pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-60655-6

High-resolution profiling of human cytomegalovirus cell-free DNA in human plasma highlights its exceptionally fragmented nature
Cited by: 3
Author(s): Vikas Peddu, Benjamin T. Bradley, Amanda M. Casto, Raj Shree, Brice G. Colbert, Hong Xie, Tracy K. Santo, Meei‐Li Huang, Edith Cheng, Eric Q. Konnick, Stephen J. Salipante, Keith R. Jerome, Christina M. Lockwood, Alexander L. Greninger
Software Mentions: 3
Published: over 6 years ago

10.1038/srep16324

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference
Cited by: 42
Author(s): Juan Pablo Isaza, Ana Luz Galván, Víctor Polanco, Bernice Huang, Andrey V. Matveyev, Myrna G. Serrano, Patrício Manque, Gregory A. Buck, Juan F. Alzate
Software Mentions: 3
Published: almost 11 years ago

10.1126/sciadv.aau8317

The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice
Cited by: 387
Author(s): Peng Zheng, Benhua Zeng, Meiling Liu, Jianjun Chen, Junxi Pan, Han Yu, Yiyun Liu, Ke Cheng, Chanjuan Zhou, Haiyang Wang, Xinyu Zhou, Siwen Gui, Seth W. Perry, Ma‐Li Wong, Júlio Licinio, Hong Wei, Peng Xie
Software Mentions: 3
Published: over 7 years ago

10.1038/srep38531

FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines
Cited by: 105
Author(s): Joshua I. Warrick, Vonn Walter, Haruo Yamashita, Eunah Chung, Lauren Shuman, Vasty Osei Amponsa, Zongyu Zheng, Wilson Chan, Tiffany Whitcomb, Feng Yue, Tejaswi Iyyanki, Yuka Imamura Kawasawa, Matthew Kaag, Wansong Guo, Jay D. Raman, Joo Seop Park, David J. DeGraff
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep46107

Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana)
Cited by: 6
Author(s): Hansheng Zhao, Huayu Sun, Lichao Li, Yonggen Lou, Rongsheng Li, Lin Qi, Zhimin Gao
Software Mentions: 2
Published: over 9 years ago

10.1038/srep08248

Whole-genome sequencing reveals that mutations in myosin-5 confer resistance to the fungicide phenamacril in Fusarium graminearum
Cited by: 58
Author(s): Zong‐Ping Zheng, Yiping Hou, Yiqiang Cai, Yu Zhang, Yanjun Li, Mingguo Zhou
Software Mentions: 2
Published: over 11 years ago

10.1038/srep08753

Transcriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production
Cited by: 25
Author(s): Yoshihiko Onda, Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Roger S. Seymour, Yui Umekawa, Stergios Pirintsos, Kazuo Shinozaki, Kikukatsu Ito
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-017-00150-7

Reciprocal regulation of γ-globin expression by exo-miRNAs: Relevance to γ-globin silencing in β-thalassemia major
Cited by: 14
Author(s): Kuo‐Ting Sun, Yu-Nan Huang, Kalaiselvi Palanisamy, Shih‐Sheng Chang, I‐Kuan Wang, Kang‐Hsi Wu, Ping Chen, Ching‐Tien Peng, Chi Yuan Li
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-03083-3

Comparative morphology and transcriptome analysis reveals distinct functions of the primary and secondary laticifer cells in the rubber tree
Cited by: 16
Author(s): Tan D, Xiaowen Hu, Lili Fu, Anuwat Kumpeangkeaw, Zehong Ding, Xiaoyan Sun, Jiaming Zhang
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-03487-1

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome
Cited by: 30
Author(s): Eugeni Belda, Boubacar Coulibaly, Abdrahamane Fofana, Abdoul Habib Béavogui, Sékou F. Traorè, Daryl M. Gohl, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 2
Published: over 9 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/s41598-017-06939-w

Circulating microRNA profiles of Hendra virus infection in horses
Cited by: 15
Author(s): Christopher Cowled, Chwan Hong Foo, Céline Deffrasnes, Christina L. Rootes, David T. Williams, Deborah Middleton, Lin‐Fa Wang, Andrew G. D. Bean, Cameron R. Stewart
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-08370-7

Regulation of tumour related genes by dynamic epigenetic alteration at enhancer regions in gastric epithelial cells infected by Epstein-Barr virus
Cited by: 26
Author(s): Atsushi Okabe, Sayaka Funata, Keisuke Matsusaka, Hiroe Namba, Masaki Fukuyo, Bahityar Rahmutulla, Motohiko Oshima, Atsushi Iwama, Masashi Fukayama, Atsushi Kaneda
Software Mentions: 2
Published: about 9 years ago

