pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-45210-2

High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material
Cited by: 5
Author(s): Anastasia Filia, Alastair Droop, Mark Harland, Helene Thygesen, Juliette Randerson-Moor, Helen Snowden, Claire Taylor, Joey Mark S. Diaz, Joanna Poźniak, Jérémie Nsengimana, Jonathan P. Laye, Julia Newton-Bishop, D. Timothy Bishop
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.24441

Identification of differentially expressed miRNAs and miRNA-targeted genes in bladder cancer
Cited by: 18
Author(s): Jong‐Young Lee, Seok Joong Yun, Pildu Jeong, Xuan‐Mei Piao, Ye‐Hwan Kim, Jihye Kim, Sathiyamoorthy Subramaniyam, Young Ho Byun, Ho Won Kang, Soonjoo Seo, Jayoung Kim, Jung Min Kim, Eun Sang Yoo, Isaac Y. Kim, Sung‐Kwon Moon, Yung Hyun Choi, Wun-jae Kim
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-019-47439-3

High prevalence of the MLH1 V384D germline mutation in patients with HER2-positive luminal B breast cancer
Cited by: 14
Author(s): Seung Eun Lee, Hye Seung Lee, Kyoung-Yeon Kim, Jung Hoon Park, Hanseong Roh, Ha Young Park, Wan-Seop Kim
Software Mentions: 1
Published: about 7 years ago

10.1038/s12276-020-0469-y

Fecal microbial transplantation and a high fiber diet attenuates emphysema development by suppressing inflammation and apoptosis
Cited by: 39
Author(s): Yoon Ok Jang, Se Hee Lee, Jong Jin Choi, Do Hyun Kim, Je-Min Choi, Min Jong Kang, Yeon Mok Oh, Young Jun Park, Yoo Seob Shin, Sei Won Lee
Software Mentions: 1
Published: over 6 years ago

10.1038/s12276-020-00487-6

Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia
Cited by: 7
Author(s): Da Hyeon Choi, Ji Won Park, Ju Kwang Choi, Kyeong Eun Lee, Won Hee Lee, Jinho Yang, Ju‐Yeon Lee, Yoon Jeong Park, Chahyun Oh, Ho-Ryun Won, Bon Seok Koo, Jae Won Chang, Yoon Shin Park
Software Mentions: 1
Published: about 6 years ago

10.3389/fcell.2021.623394

Mutations in RNA Methyltransferase Gene NSUN5 Confer High Risk of Outflow Tract Malformation
Cited by: 5
Author(s): Yifeng Wang, Tao Jiang, Jiani Xu, Yayun Gu, Yan Zhou, Yuan Lin, Yifei Wu, Wei Li, Cheng Wang, Bin Shen, Xuming Mo, Xiaowei Wang, Bin Zhou, Chenyue Ding, Zhibin Hu
Software Mentions: 1
Published: over 5 years ago

10.3389/fcell.2020.553728

Geniposide Alleviates Oxidative Stress of Mice With Depression-Like Behaviors by Upregulating Six3os1
Cited by: 18
Author(s): Tianyu Zou, Kazuo Sugimoto, Jielin Zhang, Yongxiu Liu, Yiming Zhang, Hao Liang, Yifeng Jiang, Jing Wang, Guoxiang Duan, Cheng Mei
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2017.00936

Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism
Cited by: 18
Author(s): Witold Uhrynowski, Przemysław Decewicz, Łukasz Dziewit, Monika Radlińska, Paweł S. Krawczyk, Leszek Lipiński, Dorota Adamska, Łukasz Drewniak
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-019-49065-5

A new species in the major malaria vector complex sheds light on reticulated species evolution
Cited by: 54
Author(s): Maite G. Barrón, Christophe Paupy, Nil Rahola, Ousman Akone‐Ella, Marc F. Ngangue, Theodel A. Wilson-Bahun, Marco Pombi, Pierre Kengne, Carlo Costantini, Frédéric Simard, Josefa González, Diégo Ayala
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcell.2021.645704

Mouse Retinal Organoid Growth and Maintenance in Longer-Term Culture
Cited by: 12
Author(s): Manuela Völkner, Thomas Kurth, Jana Schor, Lynn J. A. Ebner, Lara Bardtke, Cagri Kavak, Jörg Hackermüller, Mike O. Karl
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.01637

Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes
Cited by: 32
Author(s): Muhammad Ali, Dario Rangel Shaw, Mads Albertsen, Pascal E. Saikaly
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2017.00547

Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology
Cited by: 22
Author(s): Bercelin Maniangou, Nolwenn Legrand, Mehdi Alizadeh, Ulysse Guyet, Catherine Willem, Grégoire David, Éric Charpentier, Alexandre Walencik, Christelle Retière, Katia Gagne
Software Mentions: 1
Published: over 9 years ago

