pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-25963-y

Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells
Cited by: 18
Author(s): Junko Hasegawa, Takuya Sakamoto, Shinsaku Fujimoto, Tomoe Yamashita, Takamasa Suzuki, Sachihiro Matsunaga
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-28217-z

Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia pastoris
Cited by: 23
Author(s): Jinxiang Zhu, Ruiqing Gong, Qiaoyun Zhu, Qun He, Ning Xu, Yichun Xu, Menghao Cai, Xiangshan Zhou, Yuanxing Zhang, Mian Zhou
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-30530-6

Hsa-miR-10a-5p downregulation in mutant UQCRB-expressing cells promotes the cholesterol biosynthesis pathway
Cited by: 8
Author(s): Jeong Eun Kim, Ji Won Hong, Hannah S. Lee, Wankyu Kim, Jae‐Hak Lim, Yoon Shin Cho, Ho Jeong Kwon
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-019-38605-8

The long non-coding RNA Meg3 is dispensable for hematopoietic stem cells
Cited by: 15
Author(s): Pia Sommerkamp, Simon Renders, Luisa Ladel, Agnes Hotz‐Wagenblatt, Katharina Schönberger, Petra Zeisberger, Adriana Przybylla, Markus Sohn, Yunli Zhou, Anne Klibanski, Nina Cabezas-Wallscheid, Andreas Trumpp
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-39878-9

Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer
Cited by: 8
Author(s): Paul M. Krzyzanowski, Fabrice Sircoulomb, Fouad Yousif, Josée Normand, José La Rose, Kyle Francis, Fernando Suarez, Timothy Beck, John Douglas Mcpherson, Lincoln Stein, Robert Rottapel
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-41162-9

Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East
Cited by: 9
Author(s): Essam J. Alyamani, Sarah A. Marcus, Sarah M Ramirez-Busby, Chungyi Hansen, Julien Rashid, Amani El-Kholy, Daniel Spalink, Faramarz Valafar, Hussein A. Almehdar, Asif A. Jiman-Fatani, Mohammad A. Khiyami, Adel M. Talaat
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-49572-5

Ixodes scapularis salivary gland microRNAs are differentially expressed during Powassan virus transmission
Cited by: 20
Author(s): Meghan E. Hermance, Steven G. Widen, Thomas G. Wood, Saravanan Thangamani
Software Mentions: 2
Published: about 7 years ago

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

10.7554/eLife.01257

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
Cited by: 262
Author(s): Liana F. Lareau, Dustin H Hite, Gregory J. Hogan, Patrick O. Brown
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.68285

A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
Cited by: 21
Author(s): Pengyao Jiang, Anja R Ollodart, Vidha Sudhesh, Alan J. Herr, Maitreya J. Dunham, Kelley Harris
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms151018819

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome
Cited by: 14
Author(s): Magda Dudek, Jessica Adams, Martin Swain, Matthew J. Hegarty, Sharon Huws, Joe Gallagher
Software Mentions: 2
Published: about 12 years ago

10.3390/ijms18071475

Transcriptome Differences in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs in Response to Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection
Cited by: 29
Author(s): Wan Liang, Likai Ji, Yu Zhang, Yueran Zhen, Qingde Zhang, Xuewen Xu, Bang Liu
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms18081634

Transcriptome Analysis Reveals Increases in Visceral Lipogenesis and Storage and Activation of the Antigen Processing and Presentation Pathway during the Mouth-Opening Stage in Zebrafish Larvae
Cited by: 16
Author(s): Hao Xu, Enxiu Liu, Yun Li, Xiaojie Li, Chenyu Ding
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms19051481

Exploration of ABA Responsive miRNAs Reveals a New Hormone Signaling Crosstalk Pathway Regulating Root Growth of Populus euphratica
Cited by: 20
Author(s): Conglong Lian, Kun Yao, Hui Duan, Qing Li, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms20020369

Comprehensive Analysis of Differentially Expressed Unigenes under NaCl Stress in Flax (Linum usitatissimum L.) Using RNA-Seq
Cited by: 24
Author(s): Jianzhong Wu, Qian Zhao, Guangwen Wu, Hongmei Yuan, Yan Ma, Hong Lin, Liyan Pan, Suiyan Li, Dequan Sun
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms20051106

Transcriptome and Proteome-Based Network Analysis Reveals a Model of Gene Activation in Wheat Resistance to Stripe Rust
Cited by: 21
Author(s): Hong Zhang, Ying Fu, Huan Guo, Lu Zhang, Changyou Wang, Weining Song, Zhaogui Yan, Yajuan Wang, Wanquan Ji
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20122912

Cell-Free, Embryo-Specific sncRNA as a Molecular Biological Bridge between Patient Fertility and IVF Efficiency
Cited by: 17
Author(s): Timofeeva A.V. Timofeeva, Vitaliy Chagovets, Yulia S. Drapkina, Н. П. Макарова, Kalinina E.A. Kalinina, Г. Т. Сухих
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20215357

Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction
Cited by: 9
Author(s): Jianying Li, J. Joe Hull, Shi-Dong Liang, Qiongqiong Wang, Chen Luo, Qinghua Zhang, Maojun Wang, Shahid Mansoor, Xianlong Zhang, Shuangxia Jin
Software Mentions: 2
Published: about 7 years ago

10.3390/ijms21083029

Elimination of Viroids from Tobacco Pollen Involves a Decrease in Propagation Rate and an Increase of the Degradation Processes
Cited by: 13
Author(s): Jaroslav Matoušek, Lenka Steinbachová, Lenka Záveská Drábková, Tomáš Kocábek, David Potěšil, Ajay Kumar Mishra, David Honys, Gerhard Steger
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21103513

Small RNA Sequencing Analysis of miRNA Expression Reveals Novel Insihts into Root Formation under Root Restriction Cultivation in Grapevine (Vitis vinifera L.)
Cited by: 6
Author(s): Hui Li, Zhen Gao, Muhammad Zahid, Dongmei Li, Hafiz Umer Javed, Lei Wang, Shiren Song, Liping Zhao, Wenping Xu, Caixi Zhang, Chao Ma, Shiping Wang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21113846

MiRNAs Expression Profiling of Bovine (Bos taurus) Testes and Effect of bta-miR-146b on Proliferation and Apoptosis in Bovine Male Germline Stem Cells
Cited by: 21
Author(s): Yuan Gao, Fei Wu, Yaxuan Ren, Ziqing Zhou, Ningbo Chen, Yongzhen Huang, Chuzhao Lei, Hong Chen, Ruihua Dang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21165914

Comparative Transcriptomic Analysis of the Development of Sepal Morphology in Tomato (Solanum Lycopersicum L.)
Cited by: 9
Author(s): Jingyi Liu, Meijing Shi, Jing Wang, Bo Zhang, Yushun Li, Jin Wang, Ahmed H. El-Sappah, Yan Liang
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms22041563

Plasma miR-9-3p and miR-136-3p as Potential Novel Diagnostic Biomarkers for Experimental and Human Mild Traumatic Brain Injury
Cited by: 19
Author(s): Shalini Gupta, Robert Ciszek, Mette Heiskanen, Niina Lapinlampi, Janne Kukkonen, Ville Leinonen, Noora Puhakka, Asla Pitkänen
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22073568

A Tale of Two Transcriptomic Responses in Agricultural Pests via Host Defenses and Viral Replication
Cited by: 5
Author(s): Pramod Pantha, Chalivendra C. Subbaiah, Dong Ha Oh, Bret D. Elderd, Maheshi Dassanayake
Software Mentions: 2
Published: over 5 years ago

10.1523/JNEUROSCI.2673-17.2018

Loss of eIF4E Phosphorylation Engenders Depression-like Behaviors via Selective mRNA Translation
Cited by: 52
Author(s): Inês S. Amorim, Sonal Kedia, Stella Kouloulia, Konstanze Simbriger, Ilse Gantois, Seyed Mehdi Jafarnejad, Yupeng Li, Agniete Kampaite, Tine Pooters, Nicola Romanò, Christos G. Gkogkas
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.isci.2021.102790

ZBTB32 performs crosstalk with the glucocorticoid receptor and is crucial in glucocorticoid responses to starvation
Cited by: 1
Author(s): Lise Van Wyngene, Tineke Vanderhaeghen, Ιωάννα Πέττα, Steven Timmermans, Katrien Corbeels, Bart Van der Schueren, Jolien Vandewalle, Kelly Van Looveren, Charlotte Wallaeys, Melanie Eggermont, Sylviane Dewaele, Leen Catrysse, Geert Loo, Rudi Beyaert, Pieter Gillard, Toshinori Nakayama, Jan Tavernier, Karolien De Bosscher, Claude Libert
Software Mentions: 2
Published: over 5 years ago

10.1016/j.isci.2021.103093

Ezh2 harnesses the intranuclear actin cytoskeleton to remodel chromatin in differentiating Th cells
Cited by: 5
Author(s): Moran Titelbaum, Boris Brant, Daniel Baumel, Alina Burstein-Willensky, Shira Perez, Yiftah Barsheshet, Orly Avni
Software Mentions: 2
Published: about 5 years ago

10.1186/s13048-020-00709-5

Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase
Cited by: 2
Author(s): Shuai Xie, Mengxun Li, Yansen Chen, Yi Liu, Ligeng Ma, Xiaomei Sun, Yishan Sun, Ruonan Gao, Tao Huang
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.8124