10.1038/srep25039

Characterization of piRNAs across postnatal development in mouse brain
Cited by: 34
Author(s): Yanal Ghosheh, Loqmane Seridi, Tae Woo Ryu, Hazuki Takahashi, Valerio Orlando, Piero Carninci, Timothy Ravasi
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-018-24477-x

Analysis of microRNA reveals cleistogamous and chasmogamous floret divergence in dimorphic plant
Cited by: 10
Author(s): Fan Wu, Daiyu Zhang, Blaise Pascal Muvunyi, Yan Qi, Yufei Zhang, Yan Zhang, Mingshu Cao, Yanrong Wang, Jiyu Zhang
Software Mentions: 2
Published: over 8 years ago

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/srep21635

Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling
Cited by: 20
Author(s): Hadas Zur, Ranen Aviner, Tamir Tuller
Software Mentions: 2
Published: over 10 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/s41598-019-38605-8

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/srep19943

GRHL2-miR-200-ZEB1 maintains the epithelial status of ovarian cancer through transcriptional regulation and histone modification
Cited by: 115
Author(s): Vin Yee Chung, Tuan Zea Tan, Ming Tan, Ming Keong Wong, Kuee Theng Kuay, Zhe Yang, Jieru Ye, Julius Müller, Cheryl M. Koh, Ernesto Guccione, Jean Paul Thiery, Ruby Yun‐Ju Huang
Software Mentions: 2
Published: over 10 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/s41598-021-92832-6

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/s41598-019-49572-5

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: almost 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/s41598-021-95779-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

10.1038/srep11953

Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs
Cited by: 91
Author(s): Jing Lü, Ye Hou, Hui Wu, Yuanxin Miao, Xinyun Li, Jianhua Cao, John M. Brameld, Tim Parr, Zhao Song
Software Mentions: 2
Published: over 11 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/srep05559

Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process
Cited by: 55
Author(s): Oliver Smith, A. R. Clapham, Pam Rose, Yuan Liu, Jun Wang, Robin G. Allaby
Software Mentions: 2
Published: over 12 years ago

10.1038/srep41114

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes
Cited by: 55
Author(s): Olga Petrova, Fernando García-Alcalde, Claudia Zampaloni, Karin Sauer
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2013-14-11-r129

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
Cited by: 77
Author(s): Stefan Grob, Marc W. Schmid, Nathan W. Luedtke, Thomas Wicker, Ueli Grossniklaus
Software Mentions: 2
Published: almost 14 years ago

10.1016/j.ajhg.2017.01.011

Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice
Cited by: 61
Author(s): Gaëlle Carrat, Ming Hu, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Kyle J. Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, François Pattou, Isabelle Leclerc, Timothy J. Pullen, Matthew Cane, Priyanka Prabhala, William W. Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E. MacDonald, Jocelyn E. Manning Fox, Anna L. Gloyn, Philippe Froguel, Michele Solimena, Mark I. McCarthy, Guy A. Rutter
Software Mentions: 2
Published: over 9 years ago

10.1111/age.12992

Identification and characterization of miRNAs during early pregnancy in domestic sheep
Cited by: 6
Author(s): Kisun Pokharel, Jaana Peippo, Menghua Li, Juha Kantanen
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-017-1601-4

QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
Cited by: 34
Author(s): Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-12-S14-S2

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
Cited by: 417
Author(s): Qiongyi Zhao, Yi Wang, Yawei Kong, Da Luo, Xuan Li, Pei Hao
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12859-017-1873-8

riboviz: analysis and visualization of ribosome profiling datasets
Cited by: 35
Author(s): Oana Carja, Tongji Xing, Eric Wallace, Joshua B. Plotkin, Premal Shah
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-017-1548-5

Manananggal - a novel viewer for alternative splicing events
Cited by: 7
Author(s): Matthias Barann, Ralf Zimmer, Fabian Birzele
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-11-514

Data structures and compression algorithms for high-throughput sequencing technologies
Cited by: 45
Author(s): Kenneth Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi
Software Mentions: 2
Published: about 16 years ago

10.1186/s12859-015-0704-z

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering
Cited by: 18
Author(s): Mi Kyung Lee, Chae Hwa Seo, B. Alver, Sanghyuk Lee, Peter J. Park
Software Mentions: 2
Published: about 11 years ago

10.1186/s12859-018-2570-y

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
Cited by: 38
Author(s): Dmitry A. Kuzmin, Sergey Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Н. В. Орешкова, Konstantin V. Krutovsky
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04004-y

