pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-49886-4

The Human Papillomavirus (HPV) E1 protein regulates the expression of cellular genes involved in immune response
Cited by: 23
Author(s): Leonardo Josué Castro-Muñoz, Joaquín Manzo-Merino, J. Omar Muñoz-Bello, Leslie Olmedo-Nieva, Alberto Cedro‐Tanda, Luis Alfaro-Ruiz, Alfredo Hidalgo-Miranda, Vicente Madrid‐Marina, Marcela Lizano
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-51470-9

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules
Cited by: 77
Author(s): Camille Sessegolo, Corinne Cruaud, Corinne Da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien, Vincent Lacroix, Jean‐Marc Aury
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-51984-2

Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
Cited by: 35
Author(s): Aikaterini Alexaki, Gaya Hettiarachchi, John C. Athey, Upendra Katneni, Vijaya L. Simhadri, Nobuko Hamasaki-Katagiri, Puja Nanavaty, Brian C. Lin, Kazuyo Takeda, Darón I. Freedberg, Dougald M. Monroe, Joseph R. McGill, Robert Peters, Jacob Kames, David D. Holcomb, Ryan Hunt, Zuben E. Sauna, Amy D. Gelinas, Nebojša Janjić, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-56030-9

Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation
Cited by: 6
Author(s): Matthew Moran, Xiangdong Cheng, Mohamed Sham Shihabudeen Haider Ali, Nishikant Wase, Nghi M. Nguyen, Wenchao Yang, Chi Zhang, Concetta C. DiRusso, Xinghui Sun
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-59678-w

PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of multiple mRNAs
Cited by: 7
Author(s): Astrid Haas, Benedikt S. Nilges, Sebastian A. Leidel, Karl‐Heinz Klempnauer
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-73549-4

Assembly of the durian chloroplast genome using long PacBio reads
Cited by: 10
Author(s): Jeremy R. Shearman, Chutima Sonthirod, Chaiwat Naktang, Duangjai Sangsrakru, Thippawan Yoocha, Ratchanee Chatbanyong, Siriporn Vorakuldumrongchai, O. Chusri, Sithichoke Tangphatsornruang, Wirulda Pootakham
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-81637-2

Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics
Cited by: 4
Author(s): Wei Fu, Pengyu Zhu, Mingnan Qu, Zhi Wang, Yongjiang Zhang, Feiwu Li, Shuifang Zhu
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-89672-9

Osteocytes as main responders to low-intensity pulsed ultrasound treatment during fracture healing
Cited by: 18
Author(s): Tatsuya Shimizu, Naomasa Fujita, Kiyomi Tsuji‐Tamura, Yoshimasa Kitagawa, Toshiaki Fujisawa, Masato Tamura, Mari Sato
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90270-y

Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination
Cited by: 4
Author(s): Mei Mei, Jun S. Wei, Wanfeng Ai, Lijie Zhang, Xiujun Lu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-92832-6

Transcriptome analysis insight into ethylene metabolism and pectinase activity of apricot (Prunus armeniaca L.) development and ripening
Cited by: 1
Author(s): Min Xu, Weiquan Zhou, Geng WenJuan, Shirong Zhao, Yan Pan, Guoquan Fan, Shikui Zhang, Yatong Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-95779-w

Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions
Cited by: 5
Author(s): Mohammad Vatanparast, Robert T. Puckett, Deuk‐Soo Choi, Youngjin Park
Software Mentions: 2
Published: about 5 years ago

10.1186/s40064-016-2902-1

Comparative profiling of differentially expressed microRNAs between the follicular and luteal phases ovaries of goats
Cited by: 10
Author(s): Long Zhu, Tao Chen, Menghua Sui, Chunyang Han, Fugui Fang, Yuehui Ma, Mingxing Chu, Xiaorong Zhang, Cuiyan Liu, Yinghui Ling
Software Mentions: 2
Published: over 10 years ago

10.1016/j.stemcr.2016.11.014

Cytosine-5 RNA Methylation Regulates Neural Stem Cell Differentiation and Motility
Cited by: 118
Author(s): Joana V. Flores, Lucía Cordero-Espinoza, Feride Oeztuerk-Winder, Amanda Andersson-Rolf, Tommaso Selmi, Sandra Blanco, Jignesh Tailor, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13287-015-0116-z

Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species
Cited by: 559
Author(s): S. Rubina Baglio, Koos Rooijers, Danijela Koppers-Lalić, Frederik J. Verweij, M Pérez Lanzón, Nicoletta Zini, B.A. Naaijkens, Francesca Perut, Hans W.M. Niessen, Nicola Baldini, D. Michiel Pegtel
Software Mentions: 2
Published: over 11 years ago

10.7150/thno.43577

Exercise protects proliferative muscle satellite cells against exhaustion via the Igfbp7-Akt-mTOR axis
Cited by: 24
Author(s): Zhe Chen, Lei Li, Weiru Wu, Zhilong Liu, Yongxiu Huang, Li Yang, Qing Luo, Jieping Chen, Yu Hou, Guanbin Song
Software Mentions: 2
Published: almost 7 years ago

10.3390/toxins12010041

Aberrant Expressional Profiling of Known MicroRNAs in the Liver of Silver Carp (Hypophthalmichthys molitrix) Following Microcystin-LR Exposure Based on samllRNA Sequencing
Cited by: 6
Author(s): Yiyi Feng, Xi Chen, Jing Ma, Bangjun Zhang, Xiaoyü Li
Software Mentions: 2
Published: almost 7 years ago

10.1101/2020.11.16.385278

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
Cited by: 8
Author(s): Meghan Garrett, Jared Galloway, Helen Y. Chu, Hannah L. Itell, Caitlin I. Stoddard, Caitlin R Wolf, Jennifer K. Logue, Dylan McDonald, F. A. Matsen, Julie Overbaugh
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.02027-20

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses
Cited by: 32
Author(s): Jillian M. Myers, Anne E. Bonds, Rebecca A. Clemons, Natasha Thapa, D. Rabern Simmons, Derreck Carter-House, Jericho Ortañez, P. Liu, Alejandro Miralles-Durán, Alessandro Desirò, Joyce E. Longcore, Gregory Bonito, Jason E. Stajich, J. W. Spatafora, Ying Chang, Luis M. Corrochano, Andrii P. Gryganskyi, Igor V. Grigoriev, Timothy Y. James
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.03649-20

Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress
Cited by: 2
Author(s): Quinten Deparis, Jorge Duitama, María R. Foulquié-Moreno, Johan M. Thevelein
Software Mentions: 2
Published: over 5 years ago

10.1128/mSphere.00855-20

Structured RNA Contaminants in Bacterial Ribo-Seq
Cited by: 15
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: about 6 years ago

10.1128/mSystems.00673-19

Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus <i>Sulfurovum</i> in Geographically Distinct Deep-Sea Hydrothermal Vents
Cited by: 33
Author(s): Alief Moulana, R. Anderson, Caroline S. Fortunato, Julie A. Huber
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.01078-20

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
Cited by: 61
Author(s): Vojtěch Tláskal, Vendula Brabcová, Tomáš Větrovský, Mayuko Jomura, Rubén López-Mondéjar, Lummy Maria Oliveira Monteiro, J. Saraiva, Zander Rainier Human, Tomáš Cajthaml, Ulisses Nunes da Rocha, Petr Baldrián
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00704-21

Identification and Differentiation of Pseudomonas Species in Field Samples Using an <i>rpoD</i> Amplicon Sequencing Methodology
Cited by: 9
Author(s): Jonas Greve Lauritsen, Morten Lindqvist Hansen, Pernille Kjersgaard Bech, Lars Jelsbak, Lone Gram, Mikael Lenz Strube
Software Mentions: 2
Published: about 5 years ago

10.1093/hmg/ddy405

Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy
Cited by: 46
Author(s): Christopher R. S. Banerji, Maryna Panamarova, Johanna Prüller, Nicolas Figeac, Husam Hebaishi, Efthymios Fidanis, Alka Saxena, Julian Contet, Sabrina Sacconi, Simone Severini, Peter S. Zammit
Software Mentions: 2
Published: almost 8 years ago

10.1155/2015/527054

Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars
Cited by: 2
Author(s): Yan Wei, Jing Wang, Youxiang Zhou, Mingming Zhao, Yan Gong, Hua Ding, Lijun Peng, HU Ding-jin
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41388-018-0530-7

