10.7717/peerj.11820

Clinical and prognostic relevance of <i>CXCL12</i> expression in acute myeloid leukemia
Cited by: 2
Author(s): Shi-sen Wang, Zi‐jun Xu, Yue Jin, Ji‐chun Ma, Pei‐hui Xia, Xiang‐mei Wen, Zhen-wei Mao, Lin Jiang, Jun Qian
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.60645

Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation
Cited by: 28
Author(s): Christian Brion, Sheila Lutz, Frank W. Albert
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.685742

Antibiotic Intervention Affects Maternal Immunity During Gestation in Mice
Cited by: 6
Author(s): Marilen Benner, Alejandro Lopez-Rincon, Suzan Thijssen, Johan Garssen, Gerben Ferwerda, Irma Joosten, Renate G. van der Molen, Astrid Hogenkamp
Software Mentions: 4
Published: almost 5 years ago

10.3389/fimmu.2019.00555

Preferential Infiltration of Unique Vγ9Jγ2-Vδ2 T Cells Into Glioblastoma Multiforme
Cited by: 21
Author(s): Mijeong Lee, Chanho Park, Jeongmin Woo, Jin-Ho Kim, Inseong Kho, Do‐Hyun Nam, Woong-Yang Park, Yeonsoo Kim, Doo‐Sik Kong, Hye Won Lee, Tae Jin Kim
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.7295

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples
Cited by: 7
Author(s): Tonia DeBellis, Steven W. Kembel, Jean‐Philippe Lessard
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13007-020-00605-5

High-throughput method for detection and quantification of lesions on leaf scale based on trypan blue staining and digital image analysis
Cited by: 14
Author(s): Emina Mulaosmanovic, Tobias U. T. Lindblom, Marie Bengtsson, Sofia Windstam, Lars Mogren, Salla Marttila, Hartmut Stützel, Beatrix Alsanius
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.21697

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
Cited by: 43
Author(s): Lorenzo Rinaldi, Alexandra Avgustinova, Mercé Martı́n, Debayan Datta, Guiomar Solanas, Neus Prats, Salvador Aznar Benitah
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.15842

Identifying biomarkers of papillary renal cell carcinoma associated with pathological stage by weighted gene co-expression network analysis
Cited by: 29
Author(s): Zhong He, Min Sun, Ke Yuan, Rongjie Lin, Youde Xiao, Shaosheng Zhou, Hong Zhao, Yan Wang, Fuxiang Zhou, Youwen Zhou
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.20023

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey
Cited by: 68
Author(s): Yu-Ting Hsueh, Matthew R. Gronquist, Erich M. Schwarz, Ravi D. Nath, Ching-Han Lee, Shalha Gharib, Frank C. Schroeder, Paul W. Sternberg
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.67932

Wnt signaling enhances macrophage responses to IL-4 and promotes resolution of atherosclerosis
Cited by: 25
Author(s): Ada Weinstock, Karishma Rahman, Or Yaacov, Hitoo Nishi, Prashanthi Menon, Cyrus Nikain, Michela L. Garabedian, Stephanie Pena, Naveed Akbar, Brian E. Sansbury, Sean Heffron, Jianhua Liu, Gregory Marecki, Dawn Fernandez, Emily J. Brown, Kelly V. Ruggles, Stephen A. Ramsey, Chiara Giannarelli, Matthew Spite, Robin P. Choudhury, P’ng Loke, Edward A. Fisher
Software Mentions: 4
Published: over 5 years ago

10.3389/fnut.2021.640100

Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome
Cited by: 7
Author(s): Jason W. Arnold, Hunter D. Whittington, Sue F. Dagher, Jeffery Roach, M. Andrea Azcárate-Peril, José M. Bruno-Bárcena
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.691725

Severe COVID-19 Recovery Is Associated with Timely Acquisition of a Myeloid Cell Immune-Regulatory Phenotype
Cited by: 29
Author(s): A.C. Trombetta, Guilherme B. Farias, André M. C. Gomes, Ana Godinho‐Santos, Pedro Rosmaninho, Carolina M. Conceição, Joel Laia, Diana Santos, Afonso R. M. Almeida, Catarina Mota, Andréia Gomes, María Luisa Madueño Serrano, Marc Veldhoen, Ana E. Sousa, S. Fernandes
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.37892

