cran: gplots | Projects | Ecosyste.ms: Papers

10.1098/rstb.2019.0255

Dormancy dynamics and dispersal contribute to soil microbiome resilience
Cited by: 34
Author(s): Jackson W Sorensen, Ashley Shade
Software Mentions: 6
Published: over 6 years ago

AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
Cited by: 5
Author(s): Kyle Fletcher, Lin Zhang, Juliana Gil, Rongkui Han, Keri Cavanaugh, Richard W. Michelmore
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-016-0207-9

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies
Cited by: 41
Author(s): Euan Watt, Matthew Gemmell, Susan H. Berry, Mark A. Glaire, Freda Farquharson, Petra Louis, Graeme I. Murray, Emad El-Omar, Georgina L. Hold
Software Mentions: 6
Published: almost 10 years ago

10.1093/gbe/evu149

Small but Powerful, the Primary Endosymbiont of Moss Bugs, Candidatus Evansia muelleri, Holds a Reduced Genome with Large Biosynthetic Capabilities
Cited by: 33
Author(s): Diego Santos-García, Amparo Latorre, Andrés Moya, George Gibbs, Viktor Hartung, Konrad Dettner, Stefan Martin Kuechler, Francisco J. Silva
Software Mentions: 6
Published: about 12 years ago

10.1371/journal.pone.0052884

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways
Cited by: 17
Author(s): Mark L. Grimes, Wan-Jui Lee, Laurens van der Maaten, Paul Shannon
Software Mentions: 6
Published: over 13 years ago

10.1186/s12284-016-0098-1

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: over 10 years ago

10.1186/s12864-021-07526-0

Transcriptional profiling of identified neurons in leech
Cited by: 6
Author(s): Elizabeth A. C. Heath‐Heckman, Shinja Yoo, Christopher J. Winchell, Maurizio Pellegrino, James D. Angstadt, Veronica B. Lammardo, Diana M. Bautista, Francisco F. De‐Miguel, David A. Weisblat
Software Mentions: 6
Published: over 5 years ago

10.1042/BSR20210760

Identification of m6A methyltransferase-related lncRNA signature for predicting immunotherapy and prognosis in patients with hepatocellular carcinoma
Cited by: 37
Author(s): Lili Li, Rongrong Xie, Guangrong Lu
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.3001207

Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants
Cited by: 9
Author(s): Anna Laddach, Joseph C.F. Ng, Franca Fraternali
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0106084

Patterns of MiRNA Expression in Arctic Charr Development
Cited by: 24
Author(s): Kalina H. Kapralova, Sigríður Rut Franzdóttir, Hákon Jónsson, Sigurður S. Snorrason, Zophonı́as O. Jónsson
Software Mentions: 6
Published: about 12 years ago

10.7717/peerj.3411

Taxonomic richness and abundance of cryptic peracarid crustaceans in the Puerto Morelos Reef National Park, Mexico
Cited by: 9
Author(s): Luz Verónica Monroy-Velázquez, Rosa E. Rodríguez-Martínez, Fernando Álvarez
Software Mentions: 6
Published: over 9 years ago

10.1186/s12885-015-1993-3

TGFβ isoforms and receptors mRNA expression in breast tumours: prognostic value and clinical implications
Cited by: 23
Author(s): Chenfeng Chen, Kong‐Nan Zhao, Paul P. Masci, Sunil R. Lakhani, Annika Antonsson, Peter T. Simpson, Luis Vitetta
Software Mentions: 6
Published: almost 11 years ago

10.3389/fmicb.2017.01563

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle
Cited by: 28
Author(s): Chong Liu, Qinghui Meng, Yongxing Chen, Mengsi Xu, Min Shen, Rui Gao, Shangquan Gan
Software Mentions: 6
Published: about 9 years ago

10.1186/s12864-019-6375-9

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Cited by: 27
Author(s): Yanchao Xu, Richard Odongo Magwanga, Xiaomin Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Kunbo Wang, Fang Liu
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.997