Non-invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
Cited by: 108
Author(s): Danijela Koppers-Lalić, Michael Hackenberg, Renée X. de Menezes, Branislav Mišovic, Magda Wąchalska, Albert A. Geldof, Nicoletta Zini, Theo de Reijke, Thomas Würdinger, Andrè N. Vis, Jeroen van Moorselaar, D. Michiel Pegtel, Irene V. Bijnsdorp
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.14788

Acquired resistance to LY2874455 in <i>FGFR2</i>-amplified gastric cancer through an emergence of novel <i>FGFR2-ACSL5</i> fusion
Cited by: 40
Author(s): Sun Young Kim, Tae-Jin Ahn, Heejin Bang, Jun Soo Ham, Jusun Kim, Seung Tae Kim, Jiryeon Jang, Moonhee Shim, So Young Kang, Se Hoon Park, Byung Hoon Min, Hyuk Lee, Won Ki Kang, Woong-Yang Park
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.24973

Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer
Cited by: 9
Author(s): Shahrooz Rabizadeh, Chad Garner, J. Zachary Sanborn, Stephen C. Benz, Sandeep K. Reddy, Patrick Soon‐Shiong
Software Mentions: 2
Published: over 8 years ago

10.4172/2157-7633.S10-009

Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells
Cited by: 5
Author(s): Satyabrata Das, Snehalata Jena, Eun‐Mi Kim, Nicholas Zavazava, Dana N. Levasseur
Software Mentions: 2
Published: almost 15 years ago

10.1128/JVI.01515-20

Identification of a Functional Small Noncoding RNA of African Swine Fever Virus
Cited by: 8
Author(s): Laura Dunn, Alasdair Ivens, Christopher L. Netherton, Dave Chapman, Philippa M. Beard
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0199866

Genetics instability of wtAAV2 genome and AAV promoter activities in the Baculovirus/Sf9 cells system
Cited by: 5
Author(s): Adrien Savy, Minna U. Kaikkonen, Adrien Léger, Yohann Dickx, Lionel Galibert, Otto‐Wilhelm Merten
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-019-41475-9

Identification of piRNAs and piRNA clusters in the testes of the Mongolian horse
Cited by: 12
Author(s): Bei Li, Xiaolong He, Yiping Zhao, Ding Bai, Gerelchimeg Bou, Xinzhuang Zhang, Shaofeng Su, Dao Leng, Rui Li, Yuejiao Wang, Manglai Dugarjaviin
Software Mentions: 1
Published: over 7 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

10.1186/1471-2164-13-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/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.pone.0108411

Next-Generation Sequencing Analysis of MiRNA Expression in Control and FSHD Myogenesis
Cited by: 17
Author(s): Veronica Colangelo, Stéphanie François, Giulia Soldà, Raffaella Picco, Francesca Roma, Enrico Ginelli, Raffaella Meneveri
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-019-45159-2

A cross-species whole genome siRNA screen in suspension-cultured Chinese hamster ovary cells identifies novel engineering targets
Cited by: 19
Author(s): Gerald Klanert, Daniel Fernández, Marcus Weinguny, Peter Eisenhut, Eugen Bühler, Michael Melcher, Steven A. Titus, Andreas Diendorfer, Elisabeth Gludovacz, Vaibhav Jadhav, Shaobo Xiao, Beate Stern, Madhu Lal, Joseph Shiloach, Nicole Borth
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

10.1038/s41598-019-46747-y

Microbiota of the Oropharynx and Endoscope Compared to the Esophagus
Cited by: 13
Author(s): Ikenna Okereke, Aaron L. Miller, Catherine Hamilton, Adam L. Booth, Gabriel Reep, Clark L. Andersen, Sandy T. Reynolds, Richard B. Pyles
Software Mentions: 1
Published: over 7 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.pone.0110163

Integrated microRNA and mRNA Transcriptome Sequencing Reveals the Potential Roles of miRNAs in Stage I Endometrioid Endometrial Carcinoma
Cited by: 35
Author(s): Hanzhen Xiong, Qiulian Li, Shaoyan Liu, Fang Wang, Zhongtang Xiong, Juan Chen, Hui Chen, Yuexin Yang, Xuexian Tan, Qiaojie Luo, Juan Peng, Guohong Xiao, Qingping Jiang
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-019-47399-8

Multi-view Co-training for microRNA Prediction
Cited by: 8
Author(s): Mohsen Sheikh Hassani, James R. Green
Software Mentions: 1
Published: over 7 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

10.1590/1678-4685-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/s12864-018-4484-5

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/ijms21217974

A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease
Cited by: 7
Author(s): Ramakrishna Chopperla, Satendra K. Mangrauthia, Talluri Bhaskar Rao, Balakrishnan Meena, S. M. Balachandran, V. Prakasam, C. Gireesh
Software Mentions: 1
Published: about 6 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.pone.0141915

Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat
Cited by: 2
Author(s): Jincai Hou, Jianhua Fu, Dan Li, Xiao Han, Lei Li, Wenjing Song, Mingjiang Yao, Jianxun Liu
Software Mentions: 1
Published: about 11 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/s12864-019-5879-7

Construction and analysis of degradome-dependent microRNA regulatory networks in soybean
Cited by: 11
Author(s): Rui Wang, Zhongyi Yang, Yuhan Fei, Jiejie Feng, Hui Zhu, Fang Huang, Hongsheng Zhang, Ji Huang
Software Mentions: 1
Published: over 7 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.pone.0012984

Weakly Positioned Nucleosomes Enhance the Transcriptional Competency of Chromatin
Cited by: 8
Author(s): Yaakov Belch, Jingyi Yang, Yang Liu, Sridhar A. Malkaram, Rong Liu, Jean-Jack M. Riethoven, István Ladunga
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-15-920

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data
Cited by: 40
Author(s): Luis León-Novelo, Lauren M. McIntyre, Justin M. Fear, Rita M. Graze
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0122170

De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy
Cited by: 34
Author(s): Senhao Zhang, Shi Ya, Ningning Cheng, Hao Du, Wenna Fan, Chengzhang Wang
Software Mentions: 1
Published: over 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

10.1186/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.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

10.1371/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

10.1186/s12864-017-3692-8

Drosophila melanogaster retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations
Cited by: 1
Author(s): Andrew W. Harrington, Michael R. McKain, Daniel Michalski, Kaylyn M. Bauer, Joshua M. Daugherty, Mindy Steiniger
Software Mentions: 1
Published: over 9 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

10.1038/s41598-019-53102-8

Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse
Cited by: 18
Author(s): Krishnamoorthy Srikanth, Nam Young Kim, Won Cheoul Park, Jae Min Kim, Kwon Do Kim, Kyung Tai Lee, Ju Hwan Son, Han Ha Chai, Jung Woo Choi, Gul Won Jang, Heebal Kim, Youn-Chul Ryu, Jin Wu Nam, Jong Eun Park, Jun Mo Kim, Dajeong Lim
Software Mentions: 1
Published: almost 7 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

10.1371/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

10.1371/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

10.1038/s41598-019-54815-6

Draft genome of Tanacetum cinerariifolium, the natural source of mosquito coil
Cited by: 20
Author(s): Takanori Yamashiro, Akira Shiraishi, Honoo Satake, Koji Nakayama
Software Mentions: 1
Published: almost 7 years ago

10.1186/gb-2014-15-5-r69

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells
Cited by: 143
Author(s): Gilad Fuchs, Yoav Voichek, Benjamin Schwessinger, Shlomit Gilad, Ido Amit, Moshe Oren
Software Mentions: 1
Published: over 12 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

10.1186/1471-2105-13-140

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

10.1186/s13059-015-0606-4

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
Cited by: 196
Author(s): Katherine Jordan, Shichen Wang, Yanni Lun, Laura‐Jayne Gardiner, Ron MacLachlan, P. Hucl, Krysta Wiebe, Debbie Wong, Kerrie Forrest, Andrew Sharpe, Christine Sidebottom, Neil Hall, Christopher Toomajian, Timothy J. Close, Jorge Dubcovsky, Alina Akhunova, L. E. Talbert, Urmil Bansal, Harbans Bariana, Matthew Hayden, Curtis Pozniak, Jeffrey A. Jeddeloh, Anthony Hall, Eduard Akhunov
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-015-0651-z

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes
Cited by: 105
Author(s): Dmitry E. Andreev, Patrick B F O‘Connor, Alexander V. Zhdanov, Ruslan I. Dmitriev, Ivan N. Shatsky, Dmitri B. Papkovsky, Pavel V. Baranov
Software Mentions: 1
Published: over 11 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

10.1111/bju.14808

Targeted deep sequencing of urothelial bladder cancers and associated urinary <scp>DNA</scp>: a 23‐gene panel with utility for non‐invasive diagnosis and risk stratification
Cited by: 37
Author(s): Douglas G. Ward, Naheema S. Gordon, Rebecca H. Boucher, Sarah Pirrie, Laura Baxter, Sascha Ott, Lee Silcock, Celina M. Whalley, Joanne Stockton, Andrew D Beggs, Mike Griffiths, Ben Abbotts, Hanieh Ijakipour, Fathimath N. Latheef, R. A. Robinson, Andrew J. P. White, Nicholas D. James, Maurice P. Zeegers, Kar Keung Cheng, Richard T. Bryan
Software Mentions: 1
Published: over 7 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

10.1371/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

10.1371/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

10.1186/1471-2164-15-485

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

10.1186/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

10.1371/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

10.1371/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

10.1371/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

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Papers Mentioning bowtie 1,566