cran: gplots | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pgen.1009737

Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver
Cited by: 9
Author(s): Benjamin P. Flynn, Matthew T. Birnie, Yvonne M. Kershaw, Audrys G Pauža, Sohyoung Kim, Songjoon Baek, Mark F. Rogers, Alex Paterson, Diana A. Stavreva, David Murphy, Gordon L. Hager, Stafford Lightman, Becky Conway-Campbell
Software Mentions: 6
Published: about 5 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: over 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

10.1534/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

10.1534/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

10.7717/peerj.9697

Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
Cited by: 2
Author(s): Karin Hirose, Yasuhiro Ishiga, Takashi Fujikawa
Software Mentions: 6
Published: about 6 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

10.1371/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.pbio.3000741

Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei
Cited by: 32
Author(s): Eva Doleželová, Michaela Kunzová, Mario Dejung, Michal Levin, Brian Panicucci, Clément Regnault, Christian J. Janzen, Michael P. Barrett, Falk Butter, Alena Zı́ková
Software Mentions: 6
Published: over 6 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: almost 14 years ago

10.1371/journal.pbio.3000948

Absence of nuclear receptors LXRs impairs immune response to androgen deprivation and leads to prostate neoplasia
Cited by: 3
Author(s): Laura Bousset, Amandine Septier, Julio Buñay, Allison Voisin, Rachel Guiton, Christelle Damon-Soubeyrant, Yoan Renaud, Angélique De Haze, Vincent Sapin, Anne Fogli, Amandine Rambur, Cyrille de Joussineau, Ayhan Kocer, Amalia Trousson, Joëlle Henry-Berger, Marcus Höring, Gerhard Liebisch, Silke Matysik, Jean-Marc A. Lobaccaro, Laurence Morel, Silvère Baron
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pcbi.1005351

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
Cited by: 3
Author(s): Stephanie Evans, Kieran Alden, Lourdes Cucurull‐Sanchez, Christopher Larminie, Mark Coles, Marika C. Kullberg, Jon Timmis
Software Mentions: 6
Published: over 9 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/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

10.1111/tpj.14184

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes
Cited by: 91
Author(s): Genevieve M. Hoopes, John Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart, C. Robin Buell
Software Mentions: 6
Published: almost 8 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

10.3389/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

10.1002/pld3.242

Lipophilic signals lead to organ‐specific gene expression changes in Arabidopsis seedlings
Cited by: 4
Author(s): Ashley E. Cannon, Chengshi Yan, David J. Burks, Xiaolan Rao, Rajeev K. Azad, Kent D. Chapman
Software Mentions: 6
Published: over 6 years ago

10.26508/lsa.202000974

GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program
Cited by: 30
Author(s): Yôji Kojima, Chika Yamashiro, Yusuke Murase, Yukihiro Yabuta, Ikuhiro Okamoto, Chizuru Iwatani, Hideaki Tsuchiya, Masataka Nakaya, Tomoyuki Tsukiyama, Tomonori Nakamura, Takuya Yamamoto, Mitinori Saitou
Software Mentions: 6
Published: over 5 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: almost 15 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: almost 6 years ago

10.26508/lsa.202000976

Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Cited by: 5
Author(s): Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
Software Mentions: 6
Published: over 5 years ago

10.1038/leu.2015.172

Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia
Cited by: 15
Author(s): Jonathan Sive, Silvia Basilico, Rebecca Hannah, Sarah Kinston, Fernando J. Calero-Nieto, Berthold Göttgens
Software Mentions: 6
Published: over 11 years ago

10.1111/acel.13381

Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity
Cited by: 7
Author(s): Rebecca L. McIntyre, Simone Denis, Rashmi Kamble, Marte Molenaars, Michael Petr, Bauke V. Schomakers, Mizanur Rahman, Siddhartha Datta Gupta, Márton L. Tóth, Siva A. Vanapalli, Aldo Jongejan, Morten Scheibye‐Knudsen, Riekelt H. Houtkooper, Georges E. Janssens
Software Mentions: 6
Published: over 5 years ago

10.1093/bib/bbw102

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles
Cited by: 1
Author(s): Felicia Ng, David Ruau, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 6
Published: about 10 years ago

10.1371/journal.pone.0180322

Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches
Cited by: 6
Author(s): María Maqueda, Emma Roca, Daniel Brotons, José Manuel Nieto Soria, Alexandre Perera
Software Mentions: 6
Published: about 9 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

10.1098/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

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

10.1371/journal.pone.0242675

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata
Cited by: 20
Author(s): Maureen W. Ihua, Jamie A. FitzGerald, Freddy Guihéneuf, Stephen A. Jackson, Marcus J. Claesson, Dagmar B. Stengel, Alan D. W. Dobson
Software Mentions: 6
Published: almost 6 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

10.1002/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

10.3389/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

10.3389/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: over 9 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

10.3389/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

10.1371/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

10.1038/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: almost 6 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: almost 7 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: over 6 years ago