10.3389/fimmu.2021.673248

Targeted Next-Generation Sequencing Combined With Circulating-Free DNA Deciphers Spatial Heterogeneity of Resected Multifocal Hepatocellular Carcinoma
Cited by: 4
Author(s): Jianzhen Lin, Shuaiguo Zhao, Dongxu Wang, Song Yang, Yue Che, Yang Xu, Jianshan Mao, Fucun Xie, Junyu Long, Yi Bai, Xiaobo Yang, Lei Zhang, Jin Bian, Xin Lu, Xinting Sang, Jie Pan, Kai Wang, Haitao Zhao
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2021.631450

LncRNATUG1 Facilitates Th2 Cell Differentiation by Targeting the miR-29c/B7-H3 Axis on Macrophages
Cited by: 9
Author(s): Hongwei Sun, Ting Wang, Weili Zhang, Husheng Dong, Wenjing Gu, Li Huang, Yan Ya, Canhong Zhu, Zhengrong Chen
Software Mentions: 1
Published: about 5 years ago

10.1186/s13023-019-1194-2

Sequence characterization of RET in 117 Chinese Hirschsprung disease families identifies a large burden of de novo and parental mosaic mutations
Cited by: 9
Author(s): Qian Jiang, Yang Wang, Qi Li, Zhen Zhang, Ping Xiao, Hui Wang, Na Liu, Jian Wu, Feng Zhang, Aravinda Chakravarti, Wei Cai, Long Li
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-019-53283-2

Time-coursed transcriptome analysis identifies key expressional regulation in growth cessation and dormancy induced by short days in Paulownia
Cited by: 9
Author(s): Jiayuan Wang, Hongyan Wang, Tao Deng, Zhen Liu, Xuewen Wang
Software Mentions: 1
Published: almost 7 years ago

10.3389/fimmu.2017.01084

Shrimp miR-10a Is Co-opted by White Spot Syndrome Virus to Increase Viral Gene Expression and Viral Replication
Cited by: 13
Author(s): Jong Shin Huang, Shih-Ting Kang, I-Tung Chen, Li-Kwan Chang, Shih-Shun Lin, Guang Hsiung Kou, Chin‐Chou Chu, Chu Fang Lo
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-019-56662-x

Type-2 Diabetics Reduces Spatial Variation of Microbiome Based on Extracellular Vesicles from Gut Microbes across Human Body
Cited by: 19
Author(s): Geumkyung Nah, Sang-Cheol Park, Kangjin Kim, Sung-Min Kim, Jaehyun Park, Sanghun Lee, Sungho Won
Software Mentions: 1
Published: almost 7 years ago

10.1038/s12276-020-0458-1

Association between the sinus microbiota with eosinophilic inflammation and prognosis in chronic rhinosinusitis with nasal polyps
Cited by: 14
Author(s): Ji Heui Kim, Sung Hee Kim, Ji Youn Lim, Doyeon Kim, In Seong Jeong, Dong Kyu Lee, Yong Ju Jang
Software Mentions: 1
Published: over 6 years ago

10.1128/JVI.02218-20

Rapid Evolution of Enhanced Zika Virus Virulence during Direct Vertebrate Transmission Chains
Cited by: 10
Author(s): Kasen K. Riemersma, Anna S. Jaeger, Chelsea M. Crooks, Katarina M. Braun, James Weger-Lucarelli, Gregory D. Ebel, Thomas C. Friedrich, Matthew T. Aliota
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2018.01331

miR-181a-5p Regulates TNF-α and miR-21a-5p Influences Gualynate-Binding Protein 5 and IL-10 Expression in Macrophages Affecting Host Control of Brucella abortus Infection
Cited by: 24
Author(s): Patrícia Paiva Corsetti, Leonardo Augusto de Almeida, André Nicolau Aquime Gonçalves, Marco Túlio R. Gomes, Erika S. Guimarães, João Trindade Marques, Sérgio C. Oliveira
Software Mentions: 1
Published: over 8 years ago

10.3389/fcell.2020.591629

Transcriptome-Wide m6A Methylation in Skin Lesions From Patients With Psoriasis Vulgaris
Cited by: 21
Author(s): Yanan Wang, Hongzhong Jin
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-58324-9

Evaluation of the population structure and phylogeography of the Japanese Genji firefly, Luciola cruciata, at the nuclear DNA level using RAD-Seq analysis
Cited by: 12
Author(s): Dai‐ichiro Kato, Hirobumi Suzuki, Atsuhiro Tsuruta, Juri Maeda, Yoshinobu Hayashi, Kazunari Arima, Yuji Ito, Yukio Nagano
Software Mentions: 1
Published: over 6 years ago

10.1111/evo.13150

The ultimate and proximate mechanisms driving the evolution of long tails in forest deer mice
Cited by: 22
Author(s): Evan P. Kingsley, Krzysztof M. Kozak, Susanne Pfeifer, Dou‐Shuan Yang, Hopi E. Hoekstra
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-020-58659-3

