pypi: cutadapt | Projects | Ecosyste.ms: Papers

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: over 9 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 9 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: over 7 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 5 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 7 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: about 6 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 11 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: almost 10 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 9 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: almost 6 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 7 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: about 8 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 5 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: about 5 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 8 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 6 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: about 5 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 7 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 9 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 8 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 7 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 12 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 13 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: almost 9 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 8 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: almost 7 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 6 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 6 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: about 6 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: almost 6 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 5 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 5 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: almost 8 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 9 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 8 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: over 6 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 11 years ago

10.1038/s41598-020-69745-x

Systemically-delivered biodegradable PLGA alters gut microbiota and induces transcriptomic reprogramming in the liver in an obesity mouse model
Cited by: 9
Author(s): Alice Chaplin, Hanyu Gao, Courteney Asase, Rengasamy Palanivel, Bong Soo Park, Danielle Skander, Gürkan Bebek, Sanjay Rajagopalan, Andrei Maiseyeu
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-77586-x

An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
Cited by: 15
Author(s): Frédéric Jehl, Kévin Muret, Maria Bernard, Morgane Boutin, Lætitia Lagoutte, Colette Désert, Patrice Déhais, Diane Esquerré, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Frédérique Pitel, Tatiana Zerjal, Christophe Klopp, Sandrine Lagarrigue
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-78314-1

Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers
Cited by: 9
Author(s): Ezequiel Santillan, W. X. Phua, Florentin Constancias, Stefan Wuertz
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-80631-4

Response of bacterial and fungal communities to high petroleum pollution in different soils
Cited by: 40
Author(s): Polina Galitskaya, Liliya Biktasheva, Sergey Blagodatsky, Svetlana Selivanovskaya
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-81471-6

Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis
Cited by: 12
Author(s): Basharat Ahmad Bhat, Mıfftha Yaseen, Ashutosh Singh, Syed Mudasir Ahmad, Nazir Ahmad Ganai
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-86970-0

Biosyntheses characterization of alkaloids and flavonoids in Sophora flavescens by combining metabolome and transcriptome
Cited by: 9
Author(s): Guangfei Wei, Yongzhong Chen, Xiaotong Guo, Jianhe Wei, Lixin Dong, Shilin Chen
Software Mentions: 2
Published: over 5 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 5 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 5 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 5 years ago

10.1038/s41598-021-94649-9

Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
Cited by: 6
Author(s): Yong‐Bi Fu
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-96567-2

Optimized protocol for the extraction of RNA and DNA from frozen whole blood sample stored in a single EDTA tube
Cited by: 4
Author(s): Hirotaka Yamagata, Akito Kobayashi, Ryouichi Tsunedomi, Tomoe Seki, Mariko Kobayashi, Kosuke Hagiwara, Chong Chen, Shinichi Uchida, Go Okada, Manabu Fuchikami, Toshiharu Kamishikiryo, Jun‐ichi Iga, Shusuke Numata, Makoto Kinoshita, Takahiro A. Kato, Ryota Hashimoto, Hiroaki Nagano, Yasumasa Okamoto, Shu‐ichi Ueno, Tetsuro Ohmori, Shin Nakagawa
Software Mentions: 2
Published: about 5 years ago

10.3390/s20216398

Bacterial Respiration Used as a Proxy to Evaluate the Bacterial Load in Cooling Towers
Cited by: 0
Author(s): Stepan Toman, Bruno Kiilerich, Ian P. G. Marshall, Klaus Koren
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13287-015-0116-z

Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species
Cited by: 559
Author(s): S. Rubina Baglio, Koos Rooijers, Danijela Koppers-Lalić, Frederik J. Verweij, M Pérez Lanzón, Nicoletta Zini, B.A. Naaijkens, Francesca Perut, Hans W.M. Niessen, Nicola Baldini, D. Michiel Pegtel
Software Mentions: 2
Published: over 11 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: about 5 years ago

10.1038/tp.2016.87

Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia
Cited by: 36
Author(s): Shannon Ellis, Rebecca Panitch, Andrew B. West, Dan E. Arking
Software Mentions: 2
Published: over 10 years ago

10.1038/s41398-020-01159-9

Molecular pathology associated with altered synaptic transcriptome in the dorsolateral prefrontal cortex of depressed subjects
Cited by: 14
Author(s): Yuta Yoshino, Bhaskar Roy, Nilesh Kumar, M. Shahid Mukhtar, Yogesh K. Dwivedi
Software Mentions: 2
Published: over 5 years ago

10.1101/2021.07.26.453518

Increased aerosol transmission for B.1.1.7 (alpha variant) over lineage A variant of SARS-CoV-2
Cited by: 6
Author(s): Julia R Port, Claude Kwe Yinda, Victoria A. Avanzato, Jonathan Schulz, Myndi G. Holbrook, Neeltje van Doremalen, Carl Shaia, Robert J. Fischer, Vincent J. Munster
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.02041-16

Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases
Cited by: 25
Author(s): Daria Lavysh, Maria L. Sokolova, Marina Slashcheva, Konrad U. Förstner, Konstantin Severinov
Software Mentions: 2
Published: over 9 years ago

10.1128/mBio.02048-18

Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans
Cited by: 96
Author(s): Ella Shtifman Segal, Vladimir Gritsenko, Anton Levitan, Bhawna Yadav, Naama Dror, Jacob L. Steenwyk, Yael Silberberg, Kevin Mielich, Antonis Rokas, Neil A. R. Gow, Reinhard Kunze, Roded Sharan, Judith Berman
Software Mentions: 2
Published: almost 8 years ago