10.3390/biomedicines9091192

Self-Organization Provides Cell Fate Commitment in MSC Sheet Condensed Areas via ROCK-Dependent Mechanism
Cited by: 3
Author(s): Peter Nimiritsky, Ekaterina Novoseletskaya, Roman Eremichev, Natalya Alexandrushkina, Maxim Karagyaur, O. V. Vetrovoy, Nataliya Basalova, А. М. Хрусталева, Alexander Tyakht, Anastasia Efimenko, В. А. Ткачук
Software Mentions: 6
Published: about 5 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: almost 7 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

10.1038/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

10.3389/fgene.2021.675260

Aluminum or Low pH – Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress
Cited by: 16
Author(s): Miriam Szurman-Zubrzycka, Karolina Chwiałkowska, Magdalena Niemira, Mirosław Kwaśniewski, M. Nawrot, Monika Gajecka, Paul B. Larsen, Iwona Szarejko
Software Mentions: 6
Published: over 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: about 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/fcimb.2018.00020

Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals
Cited by: 20
Author(s): Lisandra Aguilar-Bultet, Pamela Nicholson, Lorenz Rychener, Margaux Dreyer, Bulent Gözel, Francesco C. Origgi, Anna Oevermann, Joachim Frey, Laurent Falquet
Software Mentions: 6
Published: over 8 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

10.1038/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: over 6 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

10.1038/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: over 6 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: almost 7 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

10.1038/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

10.1371/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: almost 11 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

10.1186/1471-2105-13-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

10.1038/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

10.1038/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

10.1371/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: almost 9 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

10.1186/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

10.1002/ece3.3142

Plant diversity has contrasting effects on herbivore and parasitoid abundance in Centaurea jacea flower heads
Cited by: 10
Author(s): Norma Nitschke, Eric Allan, H. Zwölfer, Lysett Wagner, Sylvia Creutzburg, Hannes Baur, Stefan Schmidt, Wolfgang W. Weisser
Software Mentions: 6
Published: about 9 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: over 6 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

10.1371/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/s41598-018-37397-7

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: almost 8 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/s12860-019-0199-y

Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose
Cited by: 14
Author(s): MA Wei-hua, Jaeyop Lee, Daniel Backenroth, Yu Zhou, Erin C. Bush, Peter A. Sims, Kang Liu, Yufeng Shen
Software Mentions: 5
Published: over 7 years ago

10.3390/molecules26061789

Needle Trap Device-GC-MS for Characterization of Lung Diseases Based on Breath VOC Profiles
Cited by: 14
Author(s): Fernanda Monedeiro, Maciej Monedeiro-Milanowski, Ileana-Andreea Raţiu, Beata Brożek, Tomasz Ligor, Bogusław Buszewski
Software Mentions: 5
Published: over 5 years ago

10.1002/jcsm.12643

Single‐cell RNA sequencing and lipidomics reveal cell and lipid dynamics of fat infiltration in skeletal muscle
Cited by: 33
Author(s): Zhonglin Xu, Wenjing You, Wentao Chen, Yanbing Zhou, Qiuyun Nong, Teresa G. Valencak, Yizhen Wang, Tizhong Shan
Software Mentions: 5
Published: almost 6 years ago

10.3390/ani10020356

Protection of Animals during Transport: Analysis of the Infringements Reported from 2009 to 2013 during On-Road Inspections in Italy
Cited by: 6
Author(s): Barbara Padalino, Roberta Barrasso, Daniele Tullio, Martina Zappaterra, Leonardo Nanni Costa, Giancarlo Bozzo
Software Mentions: 5
Published: over 6 years ago

10.1186/s12866-021-02123-3

Long-term stability of the urogenital microbiota of asymptomatic European women
Cited by: 13
Author(s): Magdalena Ksiezarek, Svetlana Ugarčina Perović, Júlio César Rocha, Filipa Grosso, Luı́sa Peixe
Software Mentions: 5
Published: over 5 years ago

10.3390/insects11090578

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification
Cited by: 12
Author(s): Anakena M. Castillo, Kristin Saltonstall, Carlos F. Arias, Karina Chavarria, Luis A. Ramírez‐Camejo, Luis C. Mejía, Luis F. De León
Software Mentions: 5
Published: about 6 years ago

10.3390/molecules25214894

Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach
Cited by: 8
Author(s): Michał Złoch, Paweł Pomastowski, Ewelina Maślak, Fernanda Monedeiro
Software Mentions: 5
Published: about 6 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

10.1371/journal.pone.0221862

Parameterization-induced uncertainties and impacts of crop management harmonization in a global gridded crop model ensemble
Cited by: 38
Author(s): Christian Folberth, Joshua Elliott, Christoph Müller, Juraj Balkovič, James Chryssanthacopoulos, R. C. Izaurralde, Curtis D. Jones, Nikolay Khabarov, Wenfeng Liu, Ashwan Reddy, Erwin Schmid, Rastislav Skalský, Hong Yang, Almut Arneth, Philippe Ciais, Delphine Deryng, P. Lawrence, Stefan Olin, Thomas A. M. Pugh, Alex C. Ruane, Xuhui Wang
Software Mentions: 5
Published: about 7 years ago