Deep sequencing of the viralphoHgene reveals temporal variation, depth-specific composition, and persistent dominance of the same viralphoHgenes in the Sargasso Sea
Cited by: 34
Author(s): Dawn B. Goldsmith, Rachel Parsons, Damitu Beyene, Peter Salamon, Mya Breitbart
Software Mentions: 6
Published: over 11 years ago

10.1186/s12934-016-0456-0

Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments
Cited by: 24
Author(s): Thibault Nidelet, Pascale Brial, Carole Camarasa, Sylvie Dequin
Software Mentions: 6
Published: over 10 years ago

10.1186/s12864-019-6076-4

Transcriptome analysis of the effect of C-C chemokine receptor 5 deficiency on cell response to Toxoplasma gondii in brain cells
Cited by: 7
Author(s): Kaoru Kobayashi, Kousuke Umeda, Fumie Ihara, Sadao Tanaka, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
Software Mentions: 6
Published: about 7 years ago

10.1186/1471-2164-15-353

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Cited by: 49
Author(s): Richard Landstorfer, Svenja Simon, Steffen Schober, Daniel A. Keim, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 6
Published: over 12 years ago

10.1186/s12863-021-00991-2

The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells
Cited by: 4
Author(s): Ritu Mann-Nüttel, Shafaqat Ali, Patrick Petzsch, Karl Köhrer, Judith Alferink, Stefanie Scheu
Software Mentions: 6
Published: about 5 years ago

10.3390/pathogens8040195

An Acute Stress Model in New Zealand White Rabbits Exhibits Altered Immune Response to Infection with West Nile Virus
Cited by: 5
Author(s): Willy W. Suen, Mitchell Imoda, Albert W Thomas, Nur N B M Nasir, Nawaporn Tearnsing, Wenqi Wang, Helle Bielefeldt‐Ohmann
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-018-4782-y

Gene expression profiling in the developing secondary palate in the absence of Tbx1 function
Cited by: 2
Author(s): Maria Zoupa, Guilherme M. Xavier, Stephanie Bryan, Ioannis Theologidis, Matthew Arno, Martyn T. Cobourne
Software Mentions: 6
Published: over 8 years ago

10.3389/fmicb.2020.01036

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants
Cited by: 29
Author(s): Qian Zhang, Jacquelinne J. Acuña, Nitza G. Inostroza, Paola Durán, Marı́a de la Luz Mora, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.2452

Canopy position has a profound effect on soybean seed composition
Cited by: 27
Author(s): Steven C. Huber, Kunzhi Li, Randall L. Nelson, Alexander Ulanov, Catherine M. DeMuro, Ivan Baxter
Software Mentions: 6
Published: about 10 years ago

10.3390/pathogens9010024

Genome-Wide Analysis of Cyclophilin Proteins in 21 Oomycetes
Cited by: 2
Author(s): Yan Zhang, Kyle Fletcher, Rongkui Han, Richard W. Michelmore, Ruiwu Yang
Software Mentions: 6
Published: almost 7 years ago

10.3389/fmicb.2016.02064

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
Cited by: 177
Author(s): Manoeli Lupatini, G.W. Korthals, Mattias de Hollander, Thierry Janssens, Eiko E. Kuramae
Software Mentions: 6
Published: over 9 years ago

10.1186/s13071-021-04717-2

Transcriptomic profiling of three-dimensional cholangiocyte spheroids long term exposed to repetitive Clonorchis sinensis excretory-secretory products
Cited by: 4
Author(s): Jung Woong Kim, Junyeong Yi, Jin‐Hong Park, Ji Hoon Jeong, Jin-Ho Kim, Jihee Won, Seok Chung, Tong Soo Kim, Jhang Ho Pak
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.8371

The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells
Cited by: 4
Author(s): Monika Ruszkowska, Agnieszka Sadowska, Anna Nynca, Karina Orlowska, Sylwia Świgońska, Tomasz Molcan, Łukasz Paukszto, J Jastrzebski, Renata E. Ciereszko
Software Mentions: 6
Published: over 6 years ago