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
Cited by: 7
Author(s): Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz, Giorgio Giurato
Software Mentions: 2
Published: over 5 years ago

10.1186/s12915-020-00926-w

miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling
Cited by: 26
Author(s): Bin Zhang, Lilin Zhao, Jing Ning, Jacob D. Wickham, Huanfang Tian, Xiaoming Zhang, Meiling Yang, Xiangming Wang, Sun Jian
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-213X-14-15

Integrated proteomic and transcriptomic analysis of the Aedes aegyptieggshell
Cited by: 58
Author(s): Osvaldo Marinotti, Tuan Ngo, Bianca Burini Kojin, Shao‐Pei Chou, Brian D. Nguyen, Jennifer Juhn, Rebeca Carballar-Lejarazú, Pedro N. Marinotti, Xiaofang Jiang, Marika F. Walter, Zhijian Tu, Paul D. Gershon, Anthony A. James
Software Mentions: 2
Published: over 12 years ago

10.1186/s12861-015-0089-2

MiR-21 is required for efficient kidney regeneration in fish
Cited by: 27
Author(s): Beate Hoppe, Stefan Pietsch, Martin Franke, Sven Engel, Marco Groth, Matthias Platzer, Christoph Englert
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12862-016-0844-4

Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm Osedax japonicus inferred from transcriptome and gene expression analyses
Cited by: 19
Author(s): Norio Miyamoto, Masa‐aki Yoshida, Hisao Koga, Yoshihiro Fujiwara
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-016-3271-4

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection
Cited by: 25
Author(s): Ajay Kumar Mishra, G Duraisamy, J. Matoušek, Sebastjan Radišek, Branka Javornik, Jernej Jakše
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-020-07318-y

Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes
Cited by: 17
Author(s): Yanjun Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu, Haiyun Wang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-015-1442-3

Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes
Cited by: 20
Author(s): Chen Jiao, Min Gao, Xiping Wang, Zhangjun Fei
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-415

Global transcriptome profiles of Camellia sinensis during cold acclimation
Cited by: 239
Author(s): Xinchao Wang, Qiongyi Zhao, Chun-Lei Ma, Zong Hong Zhang, Hongli Cao, Yawei Kong, Chuan Yue, Xinyuan Hao, Liang Chen, Jianqiang Ma, Jiye Jin, Xuan Li, Yajun Yang
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-015-2011-5

The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer
Cited by: 30
Author(s): Ryan A. Melnyk, John D. Coates
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-98

A genomic perspective to assessing quality of mass-reared SIT flies used in Mediterranean fruit fly (Ceratitis capitata) eradication in California
Cited by: 31
Author(s): Bernarda Calla, Brian E. Hall, Shaobin Hou, Scott M. Geib
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-020-06906-2

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element
Cited by: 16
Author(s): Ze Chen, Yibo Xuan, Guangcai Liang, Xiaolong Yang, Zhou Yu, Stephen C. Barker, Samuel Kelava, Wenjun Bu, Jingze Liu, Shan Gao
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1115

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo
Cited by: 47
Author(s): Kenji Nakahigashi, Yuki Takai, Yuh Shiwa, Masahiko Wada, Masayuki Honma, Hideki Yoshikawa, Masaru Tomita, Akio Kanai, Hirotada Mori
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-13-578

Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis
Cited by: 120
Author(s): Brian Klein, Elizabeth L Tenorio, David W. Lazinski, Andrew Camilli, Marilyn J. Duncan, Linden T. Hu
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-14-255

A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery
Cited by: 60
Author(s): Wouter J. Veneman, Oliver W. Stockhammer, Leonie de Boer, Sebastian A. J. Zaat, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-017-3556-2

Response of microRNAs to cold treatment in the young spikes of common wheat
Cited by: 60
Author(s): Guang Song, Rongzhi Zhang, Shujuan Zhang, Yulian Li, Jie Gao, Xiao Han, Mingli Chen, Jiao Wang, Wei Li, Genying Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-017-4090-y

De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly
Cited by: 19
Author(s): Monika Frazier, Martin Helmkampf, M. Renee Bellinger, Scott M. Geib, Misaki Takabayashi
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-017-3505-0

Improved annotation with de novo transcriptome assembly in four social amoeba species
Cited by: 6
Author(s): Reema Singh, Hajara M. Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J. Barton, Pauline Schaap, Christian Callebaut
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-14-298

5′ tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction
Cited by: 195
Author(s): Joseph M. Dhahbi, Stephen R. Spindler, Hani Atamna, Amy Yamakawa, Dario Boffelli, Patricia L. Mote, David I. K. Martin
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-14-273

