cran: gplots | Projects | Ecosyste.ms: Papers

10.1186/s12864-019-6034-1

De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Cited by: 19
Author(s): Eugeni Belda, Ferdinand Nanfack-Minkeu, Karin Eiglmeier, Guillaume Carissimo, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Igor V. Sharakhov, Kenneth D. Vernick
Software Mentions: 6
Published: about 7 years ago

10.1186/s12864-020-6684-z

Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines
Cited by: 7
Author(s): Ethel J. S. Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur, James Adjaye
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2164-15-1028

Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes
Cited by: 17
Author(s): M. Ono, Reiko Tanaka, Manabu Kano
Software Mentions: 6
Published: almost 13 years ago

10.1038/srep37387

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2
Cited by: 13
Author(s): Erinn M. Muller, Maoz Fine, Kim B. Ritchie
Software Mentions: 6
Published: almost 10 years ago

10.1186/1471-2164-10-270

Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events
Cited by: 110
Author(s): Sônia Sousa Melo Cavalcanti de Albuquerque, Céline Carret, Ana Rita Grosso, Alice S. Tarun, Xinxia Peng, Stefan H. I. Kappe, Miguel Prudêncio, Maria M. Mota
Software Mentions: 6
Published: over 17 years ago

10.1038/srep33696

Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests
Cited by: 247
Author(s): Kristin Kaiser, Bernd Wemheuer, Vera Korolkow, Franziska Wemheuer, Heiko Nacke, Ingo Schöning, Marion Schrumpf, Rolf Daniel
Software Mentions: 6
Published: about 10 years ago

10.1038/srep25507

CD36 is expressed in a defined subpopulation of neurons in the olfactory epithelium
Cited by: 31
Author(s): André Machado Xavier, Raissa G. Ludwig, Maíra H. Nagai, Tiago Jonas de Almeida, Hebe Mizuno Watanabe, Marcio Yukio Hirata, Tatiana R. Rosenstock, Fábio Papes, Bettina Malnic, Isaías Glezer
Software Mentions: 6
Published: over 10 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

10.3389/fimmu.2017.00246

Host Genetic Background Strongly Affects Pulmonary microRNA Expression before and during Influenza A Virus Infection
Cited by: 19
Author(s): Matthias Preuße, Klaus Schughart, Frank Peßler
Software Mentions: 6
Published: over 9 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

10.1038/s41598-017-06880-y

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis
Cited by: 29
Author(s): Fiona Fouhy, N.J. Ronan, Órla O’Sullivan, Yvonne McCarthy, Aaron M. Walsh, Desmond M. Murphy, Mary B. Daly, Evelyn Flanagan, C. Fleming, M. McCarthy, C. Shortt, Joseph A. Eustace, Fergus Shanahan, Mary C. Rea, R. Paul Ross, Catherine Stanton, Barry J. Plant
Software Mentions: 6
Published: about 9 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

10.1186/s13550-017-0355-3

A novel genomic signature predicting FDG uptake in diverse metastatic tumors
Cited by: 4
Author(s): Aurora Crespo-Jara, Maria Carmen Redal-Peña, E. Martinez-Navarro, Manuel Sureda, Francisco J. Fernández-Morejón, Francisco Javier Garcia-Cases, Ramón González Manzano, Antonio Brugarolas
Software Mentions: 6
Published: over 8 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

10.1371/journal.pone.0204542

NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis
Cited by: 9
Author(s): Manali Rupji, Bhakti Dwivedi, Jeanne Kowalski
Software Mentions: 6
Published: over 7 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: over 7 years ago

10.1074/jbc.RA120.014745

Quantitative phosphoproteomic analysis reveals involvement of PD-1 in multiple T cell functions
Cited by: 14
Author(s): Anna S. Tocheva, Michael Peled, Marianne Strazza, Kieran Adam, Shalom Lerrer, Shruti Nayak, Inbar Azoulay-Alfaguter, Connor Foster, Elliot A. Philips, Benjamin G. Neel, Beatrix Ueberheide, Adam Mor
Software Mentions: 6
Published: almost 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

10.1002/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

10.1371/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

10.26508/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

10.1186/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

10.1093/gigascience/giz050

Metabolic responses of rice cultivars with different tolerance to combined drought and heat stress under field conditions
Cited by: 48
Author(s): Lovely Mae F Lawas, Xia Li, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Ellen Zuther, Dirk K. Hincha
Software Mentions: 6
Published: over 7 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

