pypi: cutadapt | Projects | Ecosyste.ms: Papers

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: over 4 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 7 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 4 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 7 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 6 years ago

10.3389/fmicb.2020.591619

Rice Stripe Virus Coat Protein-Mediated Virus Resistance Is Associated With RNA Silencing in Arabidopsis
Cited by: 3
Author(s): Feng Sun, Peisong Hu, Wei Wang, Ying Lan, Linlin Du, Yijun Zhou, Tong Zhou
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2018.01005

A Dispensable Chromosome Is Required for Virulence in the Hemibiotrophic Plant Pathogen Colletotrichum higginsianum
Cited by: 37
Author(s): Peter-Louis Plaumann, Johannes Schmidpeter, Marlis Dahl, Leila Taher, Christian A. Koch
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2019.00005

Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria
Cited by: 10
Author(s): Anoop Alex, Agostinho Antunes
Software Mentions: 1
Published: almost 6 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: over 3 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: over 3 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 10 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 4 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 4 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: about 4 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: about 4 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: about 4 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: about 4 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: almost 11 years ago

10.1038/s41598-020-73885-5

Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes
Cited by: 9
Author(s): Robert Mukiibi, Dayle Johnston, Michael Vinsky, Carolyn Fitzsimmons, Paul Stothard, Sinéad M. Waters, Changxi Li
Software Mentions: 1
Published: about 4 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 4 years ago

10.1038/s41598-020-77639-1

Secreted sphingomyelins modulate low mammary cancer incidence observed in certain mammals
Cited by: 7
Author(s): Melissa M. Ledet, Rebecca M. Harman, Jiwei Fan, Emily Schmitt-Matzen, M. Elena Díaz-Rubio, Sheng Zhang, Gerlinde R. Van de Walle
Software Mentions: 1
Published: almost 4 years ago

10.1128/mSystems.00724-20

High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression
Cited by: 15
Author(s): Jaya Saini, Bhaswati Bandyopadhyay, AK Pandey, V G Ramachandran, Shukla Das, Vikas Sood, Arup Banerjee, Sudhanshu Vrati
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-79332-9

Molecular patterns of isolated tubulitis differ from tubulitis with interstitial inflammation in early indication biopsies of kidney allografts
Cited by: 4
Author(s): Petra Hrubá, Katelynn S. Madill‐Thomsen, Martina Macková, Jǐŕı Kléma, Jana Malušková, Luděk Voska, Alena Paříková, Janka Slatinská, Philip F. Halloran, Ondřej Viklický
Software Mentions: 1
Published: almost 4 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: almost 4 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: almost 4 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: almost 6 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 3 years ago

10.1038/s41598-021-93086-y

Acetaldehyde exposure underlies functional defects in monocytes induced by excessive alcohol consumption
Cited by: 5
Author(s): Shintaro Shiba, Nobuhiro Nakamoto, Po–Sung Chu, Keisuke Ojiro, Nobuhito Taniki, Akihiro Yamaguchi, Rei Morikawa, Tadashi Katayama, Aya Yoshida, Ryo Aoki, Toshiaki Teratani, Takahiro Suzuki, Takeshi Miyamoto, Sachiko Hara, Akira Yokoyama, Takanori Kanai
Software Mentions: 1
Published: over 3 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 4 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 3 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: about 4 years ago

10.1038/s41598-021-98168-5

The macronuclear genome of the Antarctic psychrophilic marine ciliate Euplotes focardii reveals new insights on molecular cold adaptation
Cited by: 12
Author(s): Matteo Mozzicafreddo, Sandra Pucciarelli, Estienne C. Swart, Angela Piersanti, Christiane Emmerich, Giovanna Migliorelli, Patrizia Ballarini, Cristina Miceli
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-021-98452-4

Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
Cited by: 8
Author(s): Laila Sara Arroyo Mühr, Joakim Dillner, Agustín Enrique Ure, Karin Sundström, Emilie Hultin
Software Mentions: 1
Published: about 3 years ago

10.1186/s43141-019-0006-3

Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil
Cited by: 18
Author(s): Pushpender Kumar Sharma, Vinay K. Sharma, Shailesh Sharma, Garima Bhatia, Kashmir Singh, Rohit Sharma
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-98820-0

NEIL3-deficiency increases gut permeability and contributes to a pro-atherogenic metabolic phenotype
Cited by: 4
Author(s): Tom Rune Karlsen, Xiang Yi Kong, Sverre Holm, Ana Quiles‐Jiménez, Tuva B. Dahl, Kuan Yang, Ellen Lund Sagen, Tonje Skarpengland, Jonas Øgaard, Kristian Holm, Beate Vestad, Maria Belland Olsen, Pål Aukrust, Magnar Bjørås, Johannes R. Hov, Bente Halvorsen, Ida Gregersen
Software Mentions: 1
Published: about 3 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 7 years ago