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage
Cited by: 32
Author(s): Jolinda Pollock, Adrian Muwonge, Michael R. Hutchings, Geoffrey Mainda, Barend M. deC. Bronsvoort, David L. Gally, Alexander Corbishley
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2014.00130

AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries
Cited by: 29
Author(s): Alexis Criscuolo, Sylvain Brisse
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-020-59529-8

Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles
Cited by: 53
Author(s): Da Jung Kim, Jinho Yang, Ho-Chan Seo, Won Hee Lee, Dong Hoon Lee, Sungmin Kym, Young Soo Park, Jae Gyu Kim, In Jin Jang, Yoon Keun Kim, Joo Youn Cho
Software Mentions: 1
Published: over 6 years ago

10.3389/fcell.2020.00430

Disease Activity-Associated Alteration of mRNA m5 C Methylation in CD4+ T Cells of Systemic Lupus Erythematosus
Cited by: 42
Author(s): Gangqiang Guo, Huijing Wang, Xinyu Shi, Lele Ye, Kejing Yan, Zhiyuan Chen, Huidi Zhang, Zi‐Bing Jin, Xiangyang Xue
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2014.00005

Assessment of insert sizes and adapter content in fastq data from NexteraXT libraries
Cited by: 18
Author(s): Frances Turner
Software Mentions: 1
Published: over 12 years ago

10.3389/fgene.2020.591434

Clinical Utility of Exome Sequencing and Reinterpreting Genetic Test Results in Children and Adults With Epilepsy
Cited by: 8
Author(s): Yongli Jiang, Changgeng Song, Yuanyuan Wang, Jingjing Zhao, Fang Yang, Qiong Gao, Xiuxiu Leng, Yu-lin Man, Wen Jiang
Software Mentions: 1
Published: almost 6 years ago

10.3389/fnbeh.2017.00089

Evidence for Ancestral Programming of Resilience in a Two-Hit Stress Model
Cited by: 18
Author(s): Jamshid Faraji, Nabiollah Soltanpour, Mirela Ambeskovic, Fabíola Cristina Ribeiro Zucchi, Pierre Beaumier, Igor Kovalchuk, Gerlinde A. S. Metz
Software Mentions: 1
Published: over 9 years ago

10.3389/fnagi.2020.511562

Gut Microbiome Signatures Are Biomarkers for Cognitive Impairment in Patients With Ischemic Stroke
Cited by: 47
Author(s): Yi Liu, Tianyu Gong, Junmei Zhang, Qilu Gu, Xinxin Gao, Xiongpeng Weng, Jiaming Liu, Jing Sun
Software Mentions: 1
Published: almost 6 years ago

10.3389/fgene.2021.628841

The Alteration of M6A-Tagged Transcript Profiles in the Retina of Rats After Traumatic Optic Neuropathy
Cited by: 5
Author(s): Xiaolin Qu, Kaixin Zhu, Zhenxing Li, Danfeng Zhang, Lingling Hou
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2020.612951

Transcriptome Analysis of lncRNA–mRNA Interactions in Chronic Atrophic Gastritis
Cited by: 5
Author(s): Chia-Han Yang, Jingpeng Jin, Liqiang Wang, Xiaobin Jin, Lei Yang, Bin Zhang
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.00074

Whole Exome Sequencing Identifies a Novel Predisposing Gene, MAPKAP1, for Familial Mixed Mood Disorder
Cited by: 4
Author(s): Chunxia Yang, Suping Li, X Jack, Yang Li, Aixia Zhang, Ning Sun, Yanfang Wang, Yong Xu, Kerang Zhang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-19198-0

Mutations in bassoon in individuals with familial and sporadic progressive supranuclear palsy-like syndrome
Cited by: 22
Author(s): Ichiro Yabe, Hiroaki Yaguchi, Yasutaka Kato, Yasuo Miki, Hidehisa Takahashi, Satoshi Tanikawa, Shinichi Shirai, Ikuko Takahashi, Mari Kimura, Yuka Hama, Masaaki Matsushima, Shinsuke Fujioka, Takahiro Kano, Masashi Watanabe, Shin Nakagawa, Y Kunieda, Yoshio Ikeda, Masato Hasegawa, Hiroshi Nishihara, Toshihisa Ohtsuka, Shinya Tanaka, Yoshio Tsuboi, Susumi Hatakeyama, Keiji Wakabayashi, Hidenao Sasaki
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-18091-6

Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing
Cited by: 5
Author(s): Joanna Lopacinska-Jørgensen, Jonas Nyvold Pedersen, Mads Bak, Mana M. Mehrjouy, Kristian Tølbøl Sørensen, Peter Friis Østergaard, Brian Bilenberg, Anders Kristensen, Rafael J. Taboryski, Henrik Flyvbjerg, Rodolphe Marie, Niels Tommerup, Asli N. Silahtaroglu
Software Mentions: 1
Published: almost 9 years ago