10.1038/gim.2015.156

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data
Cited by: 58
Author(s): Trevor J. Pugh, Sami S. Amr, Mark J. Bowser, Sivakumar Gowrisankar, Elizabeth Hynes, Lisa Mahanta, Heidi L. Rehm, Birgit Funke, Matthew S. Lebo
Software Mentions: 6
Published: about 10 years ago

10.1371/journal.pgen.1006750

TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells
Cited by: 50
Author(s): Juyong Brian Kim, Milos Pjanic, Trieu Nguyen, Clint L. Miller, Dharini Iyer, Boxiang Liu, Ting Wang, Olga V. Sazonova, Iván Cárcamo-Orive, Ljubica Matic, Lars Maegdefessel, Ulf Hedin, Thomas Quertermous
Software Mentions: 6
Published: over 9 years ago

10.1007/s12275-020-9536-2

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
Cited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0148016

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria
Cited by: 99
Author(s): Christina Bienhold, Lucie Zinger, Antje Boetius, Alban Ramette
Software Mentions: 6
Published: over 10 years ago

10.1007/s00239-021-10012-6

Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires
Cited by: 8
Author(s): Thomas D. Lewin, Amy H. Royall, Peter W.H. Holland
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2018.01888

Infection-Induced Changes Within the Endocytic Recycling Compartment Suggest a Roadmap of Human Cytomegalovirus Egress
Cited by: 16
Author(s): William L. Close, James Glassbrook, Stephen J. Gurczynski, Philip E. Pellett
Software Mentions: 6
Published: about 8 years ago

10.1186/s12864-021-07571-9

Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni
Cited by: 7
Author(s): Laura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve‐Codina, Kristina Gruden, María Pla
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2015.01038

Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, Brazil
Cited by: 10
Author(s): Ana Paula B. Moreira, Pedro Milet Meirelles, Eidy de Oliveira Santos, Gilberto M. Amado‐Filho, Ronaldo B. Francini‐Filho, Cristiane C. Thompson, Fabiano L. Thompson
Software Mentions: 6
Published: almost 11 years ago

10.1002/jev2.12022

Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis
Cited by: 22
Author(s): Bram Van den Broek, Isabel Pintelon, Ibrahim Hamad, Sofie Kessels, Mansour Haidar, Niels Hellings, Jerome J. A. Hendriks, Markus Kleinewietfeld, Bert Brône, Vincent Timmerman, Jean‐Pierre Timmermans, Veerle Somers, Luc Michiels, Joy Irobi
Software Mentions: 6
Published: almost 6 years ago

10.1186/1471-2105-13-S16-S10

A tutorial in displaying mass spectrometry-based proteomic data using heat maps
Cited by: 47
Author(s): Melissa Key
Software Mentions: 6
Published: almost 14 years ago

10.1371/journal.pone.0075136

Synergistic Re-Activation of Epigenetically Silenced Genes by Combinatorial Inhibition of DNMTs and LSD1 in Cancer Cells
Cited by: 31
Author(s): Han Han, Xiaojing Yang, Kurinji Pandiyan, Gangning Liang
Software Mentions: 6
Published: about 13 years ago

10.1002/1878-0261.12161

Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis
Cited by: 19
Author(s): Martín Del Castillo Velasco-Herrera, Louise van der Weyden, Jérémie Nsengimana, Anneliese O. Speak, Marcela Sjöberg, D. Timothy Bishop, Göran Jönsson, Julia Newton-Bishop, David J. Adams
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0167747

Transcriptomic Changes in Liver of Young Bulls Caused by Diets Low in Mineral and Protein Contents and Supplemented with n-3 Fatty Acids and Conjugated Linoleic Acid
Cited by: 8
Author(s): Sara Pegolo, Alessio Cecchinato, Núria Mach, Massimiliano Babbucci, Marianna Pauletto, Luca Bargelloni, Stefano Schiavon, Giovanni Bittante
Software Mentions: 6
Published: almost 10 years ago

