bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-88445-8

The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro
Cited by: 9
Author(s): Shanthi G. Parkar, Jovyn K. T. Frost, Douglas Rosendale, Halina Stoklosinski, Carel M. H. Jobsis, Duncan I. Hedderley, Pramod K. Gopal
Software Mentions: 1
Published: about 4 years ago

10.3389/fpls.2016.00715

Transcriptome Profiling of Buffalograss Challenged with the Leaf Spot Pathogen Curvularia inaequalis
Cited by: 7
Author(s): Bimal S. Amaradasa, Keenan Amundsen
Software Mentions: 1
Published: about 9 years ago

10.3389/fimmu.2020.609400

CCR8 Signaling via CCL1 Regulates Responses of Intestinal IFN-γ Producing Innate Lymphoid CelIs and Protects From Experimental Colitis
Cited by: 5
Author(s): Le Kang, Angelika Schmalzl, Tamara Leupold, Miguel Gonzalez-Acera, Raja Atreya, Markus F. Neurath, Christoph Becker, Stefan Wirtz
Software Mentions: 1
Published: over 4 years ago

10.3389/fnagi.2020.576678

Longitudinal Characterization of Transcriptomic, Functional, and Morphological Features in Human iPSC-Derived Neurons and Their Application to Investigate Translational Progranulin Disease Biology
Cited by: 3
Author(s): Gaëlle Robin, J. C. Evans, David N. Hauser, Paul Wren, Andreas Zembrzycki
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-89288-z

Biomechanical regulation of breast cancer metastasis and progression
Cited by: 10
Author(s): Adrianne Spencer, Andrew D. Sligar, Daniel Chavarria, Jason Lee, Darshil Choksi, Nikita P. Patil, HooWon Lee, Austin Veith, William J. Riley, Shubh Desai, Ali Abbaspour, Rohan Singeetham, Aaron Baker
Software Mentions: 1
Published: about 4 years ago

10.1186/s13104-018-3230-z

Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations
Cited by: 11
Author(s): Sonny T. M. Lee, Shashank Keshavmurthy, Silvia Fontana, Takuma Mezaki, Wen-Hua Chou, Chaolun Allen Chen
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-89170-y

Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures
Cited by: 5
Author(s): Yuji Ke, Maricel Podio, Joann A. Conner, Peggy Ozias‐Akins
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms21207596

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides
Cited by: 5
Author(s): Anastassia Boudichevskaia, Alevtina Ruban, Johannes Thiel, Anne Fiebig
Software Mentions: 1
Published: almost 5 years ago

10.1111/eva.12487

Transcriptional mechanisms underlying life-history responses to climate change in the three-spined stickleback
Cited by: 22
Author(s): Sin‐Yeon Kim, María M. Costa, Anna Esteve‐Codina, Alberto Velando
Software Mentions: 1
Published: about 8 years ago

10.3389/fimmu.2019.01186

Cecal CircRNAs Are Associated With the Response to Salmonella Enterica Serovar Enteritidis Inoculation in the Chicken
Cited by: 10
Author(s): Lanhong Zheng, Liying Liu, Lili Lin, Hui Tang, Xinzhong Fan, Hai Lin, Xianyao Li
Software Mentions: 1
Published: about 6 years ago

10.3390/cancers11111748

[18F] Clofarabine for PET Imaging of Hepatocellular Carcinoma
Cited by: 4
Author(s): О. Н. Сергеева, Vladimir Kepe, Yifan Zhang, Galen Miller‐Atkins, Jonathan D Keynon, Renuka Iyer, Sandra Sexton, Amad Awadallah, Xin Wei, Yogen Saunthararajah, E. Ricky Chan, Zhenghong Lee
Software Mentions: 1
Published: over 5 years ago

10.1016/j.cell.2016.08.030

Epithelia Use Butyrophilin-like Molecules to Shape Organ-Specific γδ T Cell Compartments
Cited by: 249
Author(s): Rafael Di Marco Barros, Natalie Roberts, Robin Dart, Pierre Vantourout, Anett Jandke, Oliver Nussbaumer, Livija Deban, Sara Cipolat, Rosie Hart, Maria Luisa Iannitto, Adam Laing, Bradley Spencer–Dene, Philip East, Deena L. Gibbons, Peter Irving, Pablo Pereira, Ulrich Steinhoff, Adrian Hayday
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-021-89853-6

