pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.3390/genes11080851

Transcriptome Analysis of Pistacia vera Inflorescence Buds in Bearing and Non-Bearing Shoots Reveals the Molecular Mechanism Causing Premature Flower Bud Abscission
Cited by: 9
Author(s): Jubina Benny, Francesco Paolo Marra, Antonio Giovino, Bipin Balan, Tiziano Caruso, Federico Martinelli, Annalisa Marchese
Software Mentions: 2
Published: over 4 years ago

10.1128/mSphere.00614-17

Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis, and Ixodes scapularis Ticks
Cited by: 83
Author(s): Rafal Tokarz, Stephen Sameroff, Teresa Tagliafierro, Komal Jain, Simon H. Williams, D. Moses Cucura, Ilia Rochlin, Javier Monzón, Giovanna Carpi, Danielle M. Tufts, Maria A. Diuk‐Wasser, Jory Brinkerhoff, W. Ian Lipkin
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2019.00264

TRIBE Uncovers the Role of Dis3 in Shaping the Dynamic Transcriptome in Malaria Parasites
Cited by: 9
Author(s): Meng Liu, Binbin Lu, Yanting Fan, Xiaohong He, Shijun Shen, Cizhong Jiang, Qingfeng Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/s12885-018-4304-y

RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomas
Cited by: 7
Author(s): Pilar López-Nieva, Pablo Fernández-Navarro, Concepción Vaquero-Lorenzo, María Villa‐Morales, Osvaldo Graña‐Castro, María Ángeles Cobos-Fernández, José Luis López-Lorenzo, Pilar Llamas, Laura González-Sánchez, Isabel Sastre, Marina Pollán, Marcos Malumbres, Javíer Santos, José Fernández‐Piqueras
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2017.01407

Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies
Cited by: 60
Author(s): Akshaya Ramesh, Sam Darko, Axin Hua, Glenn Overman, Amy Ransier, Joseph R. Francica, Ashley M. Trama, Georgia D. Tomaras, Barton F. Haynes, Daniel C. Douek, Thomas B. Kepler
Software Mentions: 2
Published: about 7 years ago

10.1093/molbev/msaa290

Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish
Cited by: 14
Author(s): Shao-Bing Zong, Yulong Li, Jinxian Liu
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-90548-1

Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek’s disease virus
Cited by: 7
Author(s): Aijun Sun, Rui Wang, Shuaikang Yang, Xiaojing Zhu, Ying Liu, Maikun Teng, Luping Zheng, Jun Luo, Gaiping Zhang, Guoqing Zhuang
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2018.02887

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry
Cited by: 24
Author(s): Christina Jil Fiedler, Christoph Schönher, Philipp Proksch, David Kerschbaumer, Ernest Mayr, Marija Žunabović-Pichler, Konrad J. Domig, Reinhard Perfler
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12885-020-07130-7

Defective migration and dysmorphology of neutrophil granulocytes in atypical chronic myeloid leukemia treated with ruxolitinib
Cited by: 6
Author(s): Lea Bornemann, Marc Schuster, Saskia Schmitz, Charlyn Sobczak, Clara Bessen, Simon F. Merz, Karl‐Heinz Jöckel, Thomas Haverkamp, Matthias Gunzer, Joachim R. Göthert
Software Mentions: 2
Published: over 4 years ago

10.1017/S0016672316000136

Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions
Cited by: 11
Author(s): Anna Keravnou, Marios Ioannides, Kyriakos Tsangaras, Charalambos Loizides, Michael D. Hadjidaniel, Elisavet A. Papageorgiou, Skevi Kyriakou, Pavlos Antoniou, Petros Mina, Achilleas Achilleos, Maria Neofytou, Elena Kypri, Carolina Sismani, George Koumbaris, Philippos C. Patsalis
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13601-019-0267-6

A specific synbiotic-containing amino acid-based formula restores gut microbiota in non-IgE mediated cow’s milk allergic infants: a randomized controlled trial
Cited by: 21
Author(s): Harm Wopereis, Marleen T. J. van Ampting, Aysun Cetinyurek-Yavuz, R. A. Slump, D. C. A. Candy, Assad Butt, Diego Peroni, Yvan Vandenplas, Adam Fox, Neil Shah, Guus Roeselers, Lucien F. Harthoorn, Louise J. Michaelis, Jan Knol, Christina West
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.588906

Chitin Attenuates Expression of Listeria monocytogenes Virulence Genes in vitro
Cited by: 0
Author(s): Miguel Villoria Recio, Bo-Hyung Lee, Eva Maria Sternkopf Lillebæk, Birgitte H. Kallipolitis, Cormac G. M. Gahan, Hanne Ingmer, Mona Larsen
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-91724-z

Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies
Cited by: 9
Author(s): Giwon Shin, Hee Jung Koo, Mihwa Seo, Seung-Jae Lee, Hong Gil Nam, Gyoo Yeol Jung
Software Mentions: 2
Published: over 3 years ago

10.1002/ctm2.200

The noncoding and coding transcriptional landscape of the peripheral immune response in patients with COVID‐19
Cited by: 101
Author(s): Hao Tang, Yuehan Gao, Zhaohuai Li, Yushan Miao, Zhaofeng Huang, Xiuxing Liu, Lihui Xie, Li He, Wen Wen, Yingfeng Zheng, Wenru Su
Software Mentions: 2
Published: about 4 years ago

10.1186/s12711-020-00532-y

An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens
Cited by: 12
Author(s): Dirk-Jan de Koning, Nazaret Domínguez-Gasca, Robert Fleming, Andrew C. Gill, Dominic Kurian, Andrew Law, Heather McCormack, David Morrice, Estefanía Sánchez-Rodríguez, Alejandro B. Rodrı́guez-Navarro, Rudolf Preisinger, M. Schmutz, Veronika Šmídová, Frances Turner, Peter W.F. Wilson, Rongyan Zhou, Ian C. Dunn
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2229-14-4

Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight
Cited by: 70
Author(s): Mineharu Sugimoto, Youko Oono, Oleg Gusev, Takashi Matsumoto, Takayuki Yazawa, Margarita Levinskikh, Vladimir Sychev, Gail E. Bingham, Raymond M. Wheeler, Mary E. Hummerick
Software Mentions: 2
Published: almost 11 years ago

10.1002/ece3.5614

Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genusBuxus
Cited by: 8
Author(s): Nicholas LeBlanc, Jo Anne Crouch
Software Mentions: 2
Published: about 5 years ago

10.1111/pbi.12664

RNAi-mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing
Cited by: 9
Author(s): Katja Härtl, Gregor Kalinowski, Thomas Hoffmann, Anja Preuß, Wilfried Schwab
Software Mentions: 2
Published: over 7 years ago

10.1111/pbi.12997

Tracking disease resistance deployment in potato breeding by enrichment sequencing
Cited by: 50
Author(s): Miles Armstrong, Jack H. Vossen, Joanne Tze-Yin Lim, R.C.B. Hutten, Jianfei Xu, Shona Strachan, Brian Harrower, Nicolas Champouret, Eleanor M. Gilroy, Ingo Hein
Software Mentions: 2
Published: about 6 years ago

10.1128/genomeA.00594-14

Draft Genome Sequence of Kozakia baliensis SR-745, the First Sequenced Kozakia Strain from the Family Acetobacteraceae
Cited by: 4
Author(s): Jochen Schmid, Steven Koenig, André Pick, Fabian Steffler, Shosuke Yoshida, Kenji Miyamoto, Volker Sieber
Software Mentions: 2
Published: over 10 years ago

10.1038/s41379-020-0596-y

Targeted sequencing of FH-deficient uterine leiomyomas reveals biallelic inactivating somatic fumarase variants and allows characterization of missense variants
Cited by: 17
Author(s): Bernt Popp, Ramona Erber, Cornelia Kraus, Georgia Vasileiou, Juliane Hoyer, Stefanie Burghaus, Arndt Hartmann, Matthias W. Beckmann, André Reis, Abbas Agaimy
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-91718-x

mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting body in Ophiocordyceps sinensis
Cited by: 5
Author(s): Han Zhang, Yue Pan, Xuhui Tong, Jing Bai, Jingyan Yang, Jianbin Guo
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-020-01543-7

Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques
Cited by: 17
Author(s): Nicolas Baillet, Stéphanie Reynard, Émeline Perthame, Jimmy Hortion, Alexandra Journeaux, Mathieu Mateo, Xavier Carnec, Justine Schaeffer, Caroline Picard, Laura Barrot, Stéphane Barron, Audrey Vallvé, Aurélie Duthey, Frédéric Jacquot, Cathy Boehringer, Grégory Jouvion, Natalia Pietrosemoli, Rachel Legendre, Marie‐Agnès Dillies, Richard Allan, Catherine Legras-Lachuer, Caroline Carbonnelle, Hervé Raoul, Sylvain Baize
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.01031

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System
Cited by: 38
Author(s): Nancy Merino, Mikihiko Kawai, Eric S. Boyd, Daniel R. Colman, Shawn E. McGlynn, Kenneth H. Nealson, Ken Kurokawa, Yuichi Hongoh
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.11285

Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
Cited by: 4
Author(s): Robert S. Cornman, Jennifer A. Fike, Sara J. Oyler‐McCance, Paul M. Cryan
Software Mentions: 2
Published: over 3 years ago

10.1007/s00122-021-03910-2

A Trimethylguanosine Synthase1-like (TGS1) homologue is implicated in vernalisation and flowering time control
Cited by: 8
Author(s): Candy M. Taylor, Gagan Garg, Jens Berger, Federico M. Ribalta, Janine Croser, Karam B. Singh, Wallace Cowling, Lars G. Kamphuis, Matthew N. Nelson
Software Mentions: 2
Published: over 3 years ago

10.1186/s13567-020-00786-w

Distinct transcriptome signatures of Helicobacter suis and Helicobacter heilmannii strains upon adherence to human gastric epithelial cells
Cited by: 3
Author(s): Helena Berlamont, Chloë De Witte, E Bauwens, Hannah Min Jou, Richard Ducatelle, Ellen De Meester, Yannick Gansemans, Dieter Deforce, Filip Van Nieuwerburgh, Freddy Haesebrouck, Annemieke Smet
Software Mentions: 2
Published: over 4 years ago

10.15252/embj.201694857

TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs
Cited by: 84
Author(s): Dmytro Ustianenko, Josef Pasulka, Zuzana Feketová, Lukas Bednarik, Dagmar Zigáčková, Andrea Fořtová, Mihaela Zavolan, Štěpánka Vaňáčová
Software Mentions: 2
Published: about 8 years ago

10.3390/ijms22031469

Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis
Cited by: 27
Author(s): Fiaz Rasul, Saurabh Gupta, Justyna Jadwiga Olas, Tsanko Gechev, Neerakkal Sujeeth, Bernd Mueller‐Roeber
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-014-0420-4

Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
Cited by: 24
Author(s): Erin N. Smith, Kristen Jepsen, Mahdieh Khosroheidari, Laura Z. Rassenti, Matteo D’Antonio, Emanuela M. Ghia, Dennis A. Carson, Catriona Jamieson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-014-0504-1

Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak
Cited by: 23
Author(s): Paul R. McAdam, Charles W. Vander Broek, Diane Lindsay, Melissa J. Ward, Mary Hanson, Michael Gillies, Mick Watson, Joanne M. Stevens, Giles Edwards, J. Ross Fitzgerald
Software Mentions: 2
Published: about 10 years ago

10.1186/s13059-017-1150-1

Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania
Cited by: 47
Author(s): Fumiko Kawasaki, Dario Beraldi, Robyn Hardisty, Gordon R. McInroy, Pieter van Delft, Shankar Balasubramanian
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-017-1291-2

Conservation and divergence of small RNA pathways and microRNAs in land plants
Cited by: 76
Author(s): Chenjiang You, Jie Cui, Hui Wang, Xun Qi, Li Chung Kuo, Hong Mā, Lei Gao, Beixin Mo, Xuemei Chen
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-018-1618-7

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Cited by: 623
Author(s): Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Góes de Jesus, Bradley J. Main, Amanda L Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman, Kristian G. Andersen
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-021-02319-w

Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
Cited by: 3
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: over 3 years ago

10.1093/gbe/evz125

Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths
Cited by: 23
Author(s): David A. Ray, Jenna Grimshaw, Michaela K. Halsey, Jennifer M. Korstian, Austin Osmanski, Kevin A. Sullivan, Kristen A. Wolf, Harsith Reddy, Nicole M. Foley, Richard D. Stevens, Binyamin A. Knisbacher, Orr Levy, Brian A. Counterman, Nathaniel B. Edelman, James Mallet
Software Mentions: 2
Published: over 5 years ago

10.1093/gbe/evaa175

Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids
Cited by: 29
Author(s): Atsushi Nakabachi, Jörn Piel, Igor Malenovský, Yuu Hirose
Software Mentions: 2
Published: over 4 years ago

10.1186/s13073-015-0235-2

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing
Cited by: 97
Author(s): Alexander L. Greninger, Kevin Messacar, Thelma H. Dunnebacke, Samia N. Naccache, Scot Federman, Jérôme Bouquet, David M. Mirsky, Yoshihiko Nomura, Shigeo Yagi, Carol Glaser, Michael Vollmer, Craig A. Press, Bette K. Kleinschmidt‐DeMasters, Samuel R. Dominguez, Charles Y. Chiu
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13073-016-0375-z

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
Cited by: 36
Author(s): Tanjina Kader, David Goode, Stephen Q. Wong, Jacquie Connaughton, Simone M. Rowley, Lisa Devereux, David Byrne, Stephen B. Fox, Gisela Mir Arnau, Richard W. Tothill, Ian Campbell, Kylie L. Gorringe
Software Mentions: 2
Published: about 8 years ago