10.3389/fgene.2021.641526

Dissecting the Roles of LncRNAs in the Development of Periventricular White Matter Damage
Cited by: 1
Author(s): Xinyu Wang, Heng Liu, Xiaoli Liao, Lixing Qiao, Lihua Zhu, She–Ching Wu, Yan Zhou, Yi Zhang, Bangbang Li, Lili Lin, Jingjing Ma, Qianying Gu, Jia-Ping Shu
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-12715-7

EUF1 – a newly identified gene involved in erythritol utilization in Yarrowia lipolytica
Cited by: 22
Author(s): Dorota A. Rzechonek, Cécile Neuvéglise, Hugo Devillers, Waldemar Rymowicz, Aleksandra M. Mirończuk
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-22473-9

A simple and robust real-time qPCR method for the detection of PIK3CA mutations
Cited by: 25
Author(s): Virginia Álvarez‐García, Clare Bartos, Ieva Keraite, Urmi Trivedi, Paul M. Brennan, Maïwenn Kersaudy-Kerhoas, Karim Gharbi, Olga Oikonomidou, Nicholas R. Leslie
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-22617-x

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
Cited by: 66
Author(s): Siavash Atashgahi, Bastian Hornung, Marcelle J. van der Waals, Ulisses Nunes da Rocha, Floor Hugenholtz, Bart Nijsse, Douwe Molenaar, Rob J.M. van Spanning, Alfons Johannes Maria Stams, Jan Gerritse, Hauke Smidt
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-23478-0

Cellular response to persistent foot-and-mouth disease virus infection is linked to specific types of alterations in the host cell transcriptome
Cited by: 20
Author(s): Lingling Han, Xiu Xin, Hailong Wang, Jiadai Li, Yanling Hao, Mingzhen Wang, Chengchao Zheng, Chao Shen
Software Mentions: 1
Published: over 8 years ago

10.3389/fendo.2020.00273

Analysis of Pigment-Dispersing Factor Neuropeptides and Their Receptor in a Velvet Worm
Cited by: 3
Author(s): Christine Martin, Lars Hering, Niklas Metzendorf, Sarah Hormann, Sonja Kasten, Sonja Fuhrmann, Achim Werckenthin, Friedrich W. Herberg, Monika Stengl, Georg Mayer
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-09334-7

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
Cited by: 33
Author(s): Jared Mamrot, Roxane Legaie, Stacey J. Ellery, Trevor Wilson, Torsten Seemann, David Powell, David K. Gardner, David W. Walker, Peter Temple-Smith, Anthony T. Papenfuss, Hayley Dickinson
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-26524-z

Molecular Diagnosis of 34 Japanese Families with Leber Congenital Amaurosis Using Targeted Next Generation Sequencing
Cited by: 32
Author(s): Katsuhiro Hosono, Sachiko Nishina, Tadashi Yamaguchi, Satoshi Katagiri, Hirotomo Saitsu, Kentaro Kurata, Daisuke Miyamichi, Akiko Hikoya, Kei Mizobuchi, Tadashi Nakano, Shinsei Minoshima, Maki Fukami, Hiroyuki Kondo, M. Sato, Takaaki Hayashi, Noriyuki Azuma, Yoshihiro Hotta
Software Mentions: 1
Published: over 8 years ago

10.3389/fcimb.2021.709681

Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae: In Silico and In Vitro Evidence
Cited by: 24
Author(s): Chaitra Shankar, Soumya Basu, Binesh Lal, Sathiya Shanmugam, Karthick Vasudevan, Purva Mathur, Sudha Ramaiah, Anand Anbarasu, Balaji Veeraraghavan
Software Mentions: 1
Published: about 5 years ago

10.1038/s12276-020-0470-5

Analysis of the human breast milk microbiome and bacterial extracellular vesicles in healthy mothers
Cited by: 35
Author(s): Su Yeong Kim, Dae Yong Yi
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-06256-2

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli
Cited by: 90
Author(s): Nicole Stoesser, Anna E. Sheppard, Gisele Peirano, LW Anson, Louise Pankhurst, Robert Sebra, Hang Phan, Andrew Kasarskis, Amy J Mathers, Timothy E. A. Peto, Patricia A. Bradford, Mary Motyl, A. Sarah Walker, Derrick W. Crook, Johann Pitout
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-02880-0

Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles
Cited by: 87
Author(s): Angela B. Javurek, Dhananjay Suresh, William G. Spollen, Marcia L. Hart, Sarah A. Hansen, Mark R. Ellersieck, Nathan J. Bivens, Scott A. Givan, Anandhi Upendran, Raghuraman Kannan, Cheryl S. Rosenfeld
Software Mentions: 1
Published: over 9 years ago