Acetylation of AGO2 promotes cancer progression by increasing oncogenic miR-19b biogenesis
Cited by: 50
Author(s): Hailong Zhang, Yanli Wang, Jinzhuo Dou, Yanmin Guo, Jianfeng He, Lian Li, Xiaojia Liu, Ran Chen, Rong Deng, Jian Huang, Ruiyu Xie, Xian Zhao, Jianxiu Yu
Software Mentions: 2
Published: about 8 years ago

10.1038/s41389-020-0205-4

Post-transcriptional regulation of BRG1 by FIRΔexon2 in gastric cancer
Cited by: 9
Author(s): Guzhanuer Ailiken, Kazuo Kïtamura, Tyuji Hoshino, Mamoru Satoh, Nobuko Tanaka, Toshinari Minamoto, Bahityar Rahmutulla, Sohei Kobayashi, Masayuki Kano, Tomoaki Tanaka, Atsushi Kaneda, Fumio Nomura, Hisahiro Matsubara, Hiroshi Matsushita
Software Mentions: 2
Published: over 6 years ago

10.3892/or.2019.7300

In�vivo effects of mutant RHOA on tumor formation in an orthotopic inoculation model
Cited by: 2
Author(s): Takashi Nishizawa, Kiyotaka Nakano, Etsuko Fujii, Daisuke Komura, Yoshie Kuroiwa, Chisako Ishimaru, Makoto Monnai, Hiroyuki Aburatani, Shumpei Ishikawa, Masami Suzuki
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.48725

Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb
Cited by: 21
Author(s): Joshua E. Mayfield, Seema Irani, Edwin E. Escobar, Zhao Zhang, Nathaniel T. Burkholder, Michelle Robinson, M. Rachel Mehaffey, Sarah N. Sipe, Weiwei Yang, Nicholas Adrian Prescott, Karan R. Kathuria, Zhijie Liu, Jennifer S. Brodbelt, Yan Zhang
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.06205

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse
Cited by: 142
Author(s): Marco Morselli, William A. Pastor, Barbara Montanini, Kevin Nee, Roberto Ferrari, Kai Fu, Giancarlo Bonora, Liudmilla Rubbi, Amander T. Clark, Simone Ottonello, Steven E. Jacobsen, Matteo Pellegrini
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.29938

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth
Cited by: 47
Author(s): Zheng Kuang, Sudarshan Pinglay, Hongkai Ji, Jef D. Boeke
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.06722

Quality control of transcription start site selection by nonsense-mediated-mRNA decay
Cited by: 105
Author(s): Christophe Malabat, Frank Feuerbach, Laurence Ma, Cosmin Saveanu, Alain Jacquier
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.09003

A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver
Cited by: 32
Author(s): Miyuki Suzawa, Diego A. Miranda, Karmela A Ramos, Kenny K-H Ang, Emily J. Faivre, Christopher G. Wilson, Laura Caboni, Michelle R. Arkin, Yeong-Sang Kim, Robert J. Fletterick, Aaron A. Diaz, John S. Schneekloth, Holly A. Ingraham
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.52212

MS-275, a class 1 histone deacetylase inhibitor augments glucagon-like peptide-1 receptor agonism to improve glycemic control and reduce obesity in diet-induced obese mice
Cited by: 9
Author(s): Shilpak Dilip Bele, Shravan Babu Girada, Arnab Ray, Abhishek Gupta, Srinivas Oruganti, Phanithi Prakash Babu, Rahul Sr Rayalla, Shashi Vardhan Kalivendi, Ahamed Ibrahim, Vishwajeet Puri, Venkateswar Adalla, Madhumohan R. Katika, Richard D. DiMarchi, Prasenjit Mitra
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.21615

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells
Cited by: 33
Author(s): Debjani Pal, Anja Pertot, Nitin H. Shirole, Zhan Yao, Naishitha Anaparthy, Tyler Garvin, Hilary Cox, Kenneth Chang, Fred Rollins, Jude Kendall, Leyla Edwards, Vijay A Singh, Gary C. Stone, Michael C. Schatz, James Hicks, Gregory J. Hannon, Raffaella Sordella
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.18270

MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs
Cited by: 74
Author(s): C. David Wood, Hildegonda Veenstra, Sarika Khasnis, Andrea Gunnell, Helen Webb, Claire Shannon-Lowe, Simon Andrews, Cameron S. Osborne, Michelle J. West
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.67236