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
Cited by: 57
Author(s): Amr Nassrallah, Martin Rougée, Clara Bourbousse, Stéphanie Drevensek, Sandra Fonseca, Elisa Iniesto, Ouardia Aït-Mohamed, Anne Flore Deton-Cabanillas, Gérald Zabulon, Ikhlak Ahmed, David Stroebel, Vanessa Masson, Bérangère Lombard, Dominique Eeckhout, Kris Gevaert, Damarys Loew, Auguste Genovesio, Cécile Breyton, Geert De Jaeger, Chris Bowler, Vicente Rubio, Frédy Barneche
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.66417

Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19
Cited by: 56
Author(s): Courtney Tindle, MacKenzie Fuller, Ayden G. Fonseca, Sahar Taheri, Stella‐Rita Ibeawuchi, Nathan Beutler, Gajanan D. Katkar, Amanraj Claire, Vanessa Castillo, Moises Hernandez, Hana Russo, Jason Duran, Laura E. Crotty Alexander, Ann Tipps, Grace Lin, Patricia A. Thistlethwaite, Ranajoy Chattopadhyay, Thomas F. Rogers, Debashis Sahoo, Pradipta Ghosh, Soumita Das
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.7905

Effects of plant growth-promoting rhizobacteria on co-inoculation with <i>Bradyrhizobium</i> in soybean crop: a meta-analysis of studies from 1987 to 2018
Cited by: 51
Author(s): Douglas Mariani Zeffa, Lucas Henrique Fantin, Alessandra Koltun, André Luiz Martinez de Oliveira, Maria Paula Nunes, Marcelo Giovanetti Canteri, Leandro Simões Azeredo Gonçalves
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1008502

Ablation of non-coding RNAs affects bovine leukemia virus B lymphocyte proliferation and abrogates oncogenesis
Cited by: 15
Author(s): Roghaiyeh Safari, Jean-Rock Jacques, Yves Brostaux, Luc Willems
Software Mentions: 4
Published: about 6 years ago

10.1186/s40168-021-01115-9

Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis
Cited by: 181
Author(s): Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, Guolong Zhang, Jiangchao Zhao, Junjun Wang
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.46919

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Cited by: 63
Author(s): Kirsty Sawicka, Caryn Hale, Christopher Y. Park, John Fak, Jodi Gresack, Sarah J. Van Driesche, Jaw Jou Kang, Jennifer C. Darnell, Robert B. Darnell
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.68573

Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis
Cited by: 22
Author(s): Martin H Fabry, Federica A. Falconio, Fadwa Joud, Emily K Lythgoe, Benjamin Czech, Gregory J. Hannon
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-021-01055-4

Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota
Cited by: 18
Author(s): Jennifer M. Baker, Kevin J. Hinkle, Roderick A. McDonald, Christopher Brown, Nicole R. Falkowski, Gary B. Huffnagle, Robert P. Dickson
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2020.01982

Human Regulatory Dendritic Cells Develop From Monocytes in Response to Signals From Regulatory and Helper T Cells
Cited by: 10
Author(s): Xiangyue Zhang, Pingping Zheng, Tyler R. Prestwood, Hong Zhang, Yaron Carmi, Lorna Tolentino, Nancy Wu, Okmi Choi, Daniel A. Winer, Samuel Strober, Eun‐Suk Kang, Michael N. Alonso, Edgar G. Engleman
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-020-00981-z

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
Cited by: 17
Author(s): Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Γεώργιος Μαρίνος, Christoph Kaleta, Nico Jehmlich, Christian H. Ahrens, Martin von Bergen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0177739

Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid
Cited by: 15
Author(s): Wang Hai, Shengyan Li, Shouzhen Teng, Haisheng Liang, Hongjia Xin, Hongjiang Gao, Dafang Huang, Zhihong Lang
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.62731

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis
Cited by: 22
Author(s): Markus Terrey, Scott I. Adamson, Alana L. Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55775

Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers
Cited by: 13
Author(s): Özgür Genç, Joon Yong An, Richard D. Fetter, Yelena Kulik, Giulia Zunino, Stephan J. Sanders, Graeme W. Davis
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms9091842