10.1186/s13073-017-0442-0

The genomic road to invasion—examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples
Cited by: 30
Author(s): Henry M. Wood, Catherine Daly, Rebecca Chalkley, Burcu Şengüven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, T.K. Ong, Kenneth MacLennan, Pamela Rabbitts, Caroline Conway
Software Mentions: 2
Published: over 7 years ago

10.1007/s00251-020-01181-7

High-throughput immunogenetic typing of koalas suggests possible link between MHC alleles and cancers
Cited by: 2
Author(s): Bonnie Chaban, Galit Tzipori, Kjell Nilsson, Peter Timms
Software Mentions: 2
Published: about 4 years ago

10.1111/imm.13158

Depletion of Foxp3 + regulatory T cells is accompanied by an increase in the relative abundance of Firmicutes in the murine gut microbiome
Cited by: 21
Author(s): Jan Kehrmann, Laura Effenberg, C. Matthias Wilk, Davina Schoemer, Nhi Ngo Thi Phuong, Alexandra Adamczyk, Eva Pastille, René Scholtysik, Ludger Klein-Hitpaß, Robert Klopfleisch, Astrid M. Westendorf, Jan Buer
Software Mentions: 2
Published: almost 5 years ago

10.1093/jas/sky260

Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli1,2
Cited by: 31
Author(s): Jolinda Pollock, David L. Gally, Laura Glendinning, Raksha Tiwari, Michael R. Hutchings, J.G.M. Houdijk
Software Mentions: 2
Published: over 6 years ago

10.1016/j.jbc.2021.100882

PRPF19 regulates p53-dependent cellular senescence by modulating alternative splicing of MDM4 mRNA
Cited by: 21
Author(s): Kimiyoshi Yano, Ryou‐u Takahashi, Bunsyo Shiotani, Junko Abe, Tomoki Shidooka, Yuki Sudo, Yusuke Yamamoto, Shisei Kan, Hiroki Sakagami, Hidetoshi Tahara
Software Mentions: 2
Published: over 3 years ago

10.1016/j.jbc.2021.100962

Transcriptional regulation of miR-30a by YAP impacts PTPN13 and KLF9 levels and Schwann cell proliferation
Cited by: 4
Author(s): Alyssa Shepard, Sany Hoxha, Scott Troutman, David Harbaugh, Michael S. Kareta, Joseph L. Kissil
Software Mentions: 2
Published: over 3 years ago

10.1111/jcmm.14075

BiallelicCCM3mutations cause a clonogenic survival advantage and endothelial cell stiffening
Cited by: 14
Author(s): Konrad Schwefel, Stefanie Spiegler, Sabine Ameling, Christiane D. Much, Robin A. Pilz, Oliver Otto, Uwe Völker, Ute Felbor, Matthias Rath
Software Mentions: 2
Published: almost 6 years ago

10.1111/jcmm.15101

Wilms' tumour 1‐associating protein inhibits endothelial cell angiogenesis by m6A‐dependent epigenetic silencing of desmoplakin in brain arteriovenous malformation
Cited by: 38
Author(s): Lin‐jian Wang, Yu Xue, Hao Li, Ran Huo, Zihan Yan, Jie Wang, Hongyuan Xu, Jia Wang, Yong Cao, Jizong Zhao
Software Mentions: 2
Published: over 4 years ago

10.1002/jcla.23896

Application of high‐throughput sequencing for hereditary thrombocytopenia in southwestern China
Cited by: 2
Author(s): Luying Zhang, Juanjuan Yu, Ying Xian, Xiaohong Wen, Xianmin Guan, Yuxia Guo, Ming Luo, Dou Yu
Software Mentions: 2
Published: over 3 years ago

10.3390/jcm8122077

Simultaneous Monitoring of Mutation and Chimerism Using Next-Generation Sequencing in Myelodysplastic Syndrome
Cited by: 20
Author(s): Jong-Mi Lee, Yoo-Jin Kim, Sung Soo Park, Eunhee Han, Myungshin Kim, Yonggoo Kim
Software Mentions: 2
Published: almost 5 years ago

10.1128/JCM.02337-16

Copy Number Heterogeneity of JC Virus Standards
Cited by: 18
Author(s): Alexander L. Greninger, Allen C. Bateman, Ederlyn E. Atienza, Sharon Wendt, Negar Makhsous, Keith R. Jerome, Linda Cook
Software Mentions: 2
Published: over 7 years ago

10.1128/JCM.01443-18

Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors
Cited by: 17
Author(s): Ronit R. Dalmat, Negar Makhsous, Gregory Pepper, Amalia Magaret, Keith R. Jerome, Anna Wald, Alexander L. Greninger
Software Mentions: 2
Published: almost 6 years ago