Accelerating cryoprotectant diffusion kinetics improves cryopreservation of pancreatic islets
Cited by: 8
Author(s): Nikola Doležalová, Anja V. Gruszczyk, Kerry Barkan, John Gamble, Sam G Galvin, Till Moreth, Kevin O’Holleran, Krishnaa Mahbubani, Jackie Higgins, Fiona M. Gribble, Frank Reimann, Jakub Surmacki, Simon Andrews, John Casey, Francesco Pampaloni, Michael P. Murphy, Graham Ladds, Nigel K.H. Slater, Kourosh Saeb‐Parsy
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-90148-z

Whole transcriptome RNA-seq reveals key regulatory factors involved in type 2 diabetes pathology in peripheral fat of Asian Indians
Cited by: 7
Author(s): Aditya Saxena, Navneet Mathur, Prabhat Tiwari, Sandeep Kumar Mathur
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0167003

Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool
Cited by: 2
Author(s): Marie Anson, Inês F. Amado, Marie-Pierre Mailhé, Emmanuel Donnadieu, Sylvie Garcia, François Huetz, António A. Freitas
Software Mentions: 1
Published: over 8 years ago

10.3390/cancers13081975

Profiling of Adipose and Skeletal Muscle in Human Pancreatic Cancer Cachexia Reveals Distinct Gene Profiles with Convergent Pathways
Cited by: 7
Author(s): Ashok Narasimhan, Xiaoling Zhong, Ernie D. Au, Eugene P. Ceppa, Atilla Nakeeb, Michael G. House, Nicholas J. Zyromski, C. Max Schmidt, Katheryn N. H. Schloss, Daniel Schloss, Yunlong Liu, Guanglong Jiang, Bradley A. Hancock, Milan Radovich, Joshua K. Kays, Safi Shahda, Marion E. Couch, Leonidas G. Koniaris, Teresa A. Zimmers
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0225267

Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes
Cited by: 17
Author(s): Eri Takematsu, Adrianne Spencer, Jeff Auster, Po-Chih Chen, Annette Graham, Patricia Martin, Aaron Baker
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-90467-1

PET-CT and RNA sequencing reveal novel targets for acupuncture-induced lowering of blood pressure in spontaneously hypertensive rats
Cited by: 1
Author(s): Jing Li, Chong Peng, Dongjian Lai, Yajing Fang, Daihong Luo, Zunming Zhou, Chenyun Li, Xinsheng Lai
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-90515-w

Identification of BHLHE40 expression in peripheral blood mononuclear cells as a novel biomarker for diagnosis and prognosis of hepatocellular carcinoma
Cited by: 4
Author(s): Pattapon Kunadirek, Chaiyaboot Ariyachet, Supachaya Sriphoosanaphan, Nutcha Pinjaroen, Pongserath Sirichindakul, Intawat Nookaew, Natthaya Chuaypen, Pisit Tangkijvanich
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2020.587931

Characterization of miRNAs in Extracellular Vesicles Released From Atlantic Salmon Monocyte-Like and Macrophage-Like Cells
Cited by: 15
Author(s): Nicole C. Smith, Gabriel Wajnberg, Simi Chacko, Nardos Tesfaye Woldemariam, Jacynthe Lacroix, Nicolas Crapoulet, D. Craig Ayre, Stephen M. Lewis, Matthew L. Rise, Rune Andreassen, Sherri L. Christian
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms21218119

Expression of EMT-Related Genes in Hybrid E/M Colorectal Cancer Cells Determines Fibroblast Activation and Collagen Remodeling
Cited by: 13
Author(s): Irina Druzhkova, Marina V. Shirmanova, Nadezhda Ignatova, Varvara V. Dudenkova, Maria M. Lukina, Elena V. Zagaynova, Dina Safina, Sergey V. Kostrov, D. A. Didych, A. I. Kuzmich, Г. В. Шаронов, Olga Rakitina, И. В. Алексеенко, Е. Д. Свердлов
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.57007

Notch and TLR signaling coordinate monocyte cell fate and inflammation
Cited by: 39
Author(s): Jaba Gamrekelashvili, Tamar Kapanadze, Stefan Sablotny, Corina Rațiu, Khaled Dastagir, Matthias Lochner, Susanne Karbach, Philip Wenzel, Andre Sitnow, Susanne Fleig, Tim Sparwasser, Ulrich Kalinke, Bernhard Holzmann, Hermann Haller
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2019.02070

Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Cited by: 6
Author(s): Atsadang Boonmee, Haley F. Oliver, Soraya Chaturongakul
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2018.02972

The Change of Teleost Skin Commensal Microbiota Is Associated With Skin Mucosal Transcriptomic Responses During Parasitic Infection by Ichthyophthirius multifillis
Cited by: 58
Author(s): Xiaoting Zhang, Li-Guo Ding, Yongyao Yu, Weijing Kong, Yaxing Yin, Zhenyu Huang, Xuezhen Zhang, Zhen Xu
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2018.02284

Biomarkers for Early Stages of Johne’s Disease Infection and Immunization in Goats
Cited by: 11
Author(s): Aubrey Berry, Chia-Wei Wu, Amanda J. Venturino, Adel M. Talaat
Software Mentions: 1
Published: almost 7 years ago

10.3389/fimmu.2020.00914

Identification of Altered miRNAs in Cerumen of Dogs Affected by Otitis Externa
Cited by: 5
Author(s): Cristina Lecchi, Valentina Zamarian, Giorgia Borriello, Giorgio Galiero, G. Grilli, M. Caniatti, Elisa Silvia D'Urso, P. Roccabianca, Roberta Perego, Michela Minero, Sara Legnani, Raffaele Calogero, Maddalena Arigoni, Fabrizio Ceciliani
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-90633-5

Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
Cited by: 8
Author(s): Jifang Zhang, Jian Zhao, Qunyun Tan, Xiaojun Qiu, Shuqi Mei
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.619542

Transcriptomic Basis of Serum Resistance and Virulence Related Traits in XDR P. aeruginosa Evolved Under Antibiotic Pressure in a Morbidostat Device
Cited by: 5
Author(s): Mumina Javed, Benedikt Jentzsch, Maximilian Heinrich, Viola Ueltzhoeffer, Silke Peter, Ulrich Schoppmeier, Angel Angelov, Sandra Schwarz, Matthias Willmann
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-90672-y

Rootstock effects on scion gene expression in maritime pine
Cited by: 10
Author(s): Miriam López‐Hinojosa, Nuria de María, M. Ángeles Guevara, María Dolores Vélez, José Antonio Cabezas, Luis Manuel Díaz, José Antonio Mancha, Alberto Pizarro, Lorenzo Federico Manjarrez, Carmen Collada, Carmen Dı́az-Sala, M T Cervera Goy
Software Mentions: 1
Published: about 4 years ago

10.7554/eLife.63254

BAP1/ASXL complex modulation regulates epithelial-mesenchymal transition during trophoblast differentiation and invasion
Cited by: 20
Author(s): Vicente Pérez-García, Georgia Lea, Pablo López-Jiménez, Hanneke Okkenhaug, Graham J. Burton, Ashley Moffett, Margherita Y. Turco, Myriam Hemberger
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2016.00995

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil
Cited by: 35
Author(s): Jakub Rídl, Michal Kolář, Michal Strejcek, Hynek Strnad, Petr Stursa, Jan Pačes, Tomáš Macek, Ondřej Uhlík
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-021-91269-1

Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides)
Cited by: 3
Author(s): Wangyang Ji, li E Hou, Xi Yuan, Tiantian Gu, ZhuoYu Chen, Yu Zhang, Yang Zhang, Guohong Chen, Qi Xu, Wenming Zhao
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2019.02227

LC-MS-Based Metabolomic Approach Revealed the Significantly Different Metabolic Profiles of Five Commercial Truffle Species
Cited by: 32
Author(s): Xin Li, Xiaoping Zhang, Lei Ye, Zongjing Kang, Dinghong Jia, Yang Lan, Bo Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1128/mBio.01606-21

A New Model Trypanosomatid, Novymonas esmeraldas : Genomic Perception of Its “ Candidatus Pandoraea novymonadis” Endosymbiont
Cited by: 6
Author(s): Alexandra Zakharova, Andreu Saura, Anzhelika Butenko, Lucie Podešvová, Sandra Warmusová, Alexei Y. Kostygov, Anna Nenarokova, Julius Lukeš, Frederik Opperdoes, Vyacheslav Yurchenko
Software Mentions: 1
Published: almost 4 years ago