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire
Cited by: 5
Author(s): Sara Laetitia Elphège Gnangui, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Koua, Claude Ghislaine Kouadjo, Don A. Cowan, Adolphe Zézé
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms9081564

An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma
Cited by: 6
Author(s): Yunyoung Kwak
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0115964

A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: over 11 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: about 9 years ago

10.3389/fneur.2020.582767

Added Prognostic Value of Hemorrhagic Transformation Quantification in Patients With Acute Ischemic Stroke
Cited by: 8
Author(s): Katinka R. van Kranendonk, Kilian M. Treurniet, Anna M. M. Boers, Olvert A. Berkhemer, Jonathan M. Coutinho, Hester F. Lingsma, Wim H. van Zwam, Aad van der Lugt, Robert J. van Oostenbrugge, Diederik W.J. Dippel, Yvo B.W.E.M. Roos, Henk A. Marquering, Charles B. L. M. Majoie, Clean Registry Investigators
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.58041

Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria
Cited by: 52
Author(s): Sara M. Nowinski, Ashley Solmonson, Scott F. Rusin, J. Alan Maschek, Claire Bensard, Sarah Fogarty, Mi Young Jeong, Sandra Lettlová, Jordan A. Berg, Jeffrey T. Morgan, Yeyun Ouyang, Bradley C. Naylor, João A. Paulo, Katsuhiko Funai, James E. Cox, Steven P. Gygi, Dennis R. Winge, Ralph J. DeBerardinis, Jared Rutter
Software Mentions: 4
Published: almost 6 years ago

10.1002/pld3.241

Control of translation during the unfolded protein response in maize seedlings: Life without PERKs
Cited by: 9
Author(s): Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.60987

Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons
Cited by: 9
Author(s): Bastien Saint-Leandre, Courtney J. Christopher, Mia T. Levine
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.49501

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes
Cited by: 103
Author(s): Prashant Rajbhandari, Douglas Arneson, Sydney K Hart, In Sook Ahn, Graciel Diamante, Leonardo D. Santos, Nima Zaghari, An‐Chieh Feng, Brandon J. Thomas, Laurent Vergnes, Stephen D. Lee, Abha K. Rajbhandari, Karen Reue, Stephen T. Smale, Xia Yang, Peter Tontonoz
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22147699

Impact of Long-Term Enzyme Replacement Therapy on Glucosylsphingosine (Lyso-Gb1) Values in Patients with Type 1 Gaucher Disease: Statistical Models for Comparing Three Enzymatic Formulations
Cited by: 9
Author(s): Tama Dinur, Ulrike Grittner, Shoshana Revel‐Vilk, Michal Becker‐Cohen, Majdolen Istaiti, Claudia Cozma, Arndt Rolfs, Ari Zimran
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms9091876

The Terrestrial Plastisphere: Diversity and Polymer-Colonizing Potential of Plastic-Associated Microbial Communities in Soil
Cited by: 21
Author(s): Joana MacLean, Sathish Mayanna, Liane G. Benning, Fabian Horn, Alexander Bartholomäus, Yosri Wiesner, Dirk Wagner, Susanne Liebner
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.57525

The role of the NMD factor UPF3B in olfactory sensory neurons
Cited by: 15
Author(s): Kun Tan, Samantha H. Jones, Blue B. Lake, Jennifer N Dumdie, Eleen Y. Shum, Lingjuan Zhang, Song Chen, Abhishek Sohni, Shivam Pandya, Richard L. Gallo, Kun Zhang, Heidi Cook‐Andersen, Miles Wilkinson
Software Mentions: 4
Published: almost 6 years ago

10.1093/bioinformatics/bts394

An accurate paired sample test for count data
Cited by: 58
Author(s): Thang V. Pham, Connie R. Jiménez
Software Mentions: 4
Published: almost 14 years ago

10.3390/microorganisms9081595

Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau
Cited by: 7
Author(s): Rui Wang, Wei Miao, Jing Wang, Yongjun Lin
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13073-021-00948-1