Six novel Y chromosome genes in Anophelesmosquitoes discovered by independently sequencing males and females
Cited by: 105
Author(s): Andrew Brantley Hall, Yumin Qi, Vladimir A. Timoshevskiy, Maria V. Sharakhova, Igor V. Sharakhov, Zhijian Tu
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-015-1456-x

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data
Cited by: 48
Author(s): Richard Orton, Caroline F. Wright, Marco J. Morelli, David J. King, David Paton, Donald P. King, Daniel T. Haydon
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-704

Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals
Cited by: 92
Author(s): Sebastian Baumgarten, Till Bayer, Manuel Aranda, Yi Jin Liew, Adrian R. Carr, Gos Micklem, Christian R. Voolstra
Software Mentions: 2
Published: about 13 years ago

10.1186/s12864-020-6730-x

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)
Cited by: 18
Author(s): Xiaoli Huang, Yanxin Jiang, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiaocui Ma, You Duan, L. Xia, Yaxin Chen, Nan Wu, Minjun Shi, Xiao-Qin Xia
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-1577-2

Neural transcriptome reveals molecular mechanisms for temporal control of vocalization across multiple timescales
Cited by: 29
Author(s): Ni Feng, Daniel J. Fergus, Andrew H. Bass
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-017-3570-4

Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation
Cited by: 41
Author(s): Jiaming Chen, Xiaoqiang Yang, Xiaomao Huang, Shi-Hua Duan, Chengnian Long, Jiakuan Chen, Jun Rong
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-015-2147-3

Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes
Cited by: 38
Author(s): Fotini A. Trikka, Alexandros K. Nikolaidis, Codruţa Ignea, Aphrodite Tsaballa, Leto‐Aikaterini Tziveleka, Efstathia Iοannou, Vassilios Roussis, Eleni A. Stea, Dragana Božić, Anagnostis Argiriou, Angelos K. Kanellis, Sotirios C. Kampranis, Antonios M. Makris
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-015-1965-7

Deep sequencing shows microRNA involvement in bovine mammary gland adaptation to diets supplemented with linseed oil or safflower oil
Cited by: 56
Author(s): Ran Li, Frédéric Beaudoin, Adolf A. Ammah, Nathalie Bissonnette, C. Benchaar, Xin Zhao, Chuzhao Lei, Eveline M. Ibeagha‐Awemu
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-017-3549-1

Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp.
Cited by: 25
Author(s): Alle A. Y. Lie, Zhenfeng Liu, Ramón Terrado, Avery O. Tatters, Karla B. Heidelberg, David A. Caron
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-019-5521-8

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development
Cited by: 16
Author(s): Kathleen D. DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Lingling Gao, Karen M. Frick, Karam B. Singh
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4932-2

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes
Cited by: 36
Author(s): Likai Wang, Yanpeng Xi, Sibum Sung, Hong Qiao
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-1253-6

Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights
Cited by: 27
Author(s): Jane Khudyakov, Likit Preeyanon, Cory D. Champagne, Rudy M. Ortiz, Daniel E. Crocker
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-016-2514-8

Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui')
Cited by: 21
Author(s): Songling Bai, Takanori Saito, Akiko Ito, Phạm Anh Tuấn, Ying Xu, Yuanwen Teng, Takaya Moriguchi
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-16-S13-S6

Comparison of American mink embryonic stem and induced pluripotent stem cell transcriptomes
Cited by: 24
Author(s): А. Г. Мензоров, N. M. Matveeva, Marios Nektarios Markakis, Veniamin Fishman, K. Christensen, А. А. Хабарова, Inna E. Pristyazhnyuk, Elena A. Kizilova, Susanna Cirera, Razvan Anistoroaei, O. L. Serov
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-015-1492-6

Histone modifications induced by MDV infection at early cytolytic and latency phases
Cited by: 13
Author(s): Apratim Mitra, Juan Luo, Yanghua He, Yue Gu, Huanmin Zhang, Keji Zhao, Kairong Cui, Jiuzhou Song
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-018-4533-0

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes
Cited by: 56
Author(s): Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y.R. Dent
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-1251-8

Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum
Cited by: 33
Author(s): Bin-Bin Xie, Dan Li, Wenhao Shi, Qi‐Long Qin, Xiaowei Wang, Jin-Cheng Rong, Caiyun Sun, Feng Huang, Xiying Zhang, Xiaowei Dong, Xiu-Lan Chen, Biao Zhou, Yuzhong Zhang, Xiao‐Yan Song
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-018-4463-x