10.1186/1471-2164-15-353

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

10.7717/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

10.1093/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: almost 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: almost 9 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

10.1186/s13059-021-02326-x

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: over 12 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/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

10.1042/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.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.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

10.1186/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

10.3389/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

10.3390/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

10.3390/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: 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: 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: almost 10 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: over 10 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

10.1007/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: about 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

10.1186/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

10.3389/fgene.2020.00870

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize
Cited by: 13
Author(s): Jonás A. Aguirre‐Liguori, Javier Alejandro Luna-Sanchez, Jaime Gasca-Pineda, Luis E. Eguiarte
Software Mentions: 5
Published: about 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

10.1038/s41598-018-27027-7

Immunoprofiles of human Sertoli cells infected with Zika virus reveals unique insights into host-pathogen crosstalk
Cited by: 32
Author(s): Daniel P. Strange, Richard Green, Dietmar W. Siemann, Michael Gale, Saguna Verma
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2020.00055

Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma
Cited by: 14
Author(s): Wenjie Wang, Han Wang, Ting-yan Hua, Wei Song, Jie Zhu, Jingjing Wang, Yongzhen Huang, Zhi-Liang Ding
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-018-20471-5

Development of an Immune-Pathology Informed Radiomics Model for Non-Small Cell Lung Cancer
Cited by: 104
Author(s): Chad Tang, Brian P. Hobbs, Ahmed M. Amer, Li Xiao, Carmen Behrens, Jaime Rodriguez Canales, Edwin Parra Cuentas, Pamela Villalobos, David Fried, Joe Y. Chang, David S. Hong, James Welsh, Boris Sepesi, Laurence Edward Court, Ignacio I. Wistuba, Eugene J. Koay
Software Mentions: 5
Published: over 8 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: almost 6 years ago

10.3389/fimmu.2020.01636

Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse
Cited by: 101
Author(s): Luiz Gustavo Gardinassi, Camila Oliveira Silva Souza, Helioswilton Sales‐Campos, Simone Gonçalves Fonseca
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-017-14942-4

Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Cited by: 6
Author(s): Yusuke Morita, Mikiko Ohno, Kiyoto Nishi, Yutaka Hiraoka, Sayaka Saijo, Shintaro Matsuda, Toru Kita, Takeshi Kimura, Eiichiro Nishi
Software Mentions: 5
Published: almost 9 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

10.1038/s41598-018-22977-4

Analysis of the neurotoxic effects of neuropathic organophosphorus compounds in adult zebrafish
Cited by: 11
Author(s): Melissa Faria, Inmaculada Fuertes, Eva Prats, José Luı́s Abad, Francesc Padrós, Cristian Gómez‐Canela, Josefina Casas, Jorge Estévez, Eugenio Vilanova, Benjamı́n Piña, Demetrio Raldúa
Software Mentions: 5
Published: over 8 years ago

10.3389/fchem.2020.00243

An Innovative Sequence-to-Structure-Based Approach to Drug Resistance Interpretation and Prediction: The Use of Molecular Interaction Fields to Detect HIV-1 Protease Binding-Site Dissimilarities
Cited by: 4
Author(s): Nuno G. Alves, Ana I. Mata, João Luís, Rui M. M. Brito, Carlos J. V. Simões
Software Mentions: 5
Published: over 6 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

10.3389/fcimb.2020.588155

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease
Cited by: 14
Author(s): Kai Bao, Xiaofei Li, Lucy Poveda, Weihong Qi, Nathalie Selevsek, Pınar Gümüş, Gülnur Emingil, Jonas Grossmann, Patricia I. Diaz, George Hajishengallis, Nagihan Bostancı, Georgios N. Belibasakis
Software Mentions: 5
Published: about 6 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

10.1038/s41598-017-08010-0

Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana
Cited by: 25
Author(s): Tommaso Raffaello, Fred O. Asiegbu
Software Mentions: 5
Published: about 9 years ago

10.3389/fcell.2021.648331

Fibrillarin-GFP Facilitates the Identification of Meiotic Competent Oocytes
Cited by: 6
Author(s): Ting Wang, Jie Na
Software Mentions: 5
Published: over 5 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

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