An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration
Cited by: 9
Author(s): Xanthe Brands, Bastiaan W. Haak, Augustijn M. Klarenbeek, Joe Butler, Fabrice Uhel, Wanhai Qin, Natasja A. Otto, Marja E. Jakobs, Daniel Faber, René Lutter, W. Joost Wiersinga, Tom van der Poll, Brendon P. Scicluna
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms8010008

Tissue- and Population-Level Microbiome Analysis of the Wasp Spider Argiope bruennichi Identified a Novel Dominant Bacterial Symbiont
Cited by: 22
Author(s): Monica M. Sheffer, Gabriele Uhl, Stefan Prost, Tillmann Lueders, Tim Urich, Mia M. Bengtsson
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.20949

Overcoming resistance to single-agent therapy for oncogenic <i>BRAF</i> gene fusions <i>via</i> combinatorial targeting of MAPK and PI3K/mTOR signaling pathways
Cited by: 35
Author(s): Payal Jain, Amanda Silva, Harry Han, Shih Shan Lang, Yuankun Zhu, Katie Boucher, Tiffany Smith, Aesha Vakil, Patrick Diviney, Namrata Choudhari, Pichai Raman, Christine Busch, Timothy Delaney, Xiaodong Yang, Aleksandra Olow, Sabine Mueller, Daphne A. Haas‐Kogan, Elizabeth Fox, Phillip B. Storm, Adam Resnick, Angela J. Waanders
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2020.615481

Microbial Flow Within an Air-Phyllosphere-Soil Continuum
Cited by: 19
Author(s): Shu‐Yi‐Dan Zhou, Hu Li, Madeline Giles, Roy Neilson, Xiao‐Ru Yang, Jian‐Qiang Su
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009208

A multi-omics approach to Epstein-Barr virus immortalization of B-cells reveals EBNA1 chromatin pioneering activities targeting nucleotide metabolism
Cited by: 20
Author(s): Jason Lamontagne, Samantha S. Soldan, Chenhe Su, Andreas Wiedmer, Kyoung Jae Won, Fang Lü, Aaron R. Goldman, Jayamanna Wickramasinghe, Hsin‐Yao Tang, David W. Speicher, Louise C. Showe, Andrew V. Kossenkov, Paul M. Lieberman
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9061310

Meropenem Pharmacokinetics and Target Attainment in Critically Ill Patients Are Not Affected by Extracorporeal Membrane Oxygenation: A Matched Cohort Analysis
Cited by: 12
Author(s): Matthias Gijsen, Erwin Dreesen, Pieter Annaert, Johan Nicolaï, Yves Debaveye, Joost Wauters, Isabel Spriet
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms8111729

A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes
Cited by: 7
Author(s): Kshitij Tandon, Bayanmunkh Baatar, Pei‐Wen Chiang, Dashdondog Narangarvuu, Bolormaa Oyuntsetseg, Sen‐Lin Tang
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.29132

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium
Cited by: 122
Author(s): David R. Hill, Sha Huang, Melinda S. Nagy, Veda K. Yadagiri, Courtney Fields, Dishari Mukherjee, Brooke Bons, Priya H. Dedhia, Alana M. Chin, Yu Hwai Tsai, Shrikar Thodla, Thomas M. Schmidt, Seth T. Walk, Vincent B. Young, Jason R. Spence
Software Mentions: 4
Published: over 8 years ago

10.1186/s12935-019-0950-7

A six-gene prognostic model predicts overall survival in bladder cancer patients
Cited by: 37
Author(s): Liwei Wang, Jiazhong Shi, Yaqin Huang, Sha Li, Jingqi Zhang, Hua Ding, Jin Yang, Zhiwen Chen
Software Mentions: 4
Published: almost 7 years ago

10.1183/13993003.03201-2020

Plasma metabolomics exhibit response to therapy in chronic thromboembolic pulmonary hypertension
Cited by: 23
Author(s): Emilia M. Swietlik, Pavandeep Ghataorhe, Kasia Zalewska, John Wharton, Luke Howard, Dolores Taboada, John Cannon, Nicholas W. Morrell, Martin R. Wilkins, Mark Toshner, Joanna Pepke‐Zaba, Christopher J. Rhodes
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.22130

Systematic analysis of the expression profile of non-coding RNAs involved in ischemia/reperfusion-induced acute kidney injury in mice using RNA sequencing
Cited by: 25
Author(s): Jun Zhou, Hongtao Chen, Yu Fan
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.16220