10.1038/srep46037

Intestinal microbiota link lymphopenia to murine autoimmunity via PD-1+CXCR5−/dim B-helper T cell induction
Cited by: 16
Author(s): Toshiki Eri, K. Kawahata, Takeyuki Kanzaki, Mitsuru Imamura, Koji Michishita, Lisa Akahira, Ei Bannai, Noritada Yoshikawa, Yoshinobu Kimura, Takeshi Satoh, Satoshi Uematsu, Hirotoshi Tanaka, Kazuhiko Yamamoto
Software Mentions: 1
Published: over 9 years ago

10.1038/srep43552

Genetic architecture of threshold reaction norms for male alternative reproductive tactics in Atlantic salmon (Salmo salar L.)
Cited by: 25
Author(s): Olivier Lepais, Aurélie Manicki, Stéphane Glise, Mathieu Buoro, Agnès Bardonnet
Software Mentions: 1
Published: over 9 years ago

10.3389/fcimb.2020.575613

Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities
Cited by: 63
Author(s): Hebah A. Al-Khatib, Fatiha Benslimane, Israa Elbashir, Peter Coyle, Muna Al Maslamani, Abdullatif Al‐Khal, Asmaa A. Al Thani, Hadi M. Yassine
Software Mentions: 1
Published: almost 6 years ago

10.3389/fcimb.2017.00321

Diversity of Cervical Microbiota in Asymptomatic Chlamydia trachomatis Genital Infection: A Pilot Study
Cited by: 34
Author(s): Simone Filardo, Marisa Di Pietro, Maria Grazia Porpora, Nadia Recine, Alessio Farcomeni, Maria Agnese Latino, Rosa Sessa
Software Mentions: 1
Published: about 9 years ago

10.1038/srep31326

The genetics of an early Neolithic pastoralist from the Zagros, Iran
Cited by: 57
Author(s): Marcos Gallego Llorente, Sarah Connell, Eppie R. Jones, DC Merrett, Yeonsu Jeon, Anders Eriksson, Veronika Siska, Cristina Gamba, Christopher Meiklejohn, Robert Beyer, Sungwon Jeon, Yun Sang Cho, Michael Hofreiter, Jihun Bhak, Andrea Manica, Ron Pinhasi
Software Mentions: 1
Published: about 10 years ago

10.1038/srep25719

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions
Cited by: 56
Author(s): Yingyu Law, Rasmus Hansen Kirkegaard, Angel Anisa Cokro, Xianghui Liu, Krithika Arumugam, Chao Xie, Mikkel Stokholm-Bjerregaard, Daniela I. Drautz–Moses, Per Halkjær Nielsen, Stefan Wuertz, Rohan B. H. Williams
Software Mentions: 1
Published: over 10 years ago

10.1038/srep09086

Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius
Cited by: 14
Author(s): F. Javier Cabañes, Walter Sanseverino, G. Castellá, M.R. Bragulat, Riccardo Aiese Cigliano, Armand Sánchez
Software Mentions: 1
Published: over 11 years ago

10.1186/s12977-018-0426-1

Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays
Cited by: 6
Author(s): Art F. Y. Poon, Jessica L. Prodger, Briana Lynch, Jun Lai, Steven J. Reynolds, Jingo Kasule, Adam A. Capoferri, Susanna L. Lamers, Christopher W. Rodriguez, Daniel Bruno, Stephen F. Porcella, Craig Martens, Thomas C. Quinn, Andrew D. Redd
Software Mentions: 1
Published: about 8 years ago

10.3389/fcimb.2021.628887

Functional Mapping of AGO-Associated Zika Virus-Derived Small Interfering RNAs in Neural Stem Cells
Cited by: 11
Author(s): Jianxiong Zeng, Zhifei Luo, Shupeng Dong, Xing Xie, Xinyan Liang, Youzhen Yan, Qiming Liang, Zhen Zhao
Software Mentions: 1
Published: over 5 years ago

10.1007/s43032-020-00175-w

Expression of Stromal Progesterone Receptor and Differential Methylation Patterns in the Endometrium May Correlate with Response to Progesterone Therapy in Endometrial Complex Atypical Hyperplasia
Cited by: 5
Author(s): Adam Neal, M.I. Núñez, Tiffany Lai, Anela Tosevska, Marco Morselli, M. Amneus, Mae Zakhour, Neda A. Moatamed, Matteo Pellegrini, Sanaz Memarzadeh
Software Mentions: 1
Published: over 6 years ago

10.1080/0886022X.2021.1979040

Identification of circular RNA expression profiles in renal fibrosis induced by obstructive injury
Cited by: 5
Author(s): Jiangju Huang, Zhihao Zhang, Benquan Liu, Ying Gao, Jiayi Nie, Sijian Wen, Xiaomin Lai, Hua Liu
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-41772-3