10.1038/s41396-021-00931-z

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline
Cited by: 8
Author(s): Grégoire Michoud, David Kamanda Ngugi, Alan Barozzi, Giuseppe Merlino, María Ll. Calleja, António Delgado Huertas, Xosé Anxelu G. Morán, Daniele Daffonchio
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-020-00830-z

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation
Cited by: 27
Author(s): Camilla Urbaniak, Hernan Lorenzi, James B. Thissen, Crystal Jaing, Brian Crucian, Clarence F. Sams, Duane L. Pierson, Kasthuri Venkateswaran, Satish K. Mehta
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-021-07812-x

Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss
Cited by: 9
Author(s): Daniel Oropeza, Valentina Cigliola, Agustín Romero, Simona Chera, Santiago A. Rodríguez-Seguí, Pedro Luis Herrera
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0236429

pH effect on strain-specific transcriptomes of the take-all fungus
Cited by: 1
Author(s): Kévin Gazengel, Lionel Lebreton, Nicolas Lapalu, Joëlle Amselem, Anne‐Yvonne Guillerm‐Erckelboudt, Denis Tagu, Stéphanie Daval
Software Mentions: 6
Published: about 6 years ago

10.1038/s41396-020-00844-3

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles
Cited by: 45
Author(s): Annelein Meisner, L. Basten Snoek, Joseph Nesme, Elizabeth Dent, Samuel Jacquiod, Aimée T. Classen, Anders Priemé
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1003671

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Cited by: 41
Author(s): Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng
Software Mentions: 6
Published: over 12 years ago

10.1186/s12870-016-0729-0

Gene expression profiling of the green seed problem in Soybean
Cited by: 32
Author(s): Renake Nogueira Teixeira, Wilco Ligterink, J. de B. França Neto, Henk W. M. Hilhorst, Edvaldo Aparecido Amaral da Silva
Software Mentions: 6
Published: over 10 years ago

10.15252/msb.20177974

Systematic characterization of pan‐cancer mutation clusters
Cited by: 31
Author(s): Marija Buljan, Peter Blattmann, Ruedi Aebersold, Michael Boutros
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-021-82666-7

Identification of sources resistant to a virulent Fusarium wilt strain (VCG 0124) infecting Cavendish bananas
Cited by: 14
Author(s): R Thangavelu, M. Saraswathi, S. Uma, M. Loganathan, S. Backiyarani, P. Durai, Esack Edwin Raj, Narayanan Marimuthu, G. Kannan, Rony Swennen
Software Mentions: 6
Published: over 5 years ago

10.1534/g3.117.041624

Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Cited by: 35
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Duncan M. Hendrick, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Jennifer T. Go, Gabrielle Choonoo, Sophia Jeng, Fernando P Pardo Manuel De Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale
Software Mentions: 6
Published: over 9 years ago

10.3390/cells10040921

Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR)
Cited by: 2
Author(s): Aleksandra Lipka, J Jastrzebski, Łukasz Paukszto, Karol G Makowczenko, Elżbieta Łopieńska–Biernat, Marek Gowkielewicz, Ewa Lepiarczyk, Marta Wiszpolska, Mariusz Majewski, Marta Majewska
Software Mentions: 6
Published: over 5 years ago

10.3389/fnins.2017.00363

The Role of the Interplay between Stimulus Type and Timing in Explaining BCI-Illiteracy for Visual P300-Based Brain-Computer Interfaces
Cited by: 12
Author(s): Roberta Carabalona
Software Mentions: 6
Published: about 9 years ago

10.3389/fpls.2021.675208

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum
Cited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-019-56235-y

FABP4 and MMP9 levels identified as predictive factors for poor prognosis in patients with nonalcoholic fatty liver using data mining approaches and gene expression analysis
Cited by: 32
Author(s): Audrey Coilly, Christophe Desterke, Catherine Guettier, Didier Samuel, Franck Chiappini
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-019-41336-5