Trisomy 21 consistently activates the interferon response
Cited by: 205
Author(s): Kelly D. Sullivan, Hannah C. Lewis, Amanda A. Hill, Ahwan Pandey, Leisa Jackson, Joseph M Cabral, Keith P Smith, L. Alexander Liggett, Eliana B. Gómez, Matthew D. Galbraith, James DeGregori, Joaquín M. Espinosa
Software Mentions: 4
Published: almost 10 years ago

10.3390/microorganisms7100441

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale
Cited by: 17
Author(s): Sonia S. Valencia-Agami, Daniel Cerqueda‐García, S. Putzeys, María Magdalena Uribe-Flores, Ulises García-Cruz, Daniel Pech, Jorge A. Herrera-Silveira, M. Leopoldina Aguirre-Macedo, José Q. García-Maldonado
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.ppat.1009644

Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection
Cited by: 46
Author(s): Liliana Echavarría-Consuegra, G. M. W. Cook, Idoia Busnadiego, Charlotte Lefèvre, Sarah Keep, Katherine A. Brown, Nicole Doyle, Giulia Dowgier, Krzysztof Franaszek, Nathan Moore, Stuart G. Siddell, Erica Bickerton, Benjamin G. Hale, Andrew E. Firth, Ian Brierley, Nerea Irigoyen
Software Mentions: 4
Published: about 5 years ago

10.1111/pbi.13260

The pomegranate (<i>Punica granatum</i>L.) draft genome dissects genetic divergence between soft‐ and hard‐seeded cultivars
Cited by: 59
Author(s): Xiang Luo, Haoxian Li, Zhuona Wu, Wen Yao, Peng Zhao, Da Cao, Haiyan Yu, Kaidi Li, Krishna Poudel, Dan Zhao, Fuhong Zhang, Xiaocong Xia, Lina Chen, Qi Wang, Dan Jing, Shangyin Cao
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.4088

PlantCV v2: Image analysis software for high-throughput plant phenotyping
Cited by: 191
Author(s): Malia Gehan, Arash Abbasi, Jeffrey C. Berry, Steven T. Callen, Leonardo Chavez, Andrew N. Doust, Max Feldman, Kerrigan B. Gilbert, John G. Hodge, J. Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael D. Miller, Éric Platon, Monica Tessman, Tony Sax
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2019.01253

Signal Integration of IFN-I and IFN-II With TLR4 Involves Sequential Recruitment of STAT1-Complexes and NFκB to Enhance Pro-inflammatory Transcription
Cited by: 32
Author(s): Anna Piaszyk-Borychowska, Lajos Széles, Attila Csermely, Hsüch‐Ching Chiang, Joanna Wesoły, Chien‐Kuo Lee, László Nagy, Hans A.R. Bluyssen
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.ppat.1009789

Pulmonary mesenchymal stem cells are engaged in distinct steps of host response to respiratory syncytial virus infection
Cited by: 5
Author(s): Melanie Brügger, Thomas Démoulins, G. Tuba Barut, Béatrice Zumkehr, Blandina I. Oliveira Esteves, Kemal Mehinagic, Quentin Haas, Aline Schögler, Marie‐Anne Rameix‐Welti, Jean François Eléouët, Ueli Moehrlen, Thomas Marti, Ralph A. Schmid, Artur Summerfield, Horst Posthaus, Nicolas Ruggli, Sean Hall, Marco P. Alves
Software Mentions: 4
Published: almost 5 years ago

10.3389/fimmu.2020.608895

Gentamicin Induced Microbiome Adaptations Associate With Increased BCAA Levels and Enhance Severity of Influenza Infection
Cited by: 6
Author(s): Ye Sun, Zi He, Jiajia Li, Saisai Gong, Shunzong Yuan, Tao Li, Nianzhi Ning, Xing Li, Liangyan Zhang, Fanghong Chen, Li Zhan, Jianxin Wang, Di Luo, Hui Wang
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.60681

SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Cited by: 6
Author(s): Charlotte P Choi, Rebecca J Tay, Margaret R. Starostik, Suhua Feng, James J. Moresco, Brooke E. E. Montgomery, Emily Xu, Maya A Hammonds, Michael C. Schatz, Taiowa A. Montgomery, John R. Yates, Steven E. Jacobsen, John K. Kim
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.27861

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer
Cited by: 124
Author(s): Neel Shah, Ping Wang, John Wongvipat, Wouter R. Karthaus, Wassim Abida, Joshua Armenia, Shira Rockowitz, Yotam Drier, B Bernstein, Henry W. Long, Matthew L. Freedman, Vivek Arora, Deyou Zheng, Charles L. Sawyers
Software Mentions: 4
Published: almost 9 years ago

10.7717/peerj.7705

The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma
Cited by: 30
Author(s): Jieling Li, Wang Xiao, Kai Zheng, Ying Liu, Junjun Li, Shaoqi Wang, Kaisheng Liu, Xianrang Song, Nan Li, Shouqi Xie, Shaoxiang Wang
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep42110

Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal
Cited by: 37
Author(s): Jane Khudyakov, Cory D. Champagne, Lorenzo Meneghetti, Daniel E. Crocker
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2020.00129

Broad and Fine Scale Variability in Bacterial Diversity and Cyanotoxin Quotas in Benthic Cyanobacterial Mats
Cited by: 8
Author(s): Georgia Thomson‐Laing, Jonathan Puddick, Olivier Laroche, Samantha Fulton, Konstanze Steiner, Mark W. Heath, Susanna A. Wood
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2020.00216

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells
Cited by: 26
Author(s): Noudjoud Attaf, Iñaki Cervera-Marzal, Chuang Dong, Laurine Gil, Amédée Renand, Lionel Spinelli, Pierre Milpied
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.02037

Expression Profile of Glossina pallidipes MicroRNAs During Symptomatic and Asymptomatic Infection With Glossina pallidipes Salivary Gland Hypertrophy Virus (Hytrosavirus)
Cited by: 8
Author(s): Irene K. Meki, İkbal Agah Ince, Henry M. Kariithi, Drion G. Boucias, Orhan Özcan, Andrew G. Parker, Just M. Vlak, Monique M. van Oers, Adly M. M. Abd-Alla
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.43738

Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice
Cited by: 66
Author(s): Mina Kojima, Dirk G. de Rooij, David C. Page
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.729359

Construction of Interferon-Gamma-Related Gene Signature to Characterize the Immune-Inflamed Phenotype of Glioblastoma and Predict Prognosis, Efficacy of Immunotherapy and Radiotherapy
Cited by: 9
Author(s): Hang Ji, Yixu Ba, Shuai Ma, Kezuo Hou, Shan Mi, Xin Gào, Jiaqi Jin, Qingguo Gong, Ting Liu, Fang Wang, Zhihui Liu, Shupeng Li, Jianyang Du, Shaoshan Hu
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.11020

Differential gene expression in a tripartite interaction:<i>Drosophila</i>,<i>Spiroplasma</i>and parasitic wasps
Cited by: 4
Author(s): Victor Manuel Higareda Alvear, Mariana Mateos, Diego Cortez, Cécilia Tamborindeguy, Esperanza Martínez‐Romero
Software Mentions: 4
Published: over 5 years ago

10.1093/bib/bbv019

Optimization of miRNA-seq data preprocessing
Cited by: 100
Author(s): Susan H. Tam, Ming‐Sound Tsao, John Douglas Mcpherson
Software Mentions: 4
Published: over 11 years ago

10.1186/s13062-015-0071-8

Experiences with workflows for automating data-intensive bioinformatics
Cited by: 51
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimerà, Aleksi Kallio, Eija Korpelainen, Maciej M. Kańduła, Milko Krachunov, David P. Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy, Dimitar Vassilev
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13059-021-02396-x

Chromosome-level genome assembly of a regenerable maize inbred line A188
Cited by: 28
Author(s): Guifang Lin, Cheng He, Jun Zheng, Dal Hoe Koo, Ha Le, Huakun Zheng, Tej Man Tamang, Jianqing Lin, Yan Liu, Mingxia Zhao, Yangfan Hao, Frank McFraland, Bo Wang, Qin Yang, Haibao Tang, Donald R. McCarty, Hairong Wei, Myeong Je Cho, Sunghun Park, Heidi F. Kaeppler, Shawn M. Kaeppler, Yun-Jun Liu, Nathan M. Springer, Patrick S. Schnable, Guoying Wang, Frank F. White, Sanzhen Liu
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2021.716627