Extracellular small non-coding RNA contaminants in fetal bovine serum and serum-free media
Cited by: 23
Author(s): Bettina Mannerström, Riku O. Paananen, Ahmed G. Abu-Shahba, Jukka Moilanen, Riitta Seppänen‐Kaijansinkko, Sippy Kaur
Software Mentions: 1
Published: over 7 years ago

10.3389/fcimb.2021.670935

Trehalose-Induced Remodelling of the Human Microbiota Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot Study
Cited by: 17
Author(s): Anthony M. Buckley, Ines B Moura, Norie Arai, William Spittal, Emma Clark, Yoshihiro Nishida, Hannah Harris, Karen L. de Mesy Bentley, Georgina Davis, Dapeng Wang, Suparna Mitra, Takanobu Higashiyama, Mark H. Wilcox
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2021.696913

Dynamic Changes in Lung Microbiota of Broilers in Response to Aging and Ammonia Stress
Cited by: 1
Author(s): Jian Chen, Ai Jin, Lei Huang, Yan Zhao, Yuwen Li, Haotian Zhang, Xiaojun Yang, Qingzhu Sun
Software Mentions: 1
Published: about 5 years ago

10.1186/s13148-020-00865-x

Contribution of gene mutations to Silver-Russell syndrome phenotype: multigene sequencing analysis in 92 etiology-unknown patients
Cited by: 29
Author(s): Takeshi Inoue, Akie Nakamura, Megumi Iwahashi-Odano, Kanako Tanase-Nakao, Kazuo Matsubara, Junko Nishioka, Yoshihiro Maruo, Yukihiro Hasegawa, Hiroshi Suzumura, Seiji Sato, Yoshiyuki Kobayashi, Nobuyuki Murakami, Kazuhiko Nakabayashi, Kazuki Yamazawa, Tomoko Fuke, Shunji Narumi, Akira Oka, Tsutomu Ogata, Maki Fukami, Masayo Kagami
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1007120

B cell clonal lineage alterations upon recombinant HIV-1 envelope immunization of rhesus macaques
Cited by: 3
Author(s): Christina Yacoob, Miles D. Lange, Kristen W. Cohen, Kanan Lathia, Junli Feng, Jolene A. Glenn, Sara Carbonetti, Brian G. Oliver, В. И. Вигдорович, D. Noah Sather, Leonidas Stamatatos
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1007260

Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice
Cited by: 64
Author(s): Joseph H. Skalski, Jose J. Limon, Purnima Sharma, Matthew Gargus, Christopher Nguyen, Jie Tang, Ana Lúcia Coelho, Cory M. Hogaboam, Timothy R. Crother, David Underhill
Software Mentions: 1
Published: about 8 years ago

10.3390/cells9040876

Human Peripheral Blood-Derived Endothelial Colony-Forming Cells Are Highly Similar to Mature Vascular Endothelial Cells yet Demonstrate a Transitional Transcriptomic Signature
Cited by: 29
Author(s): Anton G. Kutikhin, Alexey E. Tupikin, В. Г. Матвеева, Д. К. Шишкова, Л. В. Антонова, Мarsel R. Kabilov, Е. А. Великанова
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1007787

Circuit diversification in a biofilm regulatory network
Cited by: 68
Author(s): Manning Y. Huang, Carol A. Woolford, Gemma E. May, C. Joel McManus, Aaron P. Mitchell
Software Mentions: 1
Published: over 7 years ago

10.3390/cells8010042

Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages
Cited by: 27
Author(s): Nardos Tesfaye Woldemariam, Oleg Agafonov, Björn Hoyheim, Ross D. Houston, John B. Taggart, Rune Andreassen
Software Mentions: 1
Published: over 7 years ago

10.1038/s41419-021-04127-3

NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation
Cited by: 51
Author(s): Yuanbo Hu, Chenbin Chen, Xinya Tong, Sian Chen, Xianjing Hu, Bailin Pan, Xia Sun, Zhiyuan Chen, Xinyu Shi, Yingying Hu, Xian Shen, Xiangyang Xue, Mingdong Lu
Software Mentions: 1
Published: about 5 years ago

10.3390/ani10020176

Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding
Cited by: 13
Author(s): Jiazhong Guo, Pengfei Li, Shuai Liu, Benchun Miao, Bo Zeng, Yahui Jiang, Li Li, Linjie Wang, Yu Chen, Hongping Zhang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12866-020-01943-z

Response of the gut microbiota during the Clostridioides difficile infection in tree shrews mimics those in humans
Cited by: 3
Author(s): Wenpeng Gu, Wenge Li, Wenguang Wang, Dexuan Kuang, Wenzhu Zhang, Caixia Lü, Na Li, Pinfen Tong, Yuanyuan Han, Xiaomei Sun, Jinxing Lu, Yuan Wu, Jiejie Dai
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.03696