10.1128/JCM.01261-19

A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak
Cited by: 15
Author(s): Mitchell J. Sullivan, Deena R. Altman, Kieran I. Chacko, Brianne Ciferri, Elizabeth Webster, Theodore R. Pak, Gintaras Deikus, Martha Lewis-Sandari, Zenab Khan, Colleen Beckford, Angela Rendo, Flora Samaroo, Robert Sebra, Ramona Karam-Howlin, Tanis C. Dingle, Camille Hamula, Ali Kashif Bashir, Eric E. Schadt, Gopi Patel, Frances Wallach, Andrew Kasarskis, Kathleen Gibbs, Harm van Bakel
Software Mentions: 2
Published: almost 5 years ago

10.1093/jxb/eru373

Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin
Cited by: 387
Author(s): Shi Hong, Chuan Jiang, Tiantian Ye, Dun Xian Tan, Russel J. Reíter, Heng Zhang, Renyi Liu, Zhulong Chan
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.ppat.1003579

Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection
Cited by: 69
Author(s): João Trindade Marques, Ji Ping Wang, Xiaohong Wang, Karla Pollyanna Vieira de Oliveira, Catherine Gao, Eric Roberto Guimarães Rocha Aguiar, Nadereh Jafari, Richard W. Carthew
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.ppat.1006678

Single-cell analysis identifies cellular markers of the HIV permissive cell
Cited by: 43
Author(s): Sylvie Rato, Antonio Rausell, Miguel Muñoz, Amalio Telenti, Angela Ciuffi
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.ppat.1006954

HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes
Cited by: 65
Author(s): Thomas Hennig, Marco Michalski, Andrzej Rutkowski, Lara Djaković, Adam W. Whisnant, Marie-Sophie Friedl, Bhaskar Anand Jha, Marisa A. P. Baptista, Anne L’Hernault, Florian Erhard, Lars Dölken, Caroline C. Friedel
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008069

Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages
Cited by: 38
Author(s): Violaine Dubois, Alexandre Pawlik, Anouchka Bories, Vincent Le Moigne, Odile Sismeiro, Rachel Legendre, Hugo Varet, María del Pilar Rodríguez-Ordóñez, Jean‐Louis Gaillard, Jean‐Yves Coppée, Roland Brosch, Jean-Louis Herrmann, Fabienne Girard-Misguich
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1008091

Zygote morphogenesis but not the establishment of cell polarity in Plasmodium berghei is controlled by the small GTPase, RAB11A
Cited by: 3
Author(s): Harshal Prakash Patil, Katie R. Hughes, Leandro Lemgruber, Nisha Philip, Nicholas J. Dickens, G. Lucas Starnes, Andrew P. Waters
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1008566

Tn-Seq reveals hidden complexity in the utilization of host-derived glutathione in Francisella tularensis
Cited by: 14
Author(s): Kathryn M. Ramsey, Hannah E. Ledvina, Tenayaann M. Tresko, Jamie M. Wandzilak, Catherine A. Tower, Thomas Tallo, Caroline E. Schramm, S. Brook Peterson, Shawn J. Skerrett, Joseph D. Mougous, Simon L. Dove
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1008835

Downy Mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility
Cited by: 27
Author(s): Sarah Harvey, Priyanka Kumari, Dmitry Lapin, Thomas Griebel, Richard Hickman, Wenbin Guo, Runxuan Zhang, Jane E. Parker, Jim Beynon, Katherine J. Denby, Jens Steinbrenner
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1008904

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
Cited by: 19
Author(s): Crispín Zavala-Alvarado, Odile Sismeiro, Rachel Legendre, Hugo Varet, Giovanni Bussotti, Jan Bayram, Samuel G. Huete, Guillaume Rey, Jean‐Yves Coppée, Mathieu Picardeau, Nadia Benaroudj
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.ppat.1009430

Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype
Cited by: 34
Author(s): Rajan Guha, Anna Mathioudaki, Safiatou Doumbo, Didier Doumtabé, Jeff Skinner, Gunjan Arora, Shafiuddin Siddiqui, Shanping Li, Kassoum Kayentao, Aissata Ongoïba, Judith B. Zaugg, Boubacar Traoré, Peter D. Crompton
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1009575

Rapid progression is associated with lymphoid follicle dysfunction in SIV-infected infant rhesus macaques
Cited by: 3
Author(s): Matthew P. Wood, Chloe I. Jones, Adriana Lippy, Brian G. Oliver, Brynn Walund, Katherine A. Fancher, Bridget S. Fisher, Piper J. Wright, James T. Fuller, Patience Murapa, Jakob Habib, Maud Mavigner, Ann Chahroudi, D. Noah Sather, Deborah H. Fuller, Donald L. Sodora
Software Mentions: 2
Published: over 3 years ago