Multidrug Resistant Acinetobacter baumannii Biofilms: Evaluation of Phenotypic–Genotypic Association and Susceptibility to Cinnamic and Gallic Acids
Cited by: 7
Author(s): Mahmoud M. Sherif, Walid F. Elkhatib, Wafaa S. Khalaf, Nooran S. Elleboudy, Neveen A. Abdelaziz
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-020-6520-5

Identification of eQTLs and sQTLs associated with meat quality in beef
Cited by: 16
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Raluca G. Mateescu
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: about 7 years ago

10.3389/fmolb.2021.703307

A Potential circRNA-miRNA-mRNA Regulatory Network in Asthmatic Airway Epithelial Cells Identified by Integrated Analysis of Microarray Datasets
Cited by: 7
Author(s): Dian Chen, Wenliang Wu, Lingling Yi, Yuchen Feng, Chenli Chang, Shengchong Chen, Jiali Gao, Gongqi Chen, Guohua Zhen
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.53459

The histone modification reader ZCWPW1 links histone methylation to PRDM9-induced double-strand break repair
Cited by: 28
Author(s): Tao Huang, Shenli Yuan, Lei Gao, Mengjing Li, Xiaochen Yu, Jianhong Zhan, Yingying Yin, Chao Liu, Chuanxin Zhang, Gang Lü, Wei Li, Jiang Liu, Zi‐Jiang Chen, Hongbin Liu
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-03390-9

Aberrant plasticity of peripheral sensory axons in a painful neuropathy
Cited by: 30
Author(s): Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Software Mentions: 4
Published: about 9 years ago

10.3389/fmolb.2021.687576

A Comprehensive Analysis of the Downregulation of miRNA-1827 and Its Prognostic Significance by Targeting SPTBN2 and BCL2L1 in Ovarian Cancer
Cited by: 7
Author(s): Penghui Feng, Zhitong Ge, Zaixin Guo, Lin Lin, Qi Yu
Software Mentions: 4
Published: about 5 years ago

10.1186/s13058-020-01318-2

MDM2 inhibition in combination with endocrine therapy and CDK4/6 inhibition for the treatment of ER-positive breast cancer
Cited by: 35
Author(s): Neil Portman, Heloisa Helena Milioli, Sarah Alexandrou, Rhiannon Coulson, Aliza Yong, Kristine J. Fernandez, Karin K.M. Chia, Ensar Halilovic, Davendra Segara, Andrew Parker, Sue Haupt, Ygal Haupt, Wayne D. Tilley, Alexander Swarbrick, C. Elizabeth Caldon, Elgene Lim
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmolb.2021.690500

TRPV4 is a Prognostic Biomarker that Correlates with the Immunosuppressive Microenvironment and Chemoresistance of Anti-Cancer Drugs
Cited by: 14
Author(s): Kai Wang, Xingjun Feng, Lingzhi Zheng, Zeying Chai, Ji Hee Yu, Xinxin You, Xiaodan Li, Xiaodong Cheng
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms9081673

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types
Cited by: 2
Author(s): Andrea K. Borsodi, Márton Mucsi, Gergely Krett, Attila Szabó, Tamás Felföldi, Tibor Szili‐Kovács
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2019.03044

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti
Cited by: 34
Author(s): Víctor M. Flores‐Núñez, Citlali Fonseca-García, Damaris Desgarennes, Emiley A. Eloe‐Fadrosh, Tanja Woyke, Laila P. Partida‐Martínez
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.61531

HAT cofactor TRRAP modulates microtubule dynamics via SP1 signaling to prevent neurodegeneration
Cited by: 6
Author(s): Alicia Tapias, David Rodríguez Lázaro, Bo-Kun Yin, Seyed Mohammad Mahdi Rasa, Anna Krepelova, Erika Kelmer Sacramento, Paulius Grigaravičius, Philipp Koch, Joanna Kirkpatrick, Alessandro Ori, Francesco Neri, Zhaoqi Wang
Software Mentions: 4
Published: over 5 years ago