10.1242/dmm.034124

Epigenetic regulators Rbbp4 and Hdac1 are overexpressed in a zebrafish model of RB1 embryonal brain tumor, and are required for neural progenitor survival and proliferation
Cited by: 37
Author(s): Linda Schultz, Jeffrey A. Haltom, Maira P. Almeida, Wesley A. Wierson, Staci L. Solin, Trevor Weiss, Jordan A Helmer, Elizabeth J. Sandquist, Heather R. Shive, Maura McGrail
Software Mentions: 5
Published: over 8 years ago

10.1186/s12920-020-00740-x

Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension
Cited by: 15
Author(s): Jing Luo, Haiyan Li, Zhenwei Liu, Chenlu Li, Ruochen Wang, Jinxia Fang, Saisai Lu, Jing Guo, Xiongzhao Zhu, Xiaobing Wang
Software Mentions: 5
Published: over 6 years ago

10.1007/s12072-019-09962-3

Identification and validation of a prognostic four-genes signature for hepatocellular carcinoma: integrated ceRNA network analysis
Cited by: 41
Author(s): Yongcong Yan, Yaobin Lu, Kai Mao, Mengyu Zhang, Haohan Liu, Qicun Zhou, Jianhong Lin, Jianlong Zhang, Jie Wang, Zhiyu Xiao
Software Mentions: 5
Published: over 7 years ago

10.1007/s12035-020-01983-6

Transcriptome Analysis of iPSC-Derived Neurons from Rubinstein-Taybi Patients Reveals Deficits in Neuronal Differentiation
Cited by: 15
Author(s): Luciano Calzari, Matteo Barcella, Valentina Alari, Daniele Braga, Rafael Muñoz‐Viana, Cristina Barlassina, Palma Finelli, Cristina Gervasini, Ángel Barco, Silvia Russo, Lidia Larizza
Software Mentions: 5
Published: over 6 years ago

10.1186/s12879-018-3127-4

“Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”
Cited by: 18
Author(s): Sheetal Verma, Peicheng Du, Damalie Nakanjako, Sabine Hermans, Jessica Briggs, Lydia Nakiyingi, Jerrold J. Ellner, Yukari C. Manabe, Padmini Salgame
Software Mentions: 5
Published: over 8 years ago

10.1186/s42523-021-00095-3

Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning
Cited by: 19
Author(s): Nida Amin, Sarah Schwarzkopf, Asako Kinoshita, Johanna Tröscher-Mußotter, Sven Dänicke, Amélia Camarinha‐Silva, Korinna Huber, Jana Frahm, Jana Seifert
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pntd.0009504

Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Cited by: 16
Author(s): Arunasalam Naguleswaran, Paula Fernandes, Shubha Bevkal, Ruth Rehmann, Pamela Nicholson, Isabel Roditi
Software Mentions: 5
Published: about 5 years ago

10.1186/1471-2105-14-47

A survey of protein interaction data and multigenic inherited disorders
Cited by: 6
Author(s): Antonio M. Mora, Katerina Michalickova, Ian Donaldson
Software Mentions: 5
Published: over 13 years ago

10.3390/cells9020323

Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster Is Involved in Chromosome-Wide Gene Regulation
Cited by: 6
Author(s): Samaneh Ekhteraei-Tousi, Jacob Lewerentz, Jonas Larsson
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2164-15-749

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
Cited by: 22
Author(s): Johan Bengtsson‐Palme, Magnus Alm Rosenblad, Mikael Molin, Anders Blomberg
Software Mentions: 5
Published: almost 13 years ago

10.1186/s12864-015-2096-x

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh
Cited by: 19
Author(s): James Boocock, David Chagné, Tony R. Merriman, Michael A. Black
Software Mentions: 5
Published: about 11 years ago

10.1016/j.stem.2015.04.004

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
Cited by: 369
Author(s): Nicola K. Wilson, David G. Kent, Florian Buettner, Mona Shehata, Iain C. Macaulay, Fernando J. Calero-Nieto, Manuel Sánchez Castillo, Caroline A. Oedekoven, Evangelia Diamanti, Reiner Schulte, Chris P. Ponting, Thierry Voet, Carlos Caldas, John Stingl, Anthony Green, Fabian J. Theis, Berthold Göttgens
Software Mentions: 5
Published: over 11 years ago

10.3390/cells10081971

PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen
Cited by: 8
Author(s): Carolin Seyfferth, Bernard A. Wessels, Jorma Vahala, Jaakko Kangasjärvi, Nicolas Delhomme, Torgeir R. Hvidsten, Hannele Tuominen, Judith Lundberg‐Felten
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-016-2429-4

Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea
Cited by: 64
Author(s): Aurore Desgroux, Virginie Merot l'Anthoene, Martine Roux-Duparque, Jean-Philippe Rivière, Grégoire Aubert, Nadim Tayeh, Anne Moussart, P Mangin, Pierrick Vetel, Christophe Piriou, Rebecca J. McGee, Clarice J. Coyne, Judith Burstin, Alain Baranger, Maria Manzanares-Dauleux, Virginie Bourion, Marie‐Laure Pilet‐Nayel
Software Mentions: 5
Published: over 10 years ago

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