High-resolution, genome-wide mapping of positive supercoiling in chromosomes
Cited by: 27
Author(s): Monica S. Guo, Ryo Kawamura, Megan L Littlehale, John F. Marko, Michael T. Laub
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.06068

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch
Cited by: 85
Author(s): Benjamin Rauwel, Suk Min Jang, Marco Cassano, Adamandia Kapopoulou, Isabelle Barde, Didier Trono
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.57858

Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen
Cited by: 21
Author(s): Hao Zhang, Yang Zhang, Xinyue Zhou, Shaela Wright, Judith Hyle, Lianzhong Zhao, Jie An, Xujie Zhao, Ying Shao, Beisi Xu, Hyeong-Min Lee, Taosheng Chen, Yang Zhou, Xiang Chen, Rui Lu, Chunliang Li
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.62994

The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions
Cited by: 54
Author(s): Thierry Halter, Jingyu Wang, Delase Amesefe, Emmanuelle Lastrucci, Magali Charvin, Meenu Singla Rastogi, Lionel Navarro
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.33361

G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst
Cited by: 27
Author(s): J. Ż̷ylicz, Maud Borensztein, Frederick C K Wong, Yun Huang, Caroline Lee, Sabine Dietmann, M. Azim Surani
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.11275

Comparative analysis of viral RNA signatures on different RIG-I-like receptors
Cited by: 79
Author(s): Raul Y. Sanchez David, Chantal Combredet, Odile Sismeiro, Marie‐Agnès Dillies, Bernd Jagla, Jean‐Yves Coppée, Marie Mura, Mathilde Guerbois Galla, Philippe Desprès, Frédéric Tangy, Anastassia V. Komarova
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.17548

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage
Cited by: 208
Author(s): Caroline Townsend Stork, M Bocek, Madzia P Crossley, Julie Sollier, Lionel A. Sanz, Frédéric Chédin, Tomek Swigut, Karlene A. Cimprich
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-015-2025-z

Combined ultra-low input mRNA and whole-genome sequencing of human embryonic stem cells
Cited by: 4
Author(s): Florián Mertes, Björn Lichtner, Heiner Kuhl, Mirjam Blattner, Jörg Otte, Wasco Wruck, Bernd Timmermann, Hans Lehrach, James Adjaye
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0151826

A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads
Cited by: 1
Author(s): Hong T. Tran, Xiaowei Wu, Saima Sultana Tithi, Miao‐Kun Sun, Hehuang Xie, Liqing Zhang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0024883

A Comprehensive Expression Profile of MicroRNAs in Porcine Pituitary
Cited by: 22
Author(s): Hongyi Li, Qianyun Xi, Yuanyan Xiong, Xiao Cheng, Qien Qi, Lin Yang, Gang Shu, Lina Wang, Ping Gao, Xiaotong Zhu, Qingyan Jiang, Yongliang Zhang, Yuan Li
Software Mentions: 1
Published: about 15 years ago

10.1534/g3.114.015735

Developmental Analysis of Spliceosomal snRNA Isoform Expression
Cited by: 19
Author(s): Zhipeng Lu, A. Gregory Matera
Software Mentions: 1
Published: almost 12 years ago

10.1534/g3.115.020552

Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat
Cited by: 9
Author(s): Xidan Li, Xiaodong Liu, Javad Nadaf, Elisabeth Le Bihan‐Duval, Cécile Berri, Ian Dunn, Richard Talbot, Dirk-Jan de Koning
Software Mentions: 1
Published: about 11 years ago

10.1534/g3.115.020578

Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms
Cited by: 60
Author(s): Darin R. Rokyta, Mark J. Margres, Kate Calvin
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-14-S1-S2

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing
Cited by: 46
Author(s): Chih Hung Chou, Feng Lin, Min Te Chou, Sheng Da Hsu, Tzu Hao Chang, Shun Long Weng, Sirjana Shrestha, Chiung Chih Hsiao, Jui Hung Hung, Hsien Da Huang
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0173238

RNA-Seq analysis of salinity stress–responsive transcriptome in the liver of spotted sea bass (Lateolabrax maculatus)
Cited by: 56
Author(s): Xiaoyan Zhang, Haishen Wen, Hailiang Wang, Yuanyuan Ren, Ji Zhao, Yun Li
Software Mentions: 1
Published: over 9 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