10.3389/fgene.2020.571880

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci for Nitrite Tolerance in the Pacific White Shrimp (Litopenaeus vannamei)
Cited by: 6
Author(s): Min Peng, Dingyuan Zeng, Weilin Zhu, Xiuli Chen, Chunling Yang, Qingyun Liu, Qiangyong Li, Huanling Wang, Hong Liu, Liang JingZhen, Yong Lin, Yang Zhao
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2021.678673

Organ-Specific Transcriptome Analysis Identifies Candidate Genes Involved in the Stem Specialization of Bermudagrass (Cynodon dactylon L.)
Cited by: 4
Author(s): Si Chen, Xin Xu, Ziyan Ma, Jianxiu Liu, Bing Zhang
Software Mentions: 1
Published: about 4 years ago

10.1128/mBio.01416-21

CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii
Cited by: 12
Author(s): Yan Liao, Verena Vogel, Sabine Hauber, Jürgen Bartel, Omer S. Alkhnbashi, Sandra Maaß, Thandi S. Schwarz, Rolf Backofen, Dörte Becher, Iain G. Duggin, Anita Marchfelder
Software Mentions: 1
Published: almost 4 years ago

10.1093/molbev/msy171

Integrating embryonic development and evolutionary history to characterize tentacle-specific cell types in a ctenophore
Cited by: 22
Author(s): Leslie S. Babonis, Melissa B. DeBiasse, Warren R. Francis, Lynne M. Christianson, Anthony G. Moss, Steven H. D. Haddock, Mark Q. Martindale, Joseph F. Ryan
Software Mentions: 1
Published: almost 7 years ago

10.1128/mSphere.00030-15

A Three-Dimensional Cell Culture Model To Study Enterovirus Infection of Polarized Intestinal Epithelial Cells
Cited by: 34
Author(s): Coyne Drummond, Cheryl A. Nickerson, Carolyn B. Coyne
Software Mentions: 1
Published: over 9 years ago

10.1186/s12918-018-0652-0

scdNet: a computational tool for single-cell differential network analysis
Cited by: 12
Author(s): Yi-Chang Chiu, Tzu Hung Hsiao, Li J. Wang, Yidong Chen, Yu Shao
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2021.706341

Integrated Analysis of Hepatic miRNA and mRNA Expression Profiles in the Spontaneous Reversal Process of Liver Fibrosis
Cited by: 2
Author(s): Yang Tai, Chong Zhao, Tian Lan, Linhao Zhang, Yang Xiao, Huan Tong, Rui Li, Chengwei Tang, Jinhang Gao
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2021.671852

Small Non-coding RNA Expression Following Respiratory Syncytial Virus or Measles Virus Infection of Neuronal Cells
Cited by: 0
Author(s): Abhijeet Bakre, Catherine Duffy, Hani’ah Abdullah, S. L. Cosby, Ralph A. Tripp
Software Mentions: 1
Published: almost 4 years ago

10.1128/mSphere.00769-20

A Trypanosoma brucei ORFeome-Based Gain-of-Function Library Identifies Genes That Promote Survival during Melarsoprol Treatment
Cited by: 10
Author(s): McKenzie Carter, Stephanie Gomez, Sam Gritz, Stephen Larson, Eugenia Silva-Herzog, Hee-Sook Kim, Danae Schulz, Galadriel Hovel-Miner
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2019.00108

Integrative Analysis Reveals Key Circular RNA in Atrial Fibrillation
Cited by: 15
Author(s): Xiaofeng Hu, Linhui Chen, Shaohui Wu, Kai Xu, Weifeng Jiang, Mu Qin, Yu Zhang, Xu Liu
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2017.00213

The Dynamics of microRNA Transcriptome in Bovine Corpus Luteum during Its Formation, Function, and Regression
Cited by: 27
Author(s): Rreze M. Gecaj, Corina I. Schanzenbach, Benedikt Kirchner, Michael W. Pfaffl, Irmgard Riedmaier, Ry Y. Tweedie-Cullen, Bajram Berisha
Software Mentions: 1
Published: over 7 years ago

10.3390/cancers12082285

YB-1 Knockdown Inhibits the Proliferation of Mesothelioma Cells through Multiple Mechanisms
Cited by: 9
Author(s): Thomas G. Johnson, Karin Schelch, Kaitao Lai, Kamila A. Marzec, Marina Kennerson, Michael Grusch, Glen Reid, Andrew Burgess
Software Mentions: 1
Published: almost 5 years ago