10.1038/s41396-020-0688-1

Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut
Cited by: 9
Author(s): Mariko Takeuchi, Hiroya Kuwahara, Takumi Murakami, Kuniyuki Takahashi, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Moriya Ohkuma, Yuichi Hongoh
Software Mentions: 1
Published: over 4 years ago

10.1016/j.stemcr.2017.05.013

Fetal Therapy Model of Myelomeningocele with Three-Dimensional Skin Using Amniotic Fluid Cell-Derived Induced Pluripotent Stem Cells
Cited by: 29
Author(s): Kazuhiro Kajiwara, Tomohiro Tanemoto, Seiji Wada, Jurii Karibe, Norimasa Ihara, Yu Ikemoto, Tomoyuki Kawasaki, Yoshie Oishi, Osamu Samura, Koji Okamura, Shuji Takada, Hidenori Akutsu, Haruhiko Sago, Aikou Okamoto, Akihiro Umezawa
Software Mentions: 1
Published: over 7 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: over 7 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: about 4 years ago

10.1038/s41396-018-0157-2

Temporal dynamics of microbiota before and after host death
Cited by: 19
Author(s): David Preiswerk, Jean‐Claude Walser, Dieter Ebert
Software Mentions: 1
Published: over 6 years ago

10.1186/s13287-021-02384-9

Bone marrow mesenchymal stem cells and their derived exosomes resolve doxorubicin-induced chemobrain: critical role of their miRNA cargo
Cited by: 15
Author(s): Marwa O. El-Derany, Mohamed Noureldein
Software Mentions: 1
Published: over 3 years ago

10.1155/2017/4252974

Long Noncoding RNA uc001pwg.1 Is Downregulated in Neointima in Arteriovenous Fistulas and Mediates the Function of Endothelial Cells Derived from Pluripotent Stem Cells
Cited by: 4
Author(s): Lei Lv, Haozhe Qi, Xiaojia Guo, Qihong Ni, Zezhen Yan, Lan Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1007/s00122-019-03305-4

Genetic insights into morphometric inflorescence traits of wheat
Cited by: 31
Author(s): Gizaw M. Wolde, Corinna Trautewig, Martin Mascher, Thorsten Schnurbusch
Software Mentions: 1
Published: almost 6 years ago

10.1007/s00122-020-03743-5

Genome-wide identification of loci modifying spike-branching in tetraploid wheat
Cited by: 8
Author(s): Gizaw M. Wolde, Mona Schreiber, Corinna Trautewig, Axel Himmelbach, Shun Sakuma, Martin Mascher, Thorsten Schnurbusch
Software Mentions: 1
Published: over 3 years ago

10.3390/toxins8120378

Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs
Cited by: 11
Author(s): Donghui Xu, Xianchun Wang
Software Mentions: 1
Published: almost 8 years ago

10.1186/2047-9158-3-17

In silico analysis of regulatory networks underlines the role of miR-10b-5p and its target BDNF in huntington’s disease
Cited by: 34
Author(s): Sören Müller
Software Mentions: 1
Published: over 10 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 3 years ago

10.1007/s11250-021-02877-y

Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi
Cited by: 10
Author(s): J.N. Hakizimana, Jean‐Bosco Ntirandekura, Clara M. Yona, Lionel Nyabongo, Gladson Kamwendo, Julius L.C. Chulu, Désiré Ntakirutimana, Olivier Kamana, Hans Nauwynck, Gerald Misinzo
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.03.11.435000

ChAdOx1 nCoV-19 (AZD1222) protects Syrian hamsters against SARS-CoV-2 B.1.351 and B.1.1.7
Cited by: 18
Author(s): Robert J. Fischer, Neeltje van Doremalen, Danielle R. Adney, Claude Kwe Yinda, Julia R Port, Myndi G. Holbrook, Jonathan Schulz, Brandi N. Williamson, Tina Thomas, Kent D. Barbian, Sarah L. Anzick, Stacy Ricklefs, Brian J Smith, Dan Long, Craig Martens, Greg Saturday, Emmie de Wit, Sarah C. Gilbert, Teresa Lambe, Vincent J. Munster
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.06.17.448814

Western diet increases COVID-19 disease severity in the Syrian hamster
Cited by: 9
Author(s): Julia R Port, Danielle R. Adney, Benjamin Schwarz, Jonathan Schulz, Daniel E. Sturdevant, Brian J Smith, Victoria A. Avanzato, Myndi G. Holbrook, Jyothi N. Purushotham, Kaitlin A. Stromberg, Ian Leighton, Catharine M. Bosio, Carl Shaia, Vincent J. Munster
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.05.07.443115

Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques
Cited by: 6
Author(s): Vincent J. Munster, Meaghan Flagg, Manmeet Singh, Brandi N. Williamson, Friederike Feldmann, Lizzette Pérez-Pérez, Beniah Brumbaugh, Myndi G. Holbrook, Danielle R. Adney, Atsushi Okumura, Patrick W. Hanley, Brian J Smith, Jamie Lovaglio, Sarah L. Anzick, Craig Martens, Neeltje van Doremalen, Greg Saturday, Emmie de Wit
Software Mentions: 1
Published: over 3 years ago

10.1101/2021.08.25.457626

The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters
Cited by: 3
Author(s): Timothy D. Carroll, Douglas Fox, Neeltje van Doremalen, Erin E. Ball, Mary Kate Morris, Alicia Sotomayor-González, Venice Servellita, Arjun Rustagi, Claude Kwe Yinda, Linda Fritts, Julia R Port, Zhien Ma, Myndi G. Holbrook, Jonathan Schulz, Catherine A. Blish, Carl V. Hanson, Charles Y. Chiu, Vincent J. Munster, Sarah A. Stanley, Christopher J. Miller
Software Mentions: 1
Published: about 3 years ago

10.1128/mBio.00844-17

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity
Cited by: 23
Author(s): Ivaylo P. Ivanov, Jiajie Wei, Stephen Z. Caster, Kristina M. Smith, Audrey M. Michel, Ying Zhang, Andrew E. Firth, Michael Freitag, Jay C. Dunlap, Deborah Bell-Pedersen, John F. Atkins, Matthew S. Sachs
Software Mentions: 1
Published: over 7 years ago

10.1128/mBio.00419-18

A Viral Suppressor Modulates the Plant Immune Response Early in Infection by Regulating MicroRNA Activity
Cited by: 28
Author(s): Robert Pertermann, Selvaraj Tamilarasan, Torsten Gursinsky, Giorgio Gambino, Jana Schuck, Claus Weinholdt, Hauke Lilie, Ivo Große, Ralph Golbik, Vitantonio Pantaleo, Sven-Erik Behrens
Software Mentions: 1
Published: over 6 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 3 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 3 years ago

10.1128/mBio.01315-19

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients
Cited by: 87
Author(s): Azadeh Saffarian, Céline Mulet, Béatrice Regnault, Aurélien Amiot, J. Tran-Van-Nhieu, Jacques Ravel, Iradj Sobhani, Philippe J. Sansonetti, Thierry Pédron
Software Mentions: 1
Published: about 5 years ago

10.1128/mBio.00600-20

“ <i>Candidatus</i> Ethanoperedens,” a Thermophilic Genus of <i>Archaea</i> Mediating the Anaerobic Oxidation of Ethane
Cited by: 59
Author(s): Cedric Jasper Hahn, Rafael Laso-Pérez, Francesca Vulcano, Konstantinos-Marios Vaziourakis, Runar Stokke, Ida Helene Steen, Andreas Teske, Antje Boetius, Manuel Liebeke, Rudolf Amann, Katrin Knittel, Gunter Wegener
Software Mentions: 1
Published: over 4 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: over 4 years ago

10.1128/mBio.02052-20

Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation
Cited by: 8
Author(s): Thomas Seviour, Lan Li Wong, Yang Lü, Sudarsan Mugunthan, Qiaohui Yang, Uma Shankari, Irina Bessarab, David Liebl, Rohan B. H. Williams, Yingyu Law, Staffan Kjelleberg
Software Mentions: 1
Published: about 4 years ago

10.1128/mBio.01492-20

CaaX-Like Protease of Cyanobacterial Origin Is Required for Complex Plastid Biogenesis in Malaria Parasites
Cited by: 3
Author(s): Thomas R. Meister, Yong Tang, Michael J. Pulkoski-Gross, Ellen Yeh
Software Mentions: 1
Published: about 4 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 4 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 4 years ago

10.1128/mBio.00972-21

Expression of the Ebola Virus VP24 Protein Compromises the Integrity of the Nuclear Envelope and Induces a Laminopathy-Like Cellular Phenotype
Cited by: 5
Author(s): Santiago Vidal, María Teresa Sánchez-Aparicio, Rocio Castro Seoane, Ahmed El Motiam, Emily V Nelson, Yanis Hichem Bouzaher, Maite Baz-Martínez, Isabel García-Dorival, Susana Gonzalo, Enrique Vázquez, Anxo Vidal, César Muñoz‐Fontela, Adolfo Garcı́a-Sastre, Carmen Rivas
Software Mentions: 1
Published: about 3 years ago