10.1073/pnas.1813512115

Relationship between intact HIV-1 proviruses in circulating CD4 + T cells and rebound viruses emerging during treatment interruption
Cited by: 58
Author(s): Ching-Lan Lu, Joy A. Pai, Lilian Nogueira, Pilar Mendoza, Henning Gruell, Thiago Y. Oliveira, John P. Barton, Julio C. C. Lorenzi, Yehuda Z. Cohen, Lillian B. Cohn, Florian Klein, Marina Caskey, Michel C. Nussenzweig, Mila Janković
Software Mentions: 2
Published: about 6 years ago

10.1007/s13238-017-0475-6

Correction of β-thalassemia mutant by base editor in human embryos
Cited by: 164
Author(s): Puping Liang, Chenhui Ding, Hongwei Sun, Xiaowei Xie, Yanwen Xu, Xiya Zhang, Yu Sun, Yuanyan Xiong, Wenbin Ma, Yongxiang Liu, Yali Wang, Jian-Pei Fang, Dan Liú, Zhou Songyang, Canquan Zhou, Junjiu Huang
Software Mentions: 2
Published: about 7 years ago

10.1080/15476286.2018.1514236

Evaluation of methodologies for microRNA biomarker detection by next generation sequencing.
Cited by: 44
Author(s): Anna M.L. Coenen-Stass, Iddo Magen, Tony Brooks, Iddo Z. Ben‐Dov, Linda Greensmith, Eran Hornstein, Pietro Fratta
Software Mentions: 2
Published: about 6 years ago

10.1080/15476286.2020.1723328

Identification of RNA 3´ ends and termination sites in Haloferax volcanii
Cited by: 13
Author(s): Sarah J. Berkemer, Lisa‐Katharina Maier, Fabian Amman, Stephan H. Bernhart, Julia Wörtz, Pascal Märkle, Friedhelm Pfeiffer, Peter F. Stadler, Anita Marchfelder
Software Mentions: 2
Published: almost 5 years ago

10.1098/rsos.150196

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation
Cited by: 44
Author(s): Jessica A. Goodheart, Adam L. Bazinet, Allen G. Collins, Michael P. Cummings
Software Mentions: 2
Published: about 9 years ago

10.1186/s13045-019-0697-6

Transcriptional factor six2 promotes the competitive endogenous RNA network between CYP4Z1 and pseudogene CYP4Z2P responsible for maintaining the stemness of breast cancer cells
Cited by: 49
Author(s): Lufeng Zheng, Qianqian Guo, Chenxi Xiang, Shijia Liu, Yahui Jiang, Lanlan Gao, Haiwei Ni, Ting Wang, Qiong Zhao, Hai Liu, Yingying Xing, Yaohui Wang, Xiaoman Li, Tao Xi
Software Mentions: 2
Published: over 5 years ago

10.1038/s41388-021-01656-1

LIMK1 promotes peritoneal metastasis of gastric cancer and is a therapeutic target
Cited by: 18
Author(s): Kang Xi, Weilin Li, Weixin Liu, Han Liang, Jingyu Deng, Jun Yu, Suisheng Zhao, Wei Kang, Ka Fai To, Philip Wai Yan Chiu, Guiying Wang, Enders Kwok Wai Ng
Software Mentions: 2
Published: over 3 years ago

10.1016/j.jlr.2021.100105

A novel compound heterozygous leptin receptor mutation causes more severe obesity than in Lepr mice
Cited by: 3
Author(s): C Berger, Henrike O. Heyne, Tina Heiland, Sebastian Dommel, Corinna Höfling, Esther Guiu‐Jurado, Jana E. Lorenz, Steffen Rößner, Michael Dannemann, Janet Kelso, Peter Kovacs, Matthias Blüher, Nora Klöting
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.61991

A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch
Cited by: 9
Author(s): Zijun Wang, Christopher O. Barnes, Rajeev Gautam, Julio C. C. Lorenzi, Christian T. Mayer, Thiago Y. Oliveira, Víctor Ramos, Melissa Cipolla, Kristie Gordon, Harry B. Gristick, Anthony P. West, Yoshiaki Nishimura, Henna Raina, Michael S. Seaman, Anna Gazumyan, Malcolm A. Martin, Pamela J. Björkman, Michel C. Nussenzweig, Amelia Escolano
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.42014

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice
Cited by: 58
Author(s): João Pl Castro, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William Beluch, Ronald Naumann, Isabella Skuplik, James C. Cobb, Nicholas H. Barton, Campbell Rolian, Yingguang Frank Chan
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.49662

Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles
Cited by: 76
Author(s): Jan Janouškovec, Gita G. Paskerova, Tatiana S. Miroliubova, Kirill V. Mikhailov, Thomas Birley, Vladimir V. Aleoshin, Timur G. Simdyanov
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.52135

PCK1 and DHODH drive colorectal cancer liver metastatic colonization and hypoxic growth by promoting nucleotide synthesis
Cited by: 58
Author(s): Norihiro Yamaguchi, Ethan M. Weinberg, Alexander Nguyen, Maria V. Liberti, Hani Goodarzi, Yelena Y. Janjigian, Philip B. Paty, Leonard Saltz, T. Peter Kingham, Jia Min Loo, Elisa de Stanchina, Sohail F. Tavazoie
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.65184

Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands
Cited by: 39
Author(s): Madeleine Bossaert, Angélique Pipier, Jean‐François Riou, Céline Noirot, Linh-Trang Nguyên, Rémy-Félix Serre, Olivier Bouchez, Éric Defrancq, Patrick Calsou, Sébastien Britton, Dennis Gómez
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.28590

Fibroblast growth factors (FGFs) prime the limb specific Shh enhancer for chromatin changes that balance histone acetylation mediated by E26 transformation-specific (ETS) factors
Cited by: 10
Author(s): Silvia Peluso, Adam Douglas, Alison Hill, Carlo DeAngelis, Benjamin L. Moore, Graeme R. Grimes, Giulia Petrovich, Abdelkader Essafi, Robert E. Hill
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.22750

Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis
Cited by: 95
Author(s): Shengben Li, Brandon H. Le, Xuan Ma, Shaofang Li, Chenjiang You, Yu Yu, Bailong Zhang, Lin Liu, Lei Gao, Ting Shi, Yue Zhao, Beixin Mo, Xiaofeng Cao, Xuemei Chen
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.40037

The RNA interactome of human telomerase RNA reveals a coding-independent role for a histone mRNA in telomere homeostasis
Cited by: 12
Author(s): Roland Iványi-Nagy, Syed Moiz Ahmed, Sabrina Peter, Priya Dharshana Ramani, P.P. Ong, Oliver Dreesen, Peter Dröge
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.68068

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
Cited by: 71
Author(s): Adrian L. Sanborn, Benjamin Yeh, Jordan T. Feigerle, Cynthia V. Hao, Raphael J.L. Townshend, E Aiden, Ron O. Dror, Barbara Maier-Davis
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.42549

Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome
Cited by: 32
Author(s): Martin Wegner, Valentina Diehl, Verena Bittl, Rahel de Bruyn, Svenja Wiechmann, Yves Matthess, Marie Hebel, Michael Hayes, Simone Schaubeck, Chris Benner, Sven Heinz, Anja Bremm, Ivan Đikić, Andreas Ernst, Manuel Kaulich
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.26875

Parallel evolution of influenza across multiple spatiotemporal scales
Cited by: 107
Author(s): Katherine S Xue, Terry Stevens-Ayers, Angela P Campbell, Janet A. Englund, Steven A. Pergam, Michael Boeckh, Jesse D. Bloom
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms19030717

Comparative Transcriptome Profiling of Rice Near-Isogenic Line Carrying Xa23 under Infection of Xanthomonas oryzae pv. oryzae
Cited by: 33
Author(s): Rezwan Tariq, Chunlian Wang, Tengfei Qin, Feifei Xu, Yongchao Tang, Ying Gao, Zhiyuan Ji, Kun Zhao
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20102532

Transcriptome Analysis to Shed Light on the Molecular Mechanisms of Early Responses to Cadmium in Roots and Leaves of King Grass (Pennisetum americanum × P. purpureum)
Cited by: 21
Author(s): Junlong Zhao, Bo Xia, Yu Meng, Zhongfu Yang, Ling Pan, Man Zhou, Xinquan Zhang
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21020419

Maternal Recognition of Pregnancy in the Horse: Are MicroRNAs the Secret Messengers?
Cited by: 7
Author(s): Katrien Smits, Yannick Gansemans, Laurentijn Tilleman, Filip Van Nieuwerburgh, M. Van de Velde, Ilse Gerits, Cyrillus Ververs, K. Roels, Jan Govaere, Luc Peelman, Dieter Deforce, Ann Van Soom
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21082723

Heterogenic Origin of Micro RNAs in Atlantic Salmon (Salmo salar) Seminal Plasma
Cited by: 9
Author(s): Teshome Tilahun Bizuayehu, Igor Babiak
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21103513