10.1186/1471-2105-14-31

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

10.1186/1471-2105-13-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

10.1371/journal.pone.0166770

Intraluminal Flagellin Differentially Contributes to Gut Dysbiosis and Systemic Inflammation following Burn Injury
Cited by: 16
Author(s): Logan Grimes, Allie Doyle, Aaron L. Miller, Richard B. Pyles, Gábor Oláh, Csaba Szabó, Sarah Hoskins, Tonyia Eaves-Pyles
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0072781

Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population
Cited by: 7
Author(s): Yoshinori Taniguchi, Hideaki Matsuda, Takahisa Yamada, Toshie Sugiyama, Kosuke Homma, Yoshinori Kaneko, Satoshi Yamagishi, Hiroaki Iwaisaki
Software Mentions: 1
Published: about 13 years ago

10.1186/s12864-017-3871-7

Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
Cited by: 74
Author(s): Jingjing Jin, Hui Zhang, Jianfeng Zhang, Pingping Li, Xia Chen, Zefeng Li, Yalong Xu, Ping Lu, Peijian Cao
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0184917

Comparative analysis of miRNAs of two rapeseed genotypes in response to acetohydroxyacid synthase-inhibiting herbicides by high-throughput sequencing
Cited by: 2
Author(s): Meijiao Hu, Pu Huang, Jianqin Gao, Wei Long, Feng Chen, Wei Zhang, Xiaoyin Zhou, Qi Peng, Song Chen, Jiefu Zhang
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-2869-x

The highly expressed 5’isomiR of hsa-miR-140-3p contributes to the tumor-suppressive effects of miR-140 by reducing breast cancer proliferation and migration
Cited by: 81
Author(s): Omar Salem, Nese Erdem, Janine Jung, Ewald Münstermann, Angelika Wörner, Heike Wilhelm, Stefan Wiemann, Cindy Körner
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0028318

Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq
Cited by: 27
Author(s): Geng Chen, Kangping Yin, Leming Shi, Yunzhang Fang, Ya Qi, Peng Li, Jian Luo, Bing He, Mingyao Liu, Tieliu Shi
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0171566

Comparison of whole genome amplification techniques for human single cell exome sequencing
Cited by: 59
Author(s): Erik Borgström, Marta Paterlini, Jeff E. Mold, Jonas Frisén, Joakim Lundeberg
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0255914

Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
Cited by: 6
Author(s): M. Ardhaoui, Emna Ennaifer, Anna Christina de Matos Salim, Flávio Marcom Gomez, T. Laasili, Mohamed Samir Boubaker, Ikram Guizani
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0129190

p53 Represses the Oncogenic Sno-MiR-28 Derived from a SnoRNA
Cited by: 52
Author(s): Yu Feng, Cameron P. Bracken, Katherine A. Pillman, David Lawrence, Gregory J. Goodall, David F. Callen, Paul M. Neilsen
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0054950

Human Trace Amine-Associated Receptor TAAR5 Can Be Activated by Trimethylamine
Cited by: 93
Author(s): Ivonne Wallrabenstein, Jonas Kuklan, Lea Weber, Sandra Zborala, Markus Werner, Janine Altmüller, Christian Becker, Anna Schmidt, Hanns Hatt, Thomas Hummel, Günter Gisselmann
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0206110

Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1
Cited by: 8
Author(s): Jeffrey W. Mercante, Jason Caravas, Maliha K. Ishaq, Natalia A. Kozak-Muiznieks, Brian Raphael, Jonas M. Winchell
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0007480

Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing
Cited by: 17
Author(s): Kyoko Hayashida, Yasuko Orba, Patrícia Carvalho de Sequeira, Chihiro Sugimoto, William W. Hall, Yuki Eshita, Yutaka Suzuki, Lucky Ronald Runtuwene, Patrícia Brasil, Guilherme Amaral Calvet, Cíntia D. S. Rodrigues, Carolina Cardoso dos Santos, Maria Angélica Monteiro de Mello Mares-Guia, Junya Yamagishi, Ana María Bispo de Filippis, Hirofumi Sawa
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-13-S7-S18

Comprehensive analysis of microRNAs in breast cancer
Cited by: 37
Author(s): Hong‐Tai Chang, Sung‐Chou Li, Meng‐Ru Ho, Hung‐Wei Pan, Luo‐Ping Ger, Ling-Yueh Hu, Shou‐Yu Yu, Wen-Hsiung Li, Kuo‐Wang Tsai
Software Mentions: 1
Published: almost 14 years ago