Female novelty and male status dynamically modulate ejaculate expenditure and seminal fluid proteome over successive matings in red junglefowl
Cited by: 9
Author(s): Aitor Álvarez-Fernández, Kirill Borziak, Grant C. McDonald, Steve Dorus, Tommaso Pizzari
Software Mentions: 6
Published: over 7 years ago

10.1093/cid/ciaa1153

Investigating the Meat Pathway as a Source of Human Nontyphoidal Salmonella Bloodstream Infections and Diarrhea in East Africa
Cited by: 18
Author(s): John A. Crump, Kate M. Thomas, Jackie Benschop, Matthew A. Knox, David Wilkinson, Anne C. Midwinter, Peninah Munyua, John B. Ochieng, Godfrey Bigogo, Jennifer R. Verani, Marc‐Alain Widdowson, Gerard Prinsen, Sarah Cleaveland, Esron D. Karimuribo, Rudovick Kazwala, Blandina T. Mmbaga, Emanuel S. Swai, Nigel French, Ruth N. Zadoks
Software Mentions: 6
Published: about 6 years ago

10.3389/fnut.2019.00045

What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study
Cited by: 135
Author(s): Kimberly A. Lackey, Janet E. Williams, Courtney L. Meehan, Jessica A. Zachek, Elizabeth D. Benda, William J. Price, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Linda J. Kvist, Gloria E. Otoo, Cristina García-Carral, Esther Jiménez, Lorena Ruíz, Juan M. Rodríguez, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Michelle K. McGuire
Software Mentions: 6
Published: over 7 years ago

10.1016/j.cell.2011.11.058

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Cited by: 504
Author(s): Dominic Schmidt, Petra Schwalie, Michael D. Wilson, Benoît Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Software Mentions: 6
Published: over 14 years ago

10.1016/j.celrep.2019.12.019

Neuroinflammation-Associated Aspecific Manipulation of Mouse Predator Fear by Toxoplasma gondii
Cited by: 81
Author(s): Madlaina Boillat, Pierre‐Mehdi Hammoudi, Sunil Kumar Dogga, Stéphane Pagès, Maged Goubran, Iván Rodríguez, Dominique Soldati‐Favre
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2021.701796

L-Canavanine, a Root Exudate From Hairy Vetch (Vicia villosa) Drastically Affecting the Soil Microbial Community and Metabolite Pathways
Cited by: 7
Author(s): Hossein Mardani-Korrani, Masaru Nakayasu, Shinichi Yamazaki, Yosuke Aoki, Rumi Kaida, Takashi Motobayashi, Masaru Kobayashi, Naoko Ohkama‐Ohtsu, Yosei Oikawa, Akifumi Sugiyama, Yoshiharu Fujii
Software Mentions: 6
Published: about 5 years ago

10.1016/j.cell.2020.05.039

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Cited by: 438
Author(s): Andrew L. Ji, Adam J. Rubin, Kim Thrane, Sizun Jiang, David L. Reynolds, Robin M. Meyers, Margaret Guo, Benson M. George, Annelie Mollbrink, Joseph Bergenstråhle, Ludvig Larsson, Yunhao Bai, Bokai Zhu, Aparna Bhaduri, Jordan M. Meyers, Xavier Rovira-Clavé, S. Tyler Hollmig, Sumaira Z. Aasi, Garry P. Nolan, Joakim Lundeberg, Paul A. Khavari
Software Mentions: 6
Published: about 6 years ago

10.3390/ijms22147322

Effect of the Electromagnetic Field (EMF) Radiation on Transcriptomic Profile of Pig Myometrium during the Peri-Implantation Period—An In Vitro Study
Cited by: 6
Author(s): Ewa Monika Drzewiecka, Wiktoria Kozlowska, Łukasz Paukszto, Agata Żmijewska, Pawel Jozef Wydorski, J Jastrzebski, Anita Franczak
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-018-37397-7

Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2018.01202

Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas
Cited by: 15
Author(s): Klára Vlčková, Barbora Pafčo, Klára J. Petrželková, David Modrý, Angelique Todd, Carl J. Yeoman, Manolito Torralba, Brenda A. Wilson, Rebecca M. Stumpf, Bryan A. White, Karen E. Nelson, Steven R. Leigh, Andrés Gómez
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-018-30509-3

Drug-based perturbation screen uncovers synergistic drug combinations in Burkitt lymphoma
Cited by: 20
Author(s): Katarzyna Tomska, Roman Kurilov, Kwang Seok Lee, Jennifer Hüllein, Marina Lukas, Leopold Sellner, Tatjana Walther, Lena Wagner, Małgorzata Oleś, Benedikt Brors, Wolfgang Huber, Thorsten Zenz
Software Mentions: 6
Published: about 8 years ago

10.1186/s13148-015-0123-z

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: about 11 years ago

10.1038/s42003-020-01593-x

Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance
Cited by: 24
Author(s): Yaodong Yang, Stéphanie Bocs, Hang Fan, Alix Armero, Luc Baudouin, Pengwei Xu, Junyang Xu, Dominique This, Chantal Hamelin, Amjad Iqbal, Rashad Qadri, Lixia Zhou, Jing Li, Yi Wu, Zhiying Ma, Auguste Emmanuel Issali, Ronan Rivallan, Na Liu, Wei Xia, Ming Peng, Yong Xiao
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22116052

Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species
Cited by: 18
Author(s): Eugenia E. Montiel, Francisco Panzera, Teresa Palomeque, Pedro Lorite, Sebastián Pita
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2020.611877

Flower Production, Headspace Volatiles, Pollen Nutrients, and Florivory in Tanacetum vulgare Chemotypes
Cited by: 20
Author(s): Elisabeth J. Eilers, Sandra Kleine, Silvia Eckert, Simon Waldherr, Caroline Müller
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-66772-6

Symbiotic bacterial communities in rainforest fungus-farming ants: evidence for species and colony specificity
Cited by: 11
Author(s): Mariane Ueda Vaz Ronque, Mariana L. Lyra, Gustavo H. Migliorini, Maurício Bacci, Paulo S. Oliveira
Software Mentions: 6
Published: over 6 years ago

10.1016/j.celrep.2019.06.039

Acute Iron Deprivation Reprograms Human Macrophage Metabolism and Reduces Inflammation In Vivo
Cited by: 67
Author(s): Marie Pereira, Tai‐Di Chen, Norzawani Buang, Antoni Olona, Jeong‐Hun Ko, Maria Prendecki, Ana S.H. Costa, Efterpi Nikitopoulou, Laura Tronci, Charles D. Pusey, H. Terence Cook, Stephen P. McAdoo, Christian Frezza, Jacques Behmoaras
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-021-82379-x

Evidence for strong environmental control on bacterial microbiomes of Antarctic springtails
Cited by: 5
Author(s): Chiara Leo, Francesco Nardi, Claudio Cucini, Francesco Frati, Peter Convey, James T. Weedon, Dick Roelofs, Antonio Carapelli
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-67842-5

Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis
Cited by: 18
Author(s): Jiangang Liu, Yong Beom Cho, Hye Kyung Hong, Song Wu, Philip J. Ebert, Steven M. Bray, Suei Nee Wong, Jason C. Ting, John N. Calley, Catherine F. Whittington, Shripad V. Bhagwat, Christoph Reinhard, Robert A. Wild, Do‐Hyun Nam, Amit Aggarwal, Woo Yong Lee, Sheng-Bin Peng
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-66519-3

Interconnection of bacterial and phytoplanktonic communities with hydrochemical parameters from ice and under-ice water in coastal zone of Lake Baikal
Cited by: 10
Author(s): Yu. S. Bukin, Н. А. Бондаренко, Igor I Rusanov, Nikolai V. Pimenov, S. V. Bukin, T. V. Pogodaeva, S. M. Chernitsyna, O. V. Shubenkova, V. G. Ivanov, А. S. Zakharenko, Т. I. Zemskaya
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.58407

Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities
Cited by: 5
Author(s): Fredrick M. Mobegi, Lex E. X. Leong, Fintan Thompson, Sean Taylor, Linton Harriss, Jocelyn M. Choo, Steven Taylor, Steve Wesselingh, Robyn McDermott, Kerry L. Ivey, Geraint B. Rogers
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13148-020-00998-z

Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer
Cited by: 8
Author(s): Louis El Khoury, Shuang Fu, Ryan A. Hlady, Ryan T. Wagner, Liguo Wang, Jeanette E. Eckel‐Passow, Erik P. Castle, Melissa L. Stanton, R. Houston Thompson, Alexander S. Parker, Thai H. Ho, Keith D. Robertson
Software Mentions: 6
Published: over 5 years ago

10.1534/g3.116.027045

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides
Cited by: 20
Author(s): C. Alisha Quandt, Yanming Di, Justin Elser, Pankaj Jaiswal, Joseph W. Spatafora
Software Mentions: 6
Published: over 10 years ago

10.18632/oncotarget.20405

Cancer cell line specific co-factors modulate the FOXM1 cistrome
Cited by: 8
Author(s): Yue Wang, Matthew Ung, Tian Xia, Wenqing Cheng, Chao Cheng
Software Mentions: 5
Published: about 9 years ago

10.18632/oncotarget.13252

Prognostic and predictive values of CDK1 and MAD2L1 in lung adenocarcinoma
Cited by: 81
Author(s): Yuan-Xiang Shi, Tao Zhu, Ting Zou, Wei Zhuo, Yixin Chen, Ma-Sha Huang, Wei Zheng, Chenjing Wang, Xi Li, Xiao‐Yuan Mao, Wei Zhang, Hong‐Hao Zhou, Ji‐Ye Yin, Zhao‐Qian Liu
Software Mentions: 5
Published: almost 10 years ago

10.1038/s41598-021-84860-z

Characterisation, identification, clustering, and classification of disease
Cited by: 17
Author(s): Anthony J Webster, Kezia Gaitskell, Iain Turnbull, B J Cairns, Robert Clarke
Software Mentions: 5
Published: over 5 years ago

10.3389/fphar.2018.00084

Proteomic Analysis of Combined Gemcitabine and Birinapant in Pancreatic Cancer Cells
Cited by: 15
Author(s): Xu Zhu, Xiaomeng Shen, Jun Qu, Robert M. Straubinger, William J. Jusko
Software Mentions: 5
Published: over 8 years ago

10.3389/fpls.2019.00963

Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population
Cited by: 17
Author(s): Sophie A Harrington, Nicolás Cobo, Miroslava Karafiátová, Jaroslav Doležel, Philippa Borrill, Cristóbal Uauy
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-019-57108-0

Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
Cited by: 15
Author(s): Wilhelm Bertrams, Kathrin Griss, Maria Han, Kerstin Seidel, Andreas Klemmer, Alexandra Sittka-Stark, Stefan Hippenstiel, Norbert Suttorp, Florian Finkernagel, Jochen Wilhelm, Timm Greulich, Claus Vogelmeier, Julio Vera, Bernd Schmeck
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2017.00101

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira
Cited by: 163
Author(s): Ryan P. Bartelme, Sandra L. McLellan, Ryan J. Newton
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-021-82136-0

A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Cited by: 13
Author(s): Nivedita, Abdul Rawoof, Nirala Ramchiary, M. Z. Abdin
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-020-01477-0

Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models
Cited by: 9
Author(s): Nirosh D. Aluthge, Wesley A Tom, Alison Bartenslager, Thomas E. Burkey, Phillip S. Miller, Kelly D. Heath, Craig Kreikemeier-Bower, Hatem Kittana, Robert Schmaltz, Amanda E. Ramer‐Tait, Samodha C. Fernando
Software Mentions: 5
Published: almost 6 years ago

10.18632/oncotarget.19662

Gene expression and molecular pathway activation signatures ofMYCN-amplified neuroblastomas
Cited by: 27
Author(s): Ivan Petrov, Maria Suntsova, Elena Tarasovna Ilnitskaya, S. A. Roumiantsev, Maxim Sorokin, Andrew Garazha, Pavel Spirin, Timofey Lebedev, Нуршат Гайфуллин, Sergey Larin, Olga Kovalchuk, Д. М. Коновалов, Vladimir Prassolov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-020-66759-3

The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia
Cited by: 6
Author(s): Ximena Gómez‐Maqueo, Diana Soriano, Noé Velázquez-Rosas, Sandra Alvarado-López, Karina Jiménez‐Durán, María Del Mar Garciadiego, Alicia Gamboa‐deBuen
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-67690-3

Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-68891-6

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture
Cited by: 27
Author(s): Yustian Rovi Alfiansah, Sonja Peters, Jens Harder, Christiane Hassenrück, Astrid Gärdes
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0023024

Temporal Retinal Nerve Fiber Loss in Patients with Spinocerebellar Ataxia Type 1
Cited by: 56
Author(s): Sarah Stricker, Timm Oberwahrenbrock, Hanna Zimmermann, Jan Schroeter, Matthias Endres, Alexander U. Brandt, Friedemann Paul
Software Mentions: 5
Published: about 15 years ago

10.1038/s41598-020-66558-w

Associations among neurophysiology measures in irritable bowel syndrome (IBS) and their relevance for IBS symptoms
Cited by: 11
Author(s): Irina Midenfjord, Annikka Polster, Henrik Sjövall, Peter Friberg, Hans Törnblom, Magnus Simrén
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-66721-3

Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0235066

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies
Cited by: 3
Author(s): Rose M. Collis, Patrick J. Biggs, Anne C. Midwinter, A. Springer Browne, David Wilkinson, Hamid Irshad, Nigel French, Gale Brightwell, Adrian L. Cookson
Software Mentions: 5
Published: over 6 years ago

10.3390/genes11050499

Unmasking Intra-Tumoral Heterogeneity and Clonal Evolution in NF1-MPNST
Cited by: 2
Author(s): Chang In Moon, William Tompkins, Yuxi Wang, Abigail Godec, Xiaochun Zhang, Patrik Pipkorn, Christopher A. Miller, Carina Dehner, Sonika Dahiya, Angela C. Hirbe
Software Mentions: 5
Published: over 6 years ago

10.3390/genes12020201

Ablation of SMUG1 Reduces Cell Viability and Increases UVC-Mediated Apoptosis in Hepatocarcinoma HepG2 Cells
Cited by: 1
Author(s): Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Jung-Woong Kim
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-60065-8

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation
Cited by: 7
Author(s): Jessica Schira‐Heinen, A. Czapla, Marion Hendricks, Andreas Kloetgen, Wasco Wruck, James Adjaye, Gesine Kögler, Hans Müller, Kai Stühler, Hans‐Ingo Trompeter
Software Mentions: 5
Published: over 6 years ago

10.3390/genes12020264

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells
Cited by: 7
Author(s): Chulhong Kim, Mi Jin Kim, Jin‐Hong Park, Jin-Ho Kim, Jiyoung Kim, Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Jung-Woong Kim
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-72511-8

Burn resuscitation strategy influences the gut microbiota-liver axis in swine
Cited by: 11
Author(s): Wayne Muraoka, Jose C. Granados, Belinda I. Gómez, Susannah E. Nicholson, Kevin K. Chung, Jeffrey W. Shupp, James A. Bynum, Michael A. Dubick, David M. Burmeister
Software Mentions: 5
Published: about 6 years ago

10.1186/s12263-021-00692-6

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis
Cited by: 7
Author(s): Kaitlin Day, Aimee L. Dordevic, Helen Truby, Melissa C. Southey, Susan L. Coort, Chiara Murgia
Software Mentions: 5
Published: about 5 years ago

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Papers Mentioning gplots 2,122