10.1128/mBio.01646-20

Identification of a Novel LysR-Type Transcriptional Regulator in Staphylococcus aureus That Is Crucial for Secondary Tissue Colonization during Metastatic Bloodstream Infection
Cited by: 7
Author(s): Michaela Groma, Sarah A. Horst, Sudip Das, Bruno Huettel, Maximilian Klepsch, Thomas Rudel, Eva Medina, Martin Fraunholz
Software Mentions: 2
Published: about 6 years ago

10.1128/mSphereDirect.00552-17

Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples
Cited by: 24
Author(s): Katherine S Xue, Alexander L. Greninger, Ailyn C. Pérez-Osorio, Jesse D. Bloom
Software Mentions: 2
Published: over 8 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 8 years ago

10.1128/mSphere.00827-19

Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
Cited by: 23
Author(s): Doratha A Byrd, Rashmi Sinha, Kristi L. Hoffman, Jun Chen, Xing Hua, Jianxin Shi, Nicholas Chia, Joseph F. Petrosino, Emily Vogtmann
Software Mentions: 2
Published: over 6 years ago

10.1128/mSphere.00855-20

Structured RNA Contaminants in Bacterial Ribo-Seq
Cited by: 15
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: almost 6 years ago

10.1128/mSystems.00047-17

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice
Cited by: 16
Author(s): Koji Yasuda, Tiffany Y. Hsu, Carey Ann Gallini, Lauren J. Mclver, Emma Schwager, Andy Shi, Casey DuLong, Randall Schwager, Galeb Abu-Ali, Eric A. Franzosa, Wendy S. Garrett, Curtis Huttenhower, Xochitl C. Morgan
Software Mentions: 2
Published: about 9 years ago

10.1128/mSystems.00214-18

Ribosome Profiling Reveals HSP90 Inhibitor Effects on Stage-Specific Protein Synthesis in Leishmania donovani
Cited by: 18
Author(s): Eugenia Bifeld, Stephan Lorenzen, Katharina Bartsch, Juan-José Vasquez, T. Nicolai Siegel, Joachim Clos
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSystems.00660-19

Impacts of the Plateau Environment on the Gut Microbiota and Blood Clinical Indexes in Han and Tibetan Individuals
Cited by: 35
Author(s): Zhilong Jia, Xiaojing Zhao, Xiaoshuang Liu, Le Zhao, Qi Jia, Jianxin Shi, Xiao Xu, Hao Lü, Zhenguo Xu, Qingwen Zhong, Kang Yu, Saijia Cui, Huining Chen, Jianying Guo, Xiang Li, Yang Han, Xinyu Song, Chenghui Zhao, Xiaochen Bo, Yaping Tian, Weidong Wang, Guotong Xie, Qiang Feng, Kunlun He
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00291-21

Direct Regulons of AtxA, the Master Virulence Regulator of Bacillus anthracis
Cited by: 5
Author(s): Yoshikazu Furuta, Cheng Cheng, Tuvshinzaya Zorigt, Atmika Paudel, Shun Izumi, Mai Tsujinouchi, Tomoko Shimizu, Wim G. Meijer, Hideaki Higashi
Software Mentions: 2
Published: about 5 years ago

10.1186/s40246-019-0251-1

Investigating RNA expression profiles altered by nicotinamide mononucleotide therapy in a chronic model of alcoholic liver disease
Cited by: 12
Author(s): Mohammed A. Assiri, Hadi Ali, John Marentette, Young-Ho Yun, Juan Liu, Matthew D. Hirschey, Laura Saba, Peter Harris, Kristofer S. Fritz
Software Mentions: 2
Published: almost 7 years ago

10.1002/humu.23724

Targeted resequencing of 358 candidate genes for autism spectrum disorder in a Chinese cohort reveals diagnostic potential and genotype–phenotype correlations
Cited by: 25
Author(s): Wei‐Zhen Zhou, Jie Zhang, Ziyi Li, Xiaojing Lin, Jiarui Li, Sheng Wang, Chengliang Yang, Qixi Wu, Adam Yongxin Ye, Meng Wang, Dandan Wang, Tad Zhengzhang Pu, Yu‐Yu Wu, Liping Wei
Software Mentions: 2
Published: over 7 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
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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 7 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 5 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: over 5 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: almost 6 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 7 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: about 7 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 7 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 5 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 9 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 10 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: almost 8 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 5 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 7 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 9 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 8 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 7 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: over 6 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 6 years ago

10.3390/ijms21103513

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

10.3390/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: about 6 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 6 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: over 5 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 5 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 6 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: over 7 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: almost 9 years ago

10.1186/s12870-015-0516-3

Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures
Cited by: 26
Author(s): Chandran Nithin, Nisha Patwa, Amal Thomas, Ranjit Prasad Bahadur, Jolly Basak
Software Mentions: 1
Published: over 11 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 10 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 7 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: almost 6 years ago

10.1186/s12870-019-1794-y

Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Cited by: 42
Author(s): Jubina Benny, Antonino Pisciotta, Tiziano Caruso, Federico Martinelli
Software Mentions: 1
Published: over 7 years ago

10.3390/ani10071130

Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles
Cited by: 1
Author(s): Rui-Yi Chen, Bui Thi Ngoc Hieu, Gilbert Audira, Bao Liu, Ming‐Der Lin, Chung-Der Hsiao
Software Mentions: 1
Published: about 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 6 years ago

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