The aquatic animals’ transcriptome resource for comparative functional analysis
Cited by: 4
Author(s): Chih‐Hung Chou, Hsi‐Yuan Huang, Wei‐Chih Huang, Sheng Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yuchen Liu, Wei Huang, Meng-Lin Lee, Yi‐Chang Chen, Hsien-Da Huang
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-1042

Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes
Cited by: 36
Author(s): Isha Sethi, Satrajit Sinha, Michael Buck
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-016-3360-4

Dhurrin metabolism in the developing grain of Sorghum bicolor (L.) Moench investigated by metabolite profiling and novel clustering analyses of time-resolved transcriptomic data
Cited by: 51
Author(s): Lasse Nielsen, Peter Stuart, Martina Pičmanová, Simon Rasmussen, Carl Erik Olsen, Jesper Harholt, Birger Lindberg Møller, Nanna Bjarnholt
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-15-190

Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma
Cited by: 263
Author(s): John C. Castle, Martin Löewer, Sebastian Boegel, Jos de Graaf, Christian Bender, Arbel D. Tadmor, Valesca Boisguérin, Thomas Bukur, Patrick Sorn, Claudia Paret, Mustafa Diken, Sebastian Kreiter, Özlem Türeci, Uğur Şahin
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-15-20

Sex specific expression and distribution of small RNAs in papaya
Cited by: 21
Author(s): Rishi Aryal, Guru Jagadeeswaran, Yun Zheng, Qingyi Yu, Ramanjulu Sunkar, Ray Ming
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-14-703

Large-scale polymorphism discovery in macaque G-protein coupled receptors
Cited by: 6
Author(s): Dharmendra B. Goswami, Lisa M. Ogawa, Joshua Ward, Gregory M. Miller, Eric J. Vallender
Software Mentions: 2
Published: about 13 years ago

10.1186/s12864-017-3963-4

Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
Cited by: 48
Author(s): Bin Tian, Shichen Wang, T. C. Todd, Charles D. Johnson, Guiliang Tang, Harold N. Trick
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-15-1186

A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules
Cited by: 11
Author(s): Akshay Shah, Anja R. Oldenburg, Philippe Collas
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-015-1355-1

Learning-induced gene expression in the heads of two Nasonia species that differ in long-term memory formation
Cited by: 17
Author(s): Katja M. Hoedjes, Hans M. Smid, Elio Schijlen, Louise E. M. Vet, Joke J.F.A. van Vugt
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-13-480

Genome-wide association between DNA methylation and alternative splicing in an invertebrate
Cited by: 142
Author(s): Kevin Flores, Florian Wolschin, Jason J. Corneveaux, April N. Allen, Matthew J. Huentelman, Gro V. Amdam
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12879-016-1737-2

Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients
Cited by: 7
Author(s): Willy Ssengooba, Bouke C. de Jong, Moses Joloba, Frank Cobelens, Conor J. Meehan
Software Mentions: 2
Published: about 10 years ago

10.1186/s12920-016-0220-7

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells
Cited by: 24
Author(s): Andréanne Morin, Tony Kwan, Bing Ge, Louis Létourneau, Masashi Ban, Karolina Tandre, Maxime Caron, Johanna K. Sandling, Jonas Carlsson, Guillaume Bourque, Catherine Laprise, Alexandre Montpetit, Ann‐Christine Syvänen, Lars Rönnblom, Stephen Sawcer, Mark Lathrop, Tomi Pastinen
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2180-13-302

Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing
Cited by: 43
Author(s): Anthony Underwood, Garan Jones, M. Mentasti, Norman K. Fry, Timothy G. Harrison
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12867-018-0110-y

Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression
Cited by: 2
Author(s): Aleksandra Brzęk, Marlena Cichocka, Jakub Dolata, Wojciech Juzwa, Daniel Schümperli, Katarzyna Dorota Raczyńska
Software Mentions: 2
Published: about 8 years ago

10.1186/s12870-018-1438-7

Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus
Cited by: 32
Author(s): Meiling Yang, Zhongtian Xu, Wan Zhao, Qing Liu, Qiong Li, Lu Lu, Renyi Liu, Xiaoming Zhang, Feng Cui
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2229-13-229

Four distinct types of dehydration stress memory genes in Arabidopsis thaliana
Cited by: 191
Author(s): Yong Ding, Ning Liu, Laëtitia Virlouvet, Jean-Jack M. Riethoven, Michael Fromm, Zoya Avramova
Software Mentions: 2
Published: almost 13 years ago

Projects: pypi: bowtie

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Science Score: 90/100

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Papers Mentioning bowtie 1,566