10.1128/mSphere.00615-17

Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients
Cited by: 16
Author(s): Xuan Qin, Chuan Zhou, Danielle M. Zerr, Amanda Adler, Amin Addetia, Shuo Yuan, Alexander L. Greninger
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphere.00090-18

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis
Cited by: 31
Author(s): Clement K. M. Tsui, Ruth R. Miller, Miguel Uyaguari, Patrick Tang, Cédric Chauve, William W. L. Hsiao, Judith L. Isaac-Renton, Natalie Prystajecky
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphere.00311-18

Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches
Cited by: 16
Author(s): Simon H. Williams, Samuel Cordey, Nishit Bhuva, Florian Laubscher, Mary-Anne Hartley, Noémie Boillat‐Blanco, Zainab Mbarack, Josephine Samaka, Tarsis Mlaganile, Komal Jain, Valérie D’Acremont, Laurent Kaiser, W. Ian Lipkin
Software Mentions: 1
Published: about 6 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: about 4 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 4 years ago

10.1016/j.csbj.2021.03.034

Formation, characterization and modeling of emergent synthetic microbial communities
Cited by: 8
Author(s): Jia Wang, Dana L. Carper, Leah H. Burdick, Him K. Shrestha, Manasa R. Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz
Software Mentions: 1
Published: almost 4 years ago

10.1038/s42003-020-01425-y

Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes
Cited by: 12
Author(s): Nicolas Pitzalis, Khalid Amari, Stéfanie Graindorge, David Pflieger, Livia Donaire, Michael Wassenegger, César Llave, Manfred Heinlein
Software Mentions: 1
Published: almost 4 years ago

10.1038/cti.2016.42

Repertoire comparison of the B-cell receptor-encoding loci in humans and rhesus macaques by next-generation sequencing
Cited by: 39
Author(s): В. И. Вигдорович, Brian G. Oliver, Sara Carbonetti, Nicholas Dambrauskas, Miles D. Lange, Christina Yacoob, W. Leahy, Jonathan Callahan, Leonidas Stamatatos, D. Noah Sather
Software Mentions: 1
Published: over 8 years ago

10.1186/s13148-019-0640-2

Temple syndrome in a patient with variably methylated CpGs at the primary MEG3/DLK1:IG-DMR and severely hypomethylated CpGs at the secondary MEG3:TSS-DMR
Cited by: 11
Author(s): Masayo Kagami, Atsuhiro Yanagisawa, Masaho Ota, Katsuyoshi Matsuoka, Akie Nakamura, Kazuo Matsubara, Kazuhiko Nakabayashi, Shuji Takada, Maki Fukami, Tsutomu Ogata
Software Mentions: 1
Published: over 5 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 4 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 4 years ago

10.1186/s13148-020-00938-x

Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing
Cited by: 7
Author(s): Juozas Gordevičius, Milda Narmontė, Povilas Gibas, Kotryna Kvederavičiūtė, Vita Tomkutė, Priit Paluoja, Kaarel Krjutškov, Andres Salumets, Edita Kriukienė
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2105-14-362

iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq
Cited by: 54
Author(s): Giorgio Giurato, Maria Rosaria De Filippo, Antonio Rinaldi, Adnan Hashim, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz
Software Mentions: 1
Published: almost 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: over 6 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 4 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 4 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: over 4 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: almost 6 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: about 5 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 10 years ago

10.1186/s40478-020-01000-w

A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology
Cited by: 11
Author(s): Julia Lorenz, Tanja Rothhammer-Hampl, Saida Zoubaa, Elisabeth Bumes, Tobias Pukrop, Oliver Kölbl, Selim Corbacioglu, Nils Ole Schmidt, Martin Proescholdt, Peter Hau, Markus J. Riemenschneider
Software Mentions: 1
Published: over 4 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 3 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 4 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: over 4 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: over 4 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: about 8 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: about 4 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 8 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: over 8 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 7 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: over 4 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: over 6 years ago

10.1371/journal.pone.0095782

Extending the sRNAome of Apple by Next-Generation Sequencing
Cited by: 15
Author(s): Marike Visser, Van der Walt Anelda, Hans J. Maree, D. J. G. Rees, Johan T. Burger
Software Mentions: 1
Published: over 10 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 3 years ago

10.1371/journal.pone.0224969

A fecal sequel: Testing the limits of a genetic assay for bat species identification
Cited by: 14
Author(s): Faith M. Walker, Abby Tobin, Nancy B. Simmons, Colin J. Sobek, Daniel E. Sanchez, Christopher P. Chambers, Viacheslav Y. Fofanov
Software Mentions: 1
Published: about 5 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562