10.1093/gbe/evv115

Complete Dosage Compensation in<i>Anopheles stephensi</i>and the Evolution of Sex-Biased Genes in Mosquitoes
Cited by: 40
Author(s): Xiaofang Jiang, James K. Biedler, Yumin Qi, Andrew Brantley Hall, Zhijian Tu
Software Mentions: 4
Published: about 11 years ago

10.1007/s13238-017-0480-9

TDP-43 regulates cancer-associated microRNAs
Cited by: 28
Author(s): Xiaowei Chen, Zhen Fan, W Ambrose McGee, Mengmeng Chen, Ruirui Kong, Pushuai Wen, Tengfei Xiao, Xiaomin Chen, Jianghong Liu, Li Zhu, Runsheng Chen, Jane Y. Wu
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2020.572534

Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity
Cited by: 12
Author(s): Anny Cárdenas, Jin Ye, Maren Ziegler, Jérôme P. Payet, Ryan McMinds, Rebecca Vega Thurber, Christian R. Voolstra
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.580397

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability
Cited by: 10
Author(s): Shuting Liu, Nicholas Baetge, Jacqueline Comstock, Keri Opalk, Rachel Parsons, Elisa R. Halewood, Chance English, Stephen J. Giovannoni, Luis M. Bolaños, Craig E. Nelson, Kevin L. Vergin, Craig A. Carlson
Software Mentions: 4
Published: almost 6 years ago

10.3390/pathogens8040183

Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: almost 7 years ago

10.1111/all.14633

Single‐cell molecular profiling provides a high‐resolution map of basophil and mast cell development
Cited by: 29
Author(s): Fiona Hamey, Winnie Lau, Iwo Kuciński, Xiaonan Wang, Evangelia Diamanti, Nicola K. Wilson, Berthold Göttgens, Joakim S. Dahlin
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.6190

Forest floor temperature and greenness link significantly to canopy attributes in South Africa’s fragmented coastal forests
Cited by: 10
Author(s): Marion Pfeifer, Michael J. W. Boyle, Stuart Dunning, Pieter I. Olivier
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: almost 11 years ago

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms18050922

Transcriptomic Analysis of Calcium Remodeling in Colorectal Cancer
Cited by: 37
Author(s): Enrique Pérez-Riesgo, Lucía Gutiérrez, Daniel Ubierna, Alberto Acedo, Mary Pat Moyer, Lucı́a Núñez, Carlos Alonso
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2021.666936

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction
Cited by: 5
Author(s): Najoua Mghazli, Laila Sbabou, Rachid Hakkou, Ahmed Ouhammou, Mariam El Adnani, Odile Bruneel
Software Mentions: 4
Published: about 5 years ago

10.1093/molbev/msaa328

Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows–Wheeler Transform
Cited by: 19
Author(s): William A. Freyman, Kimberly F. McManus, Suyash Shringarpure, Ethan M. Jewett, Katarzyna Bryc, Adam Auton
Software Mentions: 4
Published: over 5 years ago

10.1007/s13238-019-0623-2

Rescue of premature aging defects in Cockayne syndrome stem cells by CRISPR/Cas9-mediated gene correction
Cited by: 42
Author(s): Si Wang, Zheying Min, Qianzhao Ji, Li Geng, Yao Su, Zunpeng Liu, Huifang Hu, Lixia Wang, Weiqi Zhang, Keiichiro Suzuiki, Yu Huang, Pu-Yao Zhang, Tie-Shan Tang, Jing Qu, Yang Yu, Guanghui Liu, Jie Qiao
Software Mentions: 4
Published: about 7 years ago

10.1038/sdata.2018.245

Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features
Cited by: 18
Author(s): Matthew P. Salomon, Javier I. J. Orozco, James S. Wilmott, Parvinder Hothi, Ayla O. Manughian-Peter, Charles S. Cobbs, Richard A. Scolyer, Dave S.B. Hoon, Diego M. Marzese
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2018.00298

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs
Cited by: 40
Author(s): Brandon J. Varela, David Lesbarrères, Roberto Ibáñez, David M. Green
Software Mentions: 4
Published: over 8 years ago