10.3390/genes10010044

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads
Cited by: 2
Author(s): Wenjing Zhang, Ning Huang, Juanjuan Zheng, Xingyu Liao, Jianxin Wang, Hongdong Li
Software Mentions: 1
Published: almost 8 years ago

10.3390/genes10020137

DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola
Cited by: 45
Author(s): Shenglin Liu, Anne Aageaard, Jesper Bechsgaard, Trine Bilde
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-021-07896-5

Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits
Cited by: 2
Author(s): Jing Jing, Xichun Jiang, Cuiyun Zhu, Qi Zheng, Qianyun Ji, Huiqun Yin, Jingtong Huang, Yixiao Zhu, Jiao Wang, Shuaiqi Qin, Yinghui Ling
Software Mentions: 1
Published: over 5 years ago

10.3390/genes10020116

Comparison of the Transcriptomes and Proteomes of Serum Exosomes from Marek’s Disease Virus-Vaccinated and Protected and Lymphoma-Bearing Chickens
Cited by: 23
Author(s): Sabari Nath Neerukonda, Phaedra Tavlarides-Hontz, Fiona M. McCarthy, Kenneth Pendarvis, Mark S. Parcells
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0002489

Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains
Cited by: 103
Author(s): Didier Ménard, E. Ricky Chan, Christophe Benedet, Arsène Ratsimbasoa, Saorin Kim, Pheaktra Chim, Catherine Do, Benoît Witkowski, Rémy Durand, Marc Thellier, Carlo Severini, Eric Legrand, Lise Musset, Bakri Y. M. Nour, Odile Mercereau–Puijalon, David Serre, Peter A. Zimmerman
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-019-6154-7

Detecting circular RNA from high-throughput sequence data with de Bruijn graph
Cited by: 9
Author(s): Xin Li, Yufeng Wu
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.59974

Ribosome recycling is not critical for translational coupling in Escherichia coli
Cited by: 15
Author(s): Kazuki Saito, Rachel Green, Allen R. Buskirk
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-018-4484-5

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)
Cited by: 71
Author(s): Mahmoud W. Yaish, Ali H. Al-Lawati, Ibtisam Al-Harrasi, Himanshu V. Patankar
Software Mentions: 1
Published: almost 9 years ago

10.3390/genes11101126

The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized
Cited by: 25
Author(s): Luohao Xu, Qi Zhou
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1003697

Masculinization of Gene Expression Is Associated with Exaggeration of Male Sexual Dimorphism
Cited by: 106
Author(s): Marie A. Pointer, Peter W. Harrison, Alison E. Wright, Judith E. Mank
Software Mentions: 1
Published: about 13 years ago

10.1186/s12864-016-2414-y

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells
Cited by: 50
Author(s): Michelle Gonzales-Cope, Simone Sidoli, Natarajan V. Bhanu, Kyoung Jae Won, Benjamin A. Garcia
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-15-485

Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms
Cited by: 75
Author(s): Rounak Nassirpour, Sachin Mathur, Mark Gosink, Yizheng Li, Ahmed Shoieb, Joanna Wood, Shawn P. O’Neil, Bruce L. Homer, Laurence O. Whiteley
Software Mentions: 1
Published: over 12 years ago

10.1590/1678-4685-GMB-2016-0055

Salt stress affects mRNA editing in soybean chloroplasts
Cited by: 26
Author(s): Nureyev Ferreira Rodrigues, Guilherme Cordenonsi da Fonseca, Franceli Rodrigues Kulcheski, Rogério Margis
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4431-5

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq)
Cited by: 8
Author(s): Jiao Yang, Ran Li, Chao Wu, Yibin Ding, Yanning Liu, Danmei Jia, Lifeng Wang, Xiang Xu, Jing Zhu, Min Zheng, Junling Jia
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-13-140

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments
Cited by: 364
Author(s): Ming Wen, Yang Shen, Suhua Shi, Tian Tang
Software Mentions: 1
Published: over 14 years ago

10.1016/j.gdata.2015.06.007

Dataset of transcriptional landscape of B cell early activation
Cited by: 2
Author(s): Alexander S. Garruss, Trent Fowler
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1004515