Small RNA Sequencing Analysis of miRNA Expression Reveals Novel Insihts into Root Formation under Root Restriction Cultivation in Grapevine (Vitis vinifera L.)
Cited by: 6
Author(s): Hui Li, Zhen Gao, Muhammad Zahid, Dongmei Li, Hafiz Umer Javed, Lei Wang, Shiren Song, Liping Zhao, Wenping Xu, Caixi Zhang, Chao Ma, Shiping Wang
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21155217

Characteristics of Circular RNA Expression Profiles of Porcine Granulosa Cells in Healthy and Atretic Antral Follicles
Cited by: 17
Author(s): Meng Li, K. J. Teerds, Tao Jiang, Hengxi Wei, Marcel Jaklofsky, Zhihong Zhao, Yao-di Liang, Li Li, Chi Chiu Wang, Shouquan Zhang
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21186452

Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
Cited by: 3
Author(s): Jung-Im Won, Jae-Moon Shin, So Young Park, Jeehee Yoon, Dong‐Hoon Jeong
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms221810154

Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing
Cited by: 11
Author(s): Tengfei Shen, Mengxuan Xu, Haoran Qi, Ying Feng, Zhangqi Yang, Meng Xu
Software Mentions: 2
Published: about 3 years ago

10.1186/s12974-020-01860-y

Evaluation of M2-like macrophage enrichment after diffuse traumatic brain injury through transient interleukin-4 expression from engineered mesenchymal stromal cells
Cited by: 27
Author(s): Syed Faaiz Enam, Sajidur Rahman Kader, Nicholas Bodkin, Johnathan G. Lyon, Mark Calhoun, Cesar Azrak, Pooja Tiwari, Daryll Vanover, Haichen Wang, Philip J. Santangelo, Ravi V. Bellamkonda
Software Mentions: 2
Published: over 4 years ago

10.1080/20002297.2019.1663084

Composition and maternal origin of the neonatal oral cavity microbiota
Cited by: 25
Author(s): Heidi Tuominen, María Carmen Collado, Jaana Rautava, Stina Syrjänen, Samuli Rautava
Software Mentions: 2
Published: almost 6 years ago

10.18632/oncotarget.21918

Integrated analysis of mRNA and miRNA expression profiles in livers of Yimeng black pigs with extreme phenotypes for backfat thickness
Cited by: 8
Author(s): Wentong Li, Yalan Yang, Ying Liu, Shuai Liu, Xiuxiu Li, Ying‐Ping Wang, Yanmin Zhang, Hui Tang, Rong Zhou, Kui Li
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.63444

Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies
Cited by: 3
Author(s): Laura Doepker, Sonja Danon, Elias Harkins, D. Ralph, Zak A. Yaffe, Meghan Garrett, Amrit Dhar, Cassia Wagner, Megan Stumpf, Dana Arenz, James A. Williams, Walter Jaoko, Kishor Mandaliya, Kelly K. Lee, F. A. Matsen, Julie Overbaugh
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13059-017-1232-0

EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels
Cited by: 18
Author(s): Josquin Daron, R. Keith Slotkin
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.43022

Random-sequence genetic oligomer pools display an innate potential for ligation and recombination
Cited by: 39
Author(s): Hannes Mutschler, Alexander I. Taylor, Benjamin T. Porebski, Alice Lightowlers, Gillian Houlihan, Mikhail Abramov, Piet Herdewijn, Philipp Holliger
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.17448

Characterization of mouse serum exosomal small RNA content: The origins and their roles in modulating inflammatory response
Cited by: 25
Author(s): Xin Zhou, Zinan Jiao, Juling Ji, Shuyuan Li, Xiaodi Huang, Xiaoshuang Lu, Heng Zhao, Jingwen Peng, Xinya Chen, Qiuhong Ji, Yuhua Ji
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.10565

Genomic DNA transposition induced by human PGBD5
Cited by: 62
Author(s): Anton Henssen, Elizabeth Hénaff, Eileen Jiang, Amy Eisenberg, Julianne Carson, Camila M. Villasante, Mondira Ray, Eric Still, Melissa Burns, Jorge Gandara, Cédric Feschotte, Christopher E. Mason, Alex Kentsis
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.16788

Next-generation sequencing reveals microRNA markers of adrenocortical tumors malignancy
Cited by: 31
Author(s): Łukasz Koperski, Marta Kotlarek, Michał Świerniak, Monika Kolanowska, Anna Klinke, Barbara Górnicka, Krystian Jażdżewski, Anna Wójcicka
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21165753

Alterations of Rice (Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus
Cited by: 6
Author(s): Linying Li, Yuqing He, Xueying Zhang, Hehong Zhang, Zongtao Sun, Junmin Li, Gaojie Hong
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562