cran: gplots | Projects | Ecosyste.ms: Papers

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: over 5 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

10.3389/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

10.1016/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

10.3389/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

10.1007/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

10.1007/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: about 5 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: about 6 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

10.1002/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: about 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

10.1038/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

10.26508/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: about 5 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

10.1038/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: about 11 years ago

10.1038/s41598-018-22488-2

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer
Cited by: 55
Author(s): Rogan Magee, Aristeidis G. Telonis, Phillipe Loher, Eric Londin, Isidore Rigoutsos
Software Mentions: 6
Published: over 8 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: about 5 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

10.3389/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: almost 8 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: over 9 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

10.1038/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

10.3389/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

10.1186/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: about 5 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: 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: almost 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: about 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: over 10 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: almost 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: 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: about 11 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: about 10 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: 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: about 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: almost 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: over 6 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: over 5 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/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.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

10.1186/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: about 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

10.1186/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

10.1093/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

10.1093/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

10.1371/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: almost 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: over 9 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

10.1186/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

10.1371/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: over 5 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: almost 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: about 6 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: about 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/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: almost 10 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/s41598-018-30509-3

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

10.1038/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

10.3390/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: about 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: about 6 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

10.1038/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: over 6 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

10.7554/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

10.3390/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/s41598-020-66519-3

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

10.1038/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/s41598-020-66721-3

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: about 6 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: almost 9 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: almost 6 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

10.3390/ijms21186488

Lipid Stores and Lipid Metabolism Associated Gene Expression in Porcine and Bovine Parthenogenetic Embryos Revealed by Fluorescent Staining and RNA-seq
Cited by: 16
Author(s): Arkadiusz Kajdasz, Ewelina Warzych, Natalia Derebecka, Zofia E. Madeja, D. Lechniak, Joanna Wesoły, Piotr Pawlak
Software Mentions: 5
Published: almost 6 years ago

10.18632/oncotarget.25350

High expression of nucleoporin 133 mRNA in bone marrow CD138+ cells is a poor prognostic factor in multiple myeloma
Cited by: 4
Author(s): Soushi Ibata, Masayoshi Kobune, Shohei Kikuchi, Masahiro Yoshida, Satoshi Miura, Hyogo Horiguchi, Kazuyuki Murase, Satoshi Iyama, Kohichi Takada, Koji Miyanishi, Junji Kato
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-021-81359-5

Aldehyde-specific responses of olfactory sensory neurons in the praying mantis
Cited by: 3
Author(s): Kota Ezaki, Takashi Yamashita, Thomas Carle, Hidehiro Watanabe, Fumio Yokohari, Yoshifumi Yamawaki
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms21218016

Enhancer of Zeste Homolog 2 (EZH2) Mediates Glucolipotoxicity-Induced Apoptosis in β-Cells
Cited by: 3
Author(s): Tina Dahlby, Christian Simon, Marie Balslev Backe, Mattias Salling Dahllöf, Edward B. Holson, Bridget K. Wagner, Marianne Böni-Schnetzler, Michał Marzec, Morten Lundh, Thomas Mandrup‐Poulsen
Software Mentions: 5
Published: almost 6 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

10.3390/ijms22031111

Detection of a DNA Methylation Signature for the Intellectual Developmental Disorder, X-Linked, Syndromic, Armfield Type
Cited by: 9
Author(s): Sadegheh Haghshenas, Michael A. Levy, Jennifer Kerkhof, Erfan Aref‐Eshghi, Haley McConkey, Tugce B. Balci, Victoria Mok Siu, Cindy Skinner, Roger E. Stevenson, Bekim Sadiković, Charles E. Schwartz
Software Mentions: 5
Published: over 5 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

10.1038/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

10.1038/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

10.1038/s41598-018-37679-0

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: over 7 years ago

10.1016/j.isci.2021.103092

The gut microbiota instructs the hepatic endothelial cell transcriptome
Cited by: 11
Author(s): Henning Formes, Joana P. Bernardes, Amrit Mann, Franziska Bayer, Giulia Pontarollo, Klytaimnistra Kiouptsi, Katrin Schäfer, Sebastian Attig, Teodora Nikolova, Thomas G. Hofmann, Jörn M. Schattenberg, Hristo Todorov, Susanne Gerber, Philip Rosenstiel, Tobias Bopp, Felix Sommer, Carsten Reinhardt
Software Mentions: 5
Published: almost 5 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

10.1038/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: about 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: about 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

10.1186/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: about 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

10.3390/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

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