10.1038/s12276-019-0352-x

Bach2 deficiency leads autoreactive B cells to produce IgG autoantibodies and induce lupus through a T cell-dependent extrafollicular pathway
Cited by: 44
Author(s): Eunkyeong Jang, Un Kyo Kim, Kiseok Jang, Young Soo Song, Ji Young, Hansol Yi, Jeehee Youn
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21218393

The Function of Oncogene B-Cell Lymphoma 6 in the Regulation of the Migration and Invasion of Trophoblastic Cells
Cited by: 4
Author(s): Andreas Ritter, Babek Khan Safdar, Britta Jasmer, Nina-Naomi Kreis, Alexandra Friemel, Susanne Roth, Christine Solbach, Frank Louwen, Juping Yuan
Software Mentions: 1
Published: over 4 years ago

10.1128/mSphere.01093-20

A 39-Amino-Acid C-Terminal Truncation of GDV1 Disrupts Sexual Commitment in Plasmodium falciparum
Cited by: 12
Author(s): Marta Tibúrcio, Eva Hitz, Igor Niederwieser, Gavin Kelly, Heledd Davies, Christian Doerig, Oliver Billker, Till S. Voss, Moritz Treeck
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0247837

The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine
Cited by: 6
Author(s): Ruwaa I. Mohamed, Salma A. Bargal, Asmaa S. Mekawy, Iman El-Shiekh, Nurcan Tunçbağ, Alaa S. Ahmed, Eman Badr, Menattallah Elserafy
Software Mentions: 1
Published: over 4 years ago

10.1128/mSphere.00443-21

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility
Cited by: 9
Author(s): Anand V. Sastry, Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner, Sibei Xu, Richard Szubin, Adam M. Feist, Victor Nizet, Jaehyung Kim
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.58064

Methotrexate attenuates vascular inflammation through an adenosine-microRNA-dependent pathway
Cited by: 8
Author(s): Dafeng Yang, Stefan Haemmig, Hong-Hao Zhou, Daniel Pérez‐Cremades, Xinghui Sun, Lei Chen, Jie Li, Jorge Haneo-Mejia, Tianlun Yang, Ivana Hollan, Mark W. Feinberg
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.03057

Cell Wall Synthesis, Development of Hyphae and Metabolic Pathways Are Processes Potentially Regulated by MicroRNAs Produced Between the Morphological Stages of Paracoccidioides brasiliensis
Cited by: 5
Author(s): Juliana Santana de Curcio, Juliano D. Paccez, Evandro Novaes, Matthias Brock, Célia Maria de Almeida Soares
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0168075

Two Subclasses of Differentially Expressed TPS1 Genes and Biochemically Active TPS1 Proteins May Contribute to Sugar Signalling in Kiwifruit Actinidia chinensis
Cited by: 3
Author(s): Charlotte Voogd, Lara Brian, Erika Varkonyi‐Gasic
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0179571

WetA bridges cellular and chemical development in Aspergillus flavus
Cited by: 34
Author(s): Ming-Yueh Wu, Matthew E. Mead, Sun-Chang Kim, Antonis Rokas, Jae-Hyuk Yu
Software Mentions: 1
Published: about 8 years ago

10.1038/s42003-021-02283-y

Guard cells control hypocotyl elongation through HXK1, HY5, and PIF4
Cited by: 9
Author(s): Gilor Kelly, Danja Brandsma, Aiman Egbaria, O. Stein, Adi Doron‐Faigenboim, Nitsan Lugassi, Eduard Belausov, Hanita Zemach, Felix Shaya, Nir Carmi, Nir Sade, David Granot
Software Mentions: 1
Published: about 4 years ago

10.3389/fgene.2018.00032

Heavy Chronic Intermittent Ethanol Exposure Alters Small Noncoding RNAs in Mouse Sperm and Epididymosomes
Cited by: 76
Author(s): Gregory Rompala, Anaïs Mounier, Cody M. Wolfe, Qishan Lin, Iliya Lefterov, Gregg E. Homanics
Software Mentions: 1
Published: over 7 years ago

10.1016/j.freeradbiomed.2020.10.322

The alarmone (p)ppGpp confers tolerance to oxidative stress during the stationary phase by maintenance of redox and iron homeostasis in Staphylococcus aureus
Cited by: 22
Author(s): