey L. Platt, Jorge A. Piedrahita
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0107365

Vernalization Mediated Changes in the Lolium perenne Transcriptome
Cited by: 17
Author(s): Cristiana Paina, Stephen Byrne, C. Domnisoru, Torben Asp
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0158846

Analysis of Genetic Variation across the Encapsidated Genome of Microplitis demolitor Bracovirus in Parasitoid Wasps
Cited by: 3
Author(s): Gaelen R. Burke
Software Mentions: 1
Published: over 10 years ago

10.1186/1756-0500-5-275

BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data
Cited by: 6
Author(s): Peter E. Larsen, F. Collart
Software Mentions: 1
Published: over 14 years ago

10.1038/s42003-020-01525-9

Natural epialleles of Arabidopsis SUPERMAN display superwoman phenotypes
Cited by: 9
Author(s): Ramesh Bondada, Saravanakumar Somasundaram, Mohan Premanand Marimuthu, Mohammed Afsal Badarudeen, Vaishak Kanjirakol Puthiyaveedu, Maruthachalam Ravi
Software Mentions: 1
Published: almost 6 years ago

10.1038/s42003-019-0500-9

Genome assembly of Nannochloropsis oceanica provides evidence of host nucleus overthrow by the symbiont nucleus during speciation
Cited by: 26
Author(s): Li Guo, Sijie Liang, Zhongyi Zhang, Huan Liu, Songwen Wang, Kehou Pan, Jian Xu, Xue Ren, Surui Pei, Guanpin Yang
Software Mentions: 1
Published: over 7 years ago

10.1038/s42003-020-01125-7

Improving the diversity of captured full-length isoforms using a normalized single-molecule RNA-sequencing method
Cited by: 8
Author(s): Yueming Hu, Xing-sheng Shu, Jiaxian Yu, Ming-an Sun, Zewei Chen, Xianming Liu, Qiongfang Fang, Wei Zhang, Xinjie Hui, Ying Ying, Li Fu, Desheng Lu, Rakesh Kumar, Yejun Wang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0040366

Prevalence and Clinical Features of Hearing Loss Patients with CDH23 Mutations: A Large Cohort Study
Cited by: 55
Author(s): Maiko Miyagawa, Shin‐ya Nishio, Shin‐ichi Usami
Software Mentions: 1
Published: over 14 years ago

10.1186/1753-6561-8-S4-P96

Advancing palm genomics by developing a high-density battery of molecular markers for Elaeis oleifera for future downstream applications
Cited by: 0
Author(s): Alexandre Alonso Alves, Valquíria Martins Pereira, André Pereira Leão, Eduardo Fernandes Formigheri, Guy de Capdeville, Manoel Teixeira Souza Júnior
Software Mentions: 1
Published: about 12 years ago

10.1038/s42003-019-0519-y

Amplification-free library preparation with SAFE Hi-C uses ligation products for deep sequencing to improve traditional Hi-C analysis
Cited by: 16
Author(s): Longjian Niu, Wei Shen, Yingzhang Huang, Na He, Yuedong Zhang, Jialei Sun, Wan J, Daxin Jiang, Manyun Yang, Yu Chung Tse, Li Li, Chaoqi Hou
Software Mentions: 1
Published: over 7 years ago

10.1038/s42003-019-0563-7

Adipocyte metabolism is improved by TNF receptor-targeting small RNAs identified from dried nuts
Cited by: 43
Author(s): Katia Aquilano, Veronica Ceci, Angelo Gismondi, Susanna De Stefano, Federico Iacovelli, Raffaella Faraonio, Gabriele Di Marco, Noemi Poerio, Antonella Minutolo, Giuseppina Minopoli, Antonia Marcone, Maurizio Fraziano, Flavia Tortolici, Simona Sennato, Stefano Casciardi, Marina Potestà, Roberta Bernardini, Maurizio Mattei, Mattia Falconi, Carla Montesano, Stefano Rufini, Antonella Canini, Daniele Lettieri Barbato
Software Mentions: 1
Published: about 7 years ago

10.1080/19420889.2020.1776568

Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms
Cited by: 6
Author(s): Takuro Nakayama, Kazuya Takahashi, Ryoma Kamikawa, Mitsunori Iwataki, Yuji Inagaki, Goro Tanifuji
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0167088

Determination of a Screening Metric for High Diversity DNA Libraries
Cited by: 0
Author(s): Nicholas Guido, Steven Handerson, Elaine M. Joseph, Devin Leake, Li Kung
Software Mentions: 1
Published: almost 10 years ago

10.1093/dnares/dsw008

Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling
Cited by: 68
Author(s): Kenji Nakahigashi, Yuki Takai, Michiko Kimura, Nozomi Abe, Toru Nakayashiki, Yuh Shiwa, Hideki Yoshikawa, Barry L. Wanner, Yasushi Ishihama, Hirotada Mori
Software Mentions: 1
Published: over 10 years ago

10.1016/j.dib.2018.12.042

Data of de novo assembly and functional annotation of the leaf transcriptome of Impatiens balsamina
Cited by: 1
Author(s): Lian Chee Foong, Anthony Siong Hock Ho, Brandon Pei Hui Yeo, Yang Mooi Lim, Sheh May Tam
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0090859

Circular RNA Is Expressed across the Eukaryotic Tree of Life
Cited by: 533
Author(s): Peter L. Wang, Yun Bao, Muh-Ching Yee, Steven P. Barrett, Gregory J. Hogan, Mari Olsen, José R. Dinneny, Patrick O. Brown, Julia Salzman
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-018-21268-2

Comparative transcriptomics provides novel insights into the mechanisms of selenium tolerance in the hyperaccumulator plant Cardamine hupingshanensis
Cited by: 37
Author(s): Yang Zhou, Tang Qiao-yu, Meiru Wu, Di Mou, Hui Liu, Shouchuang Wang, Chi Zhang, Ding Li, Jie Luo
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12870-021-03136-w

Integrated ionomic and transcriptomic dissection reveals the core transporter genes responsive to varying cadmium abundances in allotetraploid rapeseed
Cited by: 3
Author(s): Ting Zhou, Caipeng Yue, Tianyu Zhang, Ying Liu, Jinyong Huang, Yingpeng Hua
Software Mentions: 1
Published: over 5 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

10.3389/fmicb.2019.00083

milR4 and milR16 Mediated Fruiting Body Development in the Medicinal Fungus Cordyceps militaris
Cited by: 18
Author(s): Ying Shao, Jin Tang, Shanglong Chen, Yonghua Wu, Kun Wang, Bin Ma, Qun Zhou, Anhui Chen, Yulong Wang
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0158142

Mining and Analysis of SNP in Response to Salinity Stress in Upland Cotton (Gossypium hirsutum L.)
Cited by: 10
Author(s): Xiaoge Wang, Xuke Lu, Junjuan Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Wuwei Ye
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2016.01977

Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters
Cited by: 10
Author(s): Gleb Y. Fisunov, Irina Garanina, Daria V. Evsyutina, Tatiana A. Semashko, Anastasia S. Nikitina, Vadim M. Govorun
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-018-24515-8

Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map
Cited by: 12
Author(s): Thomas J. Hardcastle, Sebastian Müller, David C. Baulcombe
Software Mentions: 1
Published: over 8 years ago

10.1186/s12870-015-0553-y

Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons
Cited by: 27
Author(s): Anne V. Brown, Karen A. Hudson
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0136383

MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata
Cited by: 10
Author(s): Xiaolu Wang, Danqing Yin, Peng Li, Shaowu Yin, Li Wang, Yong Jia, Xinhua Shu
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0227749

Molecular and biological analysis revealed genetic diversity and high virulence strain of Toxoplasma gondii in Japan
Cited by: 6
Author(s): Junpei Fukumoto, Akinori Yamano, Motomichi Matsuzaki, Hisako Kyan, Tsutomu Matsui, Tomohide Matsuo, Toshihiro Matsui, Mami Murakami, Yasuhiro Takashima, Ryuma Matsubara, Michiru Tahara, Takaya Sakura, Fumihiko Takeuchi, Kisaburo Nagamune
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2017.00858

The Mechanism of Starch Over-Accumulation in Chlamydomonas reinhardtii High-Starch Mutants Identified by Comparative Transcriptome Analysis
Cited by: 26
Author(s): Kwang Min Koo, Sera Jung, Beom S. Lee, Jin Baek Kim, Yeong Deuk Jo, Hong Il Choi, Si Yong Kang, Gook Hyun Chung, Won Joong Jeong, Joon-Woo Ahn
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0022544

Integrated Expression Profiling and Genome-Wide Analysis of ChREBP Targets Reveals the Dual Role for ChREBP in Glucose-Regulated Gene Expression
Cited by: 123
Author(s): Yun Seung Jeong, Deokhoon Kim, Yong Seok Lee, Ha Jung Kim, Jung Youn Han, Seung Soon Im, Hansook Kim Chong, Je Keun Kwon, Yun Ho Cho, Woo Kyung Kim, Timothy F. Osborne, Jay D. Horton, Hee-Sook Jun, Yeon Soon Ahn, Sung Min Ahn, Jung Han Young
Software Mentions: 1
Published: over 15 years ago

10.3389/fmicb.2017.00270

Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells
Cited by: 24
Author(s): Andreas Dix, Kristin Czakai, Ines Leonhardt, Karin Schäferhoff, Michael Bonin, Reinhard Guthke, Hermann Einsele, Oliver Kurzai, Jürgen Löffler, Jörg Linde
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0116528

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing
Cited by: 28
Author(s): Modhumita Ghosh Dasgupta, Veeramuthu Dharanishanthi, Ishangi Agarwal, Konstantin V. Krutovsky
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0114612

Genome-Wide Identification of Different Dormant Medicago sativa L. MicroRNAs in Response to Fall Dormancy
Cited by: 18
Author(s): Wenna Fan, Senhao Zhang, Hao Du, Xuejun Sun, Shi Ya, Chengzhang Wang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0050013

Function Annotation of Hepatic Retinoid x Receptor α Based on Genome-Wide DNA Binding and Transcriptome Profiling
Cited by: 10
Author(s): Qimin Zhan, Yaping Fang, Yuqi He, Hui‐Xin Liu, Jianwen Fang, Yu‐Jui Yvonne Wan
Software Mentions: 1
Published: almost 14 years ago

Projects: pypi: bowtie

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Papers Mentioning bowtie 1,566