The neural crest is a source of mesenchymal stem cells with specialized hematopoietic stem cell niche function
Cited by: 229
Author(s): Joan Isern, Andrés García‐García, Ana María Díaz Martín, Lorena Arranz, Daniel Martín-Pérez, Carlos Torroja, Fátima Sánchez-Cabo, Simón Méndez-Ferrer
Software Mentions: 1
Published: about 12 years ago

10.1186/s12866-014-0298-z

Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae
Cited by: 28
Author(s): Benjamin J. Perry, Christopher K. Yost
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41419-020-2500-6

Histone deacetylase 1 and 2 drive differentiation and fusion of progenitor cells in human placental trophoblasts
Cited by: 28
Author(s): Gargi Jaju Bhattad, Mariyan Jeyarajah, Megan McGill, Vanessa Dumeaux, Hiroaki Okae, Takahiro Arima, Patrick Lajoie, Nathalie G. Bérubé, Stephen J. Renaud
Software Mentions: 1
Published: over 6 years ago

10.1186/s12881-020-01161-4

Novel nonsense mutation p. Gln264Ter in the ANK1 confirms causative role for hereditary spherocytosis: a case report
Cited by: 5
Author(s): Senmao Chai, Rong Jiao, Xiaodong Sun, Pan Fu, Qiang Zhao, Ming Sang
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12916-020-01667-x

Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing
Cited by: 20
Author(s): Haikun Zhang, Paul R Dong, Shicheng Guo, Chengcheng Tao, Wei Chen, Wenling Zhao, Jia-Kang Wang, Ramsey Cheung, Augusto Villanueva, Fan Jian, Huiguo Ding, Steven J. Schrodi, Dake Zhang, Changqing Zeng
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-13-571

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes
Cited by: 102
Author(s): Hamid Ashrafi, Theresa Hill, Kevin Stoffel, Alexander Kozik, Jiqiang Yao, Sebastián Reyes Chin-Wo, Allen Van Deynze
Software Mentions: 1
Published: almost 15 years ago

10.3390/cancers12092346

Diversity in the Extracellular Vesicle-Derived Microbiome of Tissues According to Tumor Progression in Pancreatic Cancer
Cited by: 14
Author(s): Jin‐Yong Jeong, Tae‐Bum Kim, Jinju Kim, Hwi Wan Choi, Eo Jin Kim, Hyun Ju Yoo, Song Lee, Hye Ryeong Jun, Wonbeak Yoo, Seokho Kim, Song Cheol Kim, Eunsung Jun
Software Mentions: 1
Published: about 6 years ago

10.3390/cancers12082224

TERT Promoter Mutation as an Independent Prognostic Marker for Poor Prognosis MAPK Inhibitors-Treated Melanoma
Cited by: 7
Author(s): Pauline Blateau, Étienne Coyaud, Estelle Laurent, Benoît Béganton, Vincent Ducros, Géraldine Chauchard, Julie A. Vendrell, Jérôme Solassol
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0164228

DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data
Cited by: 27
Author(s): Junko Tsuji, Zhiping Weng
Software Mentions: 1
Published: almost 10 years ago

10.1098/rspb.2017.2654

Multi-omics analysis of thermal stress response in a zooxanthellate cnidarian reveals the importance of associating with thermotolerant symbionts
Cited by: 56
Author(s): Maha J. Cziesielski, Yi Jin Liew, Guoxin Cui, Sebastian Schmidt‐Roach, Sara Campana, Claudius Marondedze, Manuel Aranda
Software Mentions: 1
Published: over 8 years ago

10.1098/rspb.2018.0214

Resolving the phylogenetic position of Darwin's extinct ground sloth ( <i>Mylodon darwinii</i> ) using mitogenomic and nuclear exon data
Cited by: 15
Author(s): Frédéric Delsuc, Melanie Kuch, Gillian C. Gibb, Jonathan J. Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T. Duggan, Hendrik N. Poinar
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0149756

Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer
Cited by: 67
Author(s): Douglas G. Ward, Laura Baxter, Naheema S. Gordon, Sascha Ott, Richard S. Savage, Andrew D Beggs, Jonathan James, Jennifer Lickiss, Shaun Green, Yvonne Wallis, Wenbin Wei, Nicholas D. James, Maurice P. Zeegers, Kar Keung Cheng, Glenn M. Mathews, Prashant Patel, Michael Griffiths, Richard T. Bryan
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-021-07619-w

Transcriptome-wide N6-methyladenosine modification profiling of long non-coding RNAs during replication of Marek’s disease virus in vitro
Cited by: 9
Author(s): Aijun Sun, Xiaojing Zhu, Ying Liu, Rui Wang, Shuaikang Yang, Maikun Teng, Luping Zheng, Jun Luo, Gaiping Zhang, Guoqing Zhuang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0158565