A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters
Cited by: 26
Author(s): Özlem Yıldırım, Jui-Hung Hung, Ryan J. Cedeno, Zhiping Weng, Christopher J. Lengner, Oliver J. Rando
Software Mentions: 1
Published: over 12 years ago

10.1016/j.gdata.2015.08.024

Transcriptome analysis of genetic mechanism of growth curve inflection point using a pig model
Cited by: 0
Author(s): Linyuan Shen, Shunhua Zhang, Li Zhu
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-018-5400-8

A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress
Cited by: 12
Author(s): Yachun Su, Xinhuan Xiao, Hui Ling, Ning Huang, Feng Liu, Weihua Su, Yuye Zhang, Liping Xu, Khushi Muhammad, Youxiong Que
Software Mentions: 1
Published: almost 8 years ago

10.1186/gb-2009-10-9-r98

Simultaneous alignment of short reads against multiple genomes
Cited by: 222
Author(s): Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pgen.1005443

Functional Activation of the Flagellar Type III Secretion Export Apparatus
Cited by: 14
Author(s): Andrew Phillips, Rebecca A. Calvo, Daniel B. Kearns
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-14-2

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation
Cited by: 144
Author(s): J. A. Ward, J. S. Bhangoo, Felicidad Fernández-Fernández, Patrick P. Moore, Jd. Swanson, Roberto Viola, Riccardo Velasco, Nahla V. Bassil, Courtney Weber, Daniel J. Sargent
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1003512

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences
Cited by: 11
Author(s): Ephraim Kenigsberg, Amos Tanay
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1004831

The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle
Cited by: 108
Author(s): Bo Zhou, Jared M. Schrader, Virginia S. Kalogeraki, Eduardo Abeliuk, Cong B. Dinh, James Q. Pham, Zhongying Z. Cui, David L. Dill, Harley H. McAdams, Lucy Shapiro
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1004355

A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium
Cited by: 49
Author(s): Jean‐François Pombert, Nicolas A. Blouin, Christopher E. Lane, Drion G. Boucias, Patrick J. Keeling
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2011-12-9-r88

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
Cited by: 124
Author(s): Cyrille Saintenac, Dayou Jiang, Eduard Akhunov
Software Mentions: 1
Published: almost 16 years ago

10.1186/gb-2012-13-10-r93

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome
Cited by: 74
Author(s): John P. Thomson, Harri Lempiäinen, Jim Hackett, Colm E. Nestor, Arne Müller, Federico Bolognani, Edward J. Oakeley, Dirk Schübeler, Rémi Terranova, Diana Reinhardt, Jonathan G. Moggs, Richard R. Meehan
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1005064

Bacterial Infection Drives the Expression Dynamics of microRNAs and Their isomiRs
Cited by: 57
Author(s): Katherine J. Siddle, Ludovic Tailleux, Matthieu Deschamps, Yong-Hwee Eddie Loh, Cécile Deluen, Brigitte Gicquel, Christophe Antoniewski, Luis B. Barreiro, Laurent Farinelli, Lluı́s Quintana-Murci
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1004204

RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin throughout Mitosis, Suggesting a Role in Mitotic Bookmarking
Cited by: 70
Author(s): Robert J. Lake, Pei-Fang Tsai, In-Chan Choi, Kyoung Jae Won, Hua-Ying Fan
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-12-158

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing
Cited by: 64
Author(s): Marten Jäger, Claus‐Eric Ott, Johannes Grünhagen, Jochen Hecht, Hanna Schell, Stefan Mundlos, Georg N. Duda, Peter N. Robinson, Jasmin Lienau
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-15-743

The I2 resistance gene homologues in Solanum have complex evolutionary patterns and are targeted by miRNAs
Cited by: 20
Author(s): Chunhua Wei, Hanhui Kuang, Li Feng, Jiongjiong Chen
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-017-3869-1

Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing
Cited by: 89
Author(s): Minmin Liu, Huiyang Yu, Gangjun Zhao, Qiufeng Huang, Yongen Lu, Bo Ouyang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1007170

Cdc73 suppresses genome instability by mediating telomere homeostasis
Cited by: 14
Author(s): Rahul V. Nene, Christopher D. Putnam, Bin-Zhong Li, Katarina G. Nguyen, Anjana Srivatsan, Christopher S. Campbell, Arshad Desai, Richard D. Kolodner
Software Mentions: 1
Published: almost 9 years ago

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Papers Mentioning bowtie 1,566