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus
Cited by: 39
Author(s): Ahmed Sayadi, Elina Immonen, Helen Bayram, Göran Arnqvist
Software Mentions: 1
Published: about 10 years ago

10.3390/ijms19020642

Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A
Cited by: 14
Author(s): Regina Stoltenburg, Beate Strehlitz
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.102657

Low-abundance mutations in colorectal cancer patients and healthy adults
Cited by: 1
Author(s): Yanfei Li, Zhengsheng Dai, Gang Huang, Yueling Jin, Zhongping Ning, Junwei Shen
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-6145-8

Genomic characterization of Haemophilus influenzae: a focus on the capsule locus
Cited by: 25
Author(s): Caelin Cubeñas-Potts, Nadav Topaz, Lorraine D. Rodriguez‐Rivera, Fang Hu, How-Yi Chang, Melissa Whaley, Susanna Schmink, Adam C. Retchless, Alexander Chen, Edward Ramos, Gregory Doho, Xin Wang
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-015-1310-1

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
Cited by: 156
Author(s): Nahla V. Bassil, Thomas M. Davis, Hailong Zhang, Stephen P. Ficklin, Mike Mittmann, Teresa A. Webster, Lise L. Mahoney, David Wood, Elisabeth S Alperin, Umesh R. Rosyara, Herma Koehorst-vanc Putten, Amparo Monfort, Daniel J. Sargent, Iraida Amaya, B. Denoyés-Rothan, Luca Bianco, T. van Dijk, Ali Pirani, Amy Iezzoni, Dorrie Main, Cameron Peace, Yayuan Yang, Vance M. Whitaker, Sujeet Verma, Laurent Bellon, Fiona Brew, Raúl Herrera, Eric van de Weg
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms20020290

RNA Sequencing Reveals Differential Gene Expression of Cerrena Unicolor in Response to Variable Lighting Conditions
Cited by: 8
Author(s): Anna Pawlik, Andrzej Mazur, Jerzy Wielbo, Piotr Koper, Kamil Żebracki, Agnieszka Kubik-Komar, Grzegorz Janusz
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-71562-1

Kinship analysis on single cells after whole genome amplification
Cited by: 6
Author(s): Jana Weymaere, Ann-Sophie Vander Plaetsen, Laurentijn Tilleman, Olivier Tytgat, Kaat Rubben, Sofie Geeraert, Dieter Deforce, Filip Van Nieuwerburgh
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0174886

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing
Cited by: 29
Author(s): Endre Neparáczki, Klaudia Kocsy, Gábor Endre Tóth, Zoltán Maróti, Tibor Kalmár, Péter Bihari, István Nagy, György Paragh, Erika Molnár, István Raskó, Tibor Török
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-72242-w

Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics
Cited by: 16
Author(s): Ji‐Hyang Lee, Jun-Pyo Choi, Jinho Yang, Ha-Kyeong Won, Chan Sun Park, Woo-Jung Song, Hyouk‐Soo Kwon, Tae‐Bum Kim, Eui Chong Kim, Hae‐Sim Park, You Sook Cho
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-73501-6

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)
Cited by: 27
Author(s): Zac H. Forsman, Raphael Ritson‐Williams, Kaho H. Tisthammer, Ingrid S. Knapp, Robert J. Toonen
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-74163-0

Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe
Cited by: 1
Author(s): Mateusz Malinowski, Mashal Alawi, Ines Krohn, S. Emil Ruff, Daniela Indenbirken, Matthias Karrasch, Rolf Lüschow, Wolfgang R. Streit, Günter Timmermann, Andreas Pommerening‐Röser
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-75069-7

Genome-wide identification of AP2/ERF transcription factor-encoding genes in California poppy (Eschscholzia californica) and their expression profiles in response to methyl jasmonate
Cited by: 16
Author(s): Yasuyuki Yamada, S. Nishida, Nobukazu Shitan, Fumihiko Sato
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-75801-3

Single-cell RNA profiling links ncRNAs to spatiotemporal gene expression during C. elegans embryogenesis
Cited by: 2
Author(s): Yan Sun, Qichao Yu, Lei Li, Zhanlong Mei, Biaofeng Zhou, Shang Liu, Tao Pan, Liang Wu, Ying Lei, Longqi Liu, Radoje Drmanac, Kun Ma, Shiping Liu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0235853

An efficient ORF selection system for DNA fragment libraries based on split beta-lactamase complementation
Cited by: 0
Author(s): Vaishali Verma, Gopal Joshi, Amita Gupta, Vijay Chaudhary
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0200599

Supplementation stocking of Lake Trout (Salvelinus namaycush) in small boreal lakes: Ecotypes influence on growth and condition
Cited by: 13
Author(s): Olivier Morissette, Pascal Sirois, Nigel P. Lester, Chris C. Wilson, Louis Bernatchez
Software Mentions: 1
Published: about 8 years ago

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Papers Mentioning cutadapt 1,562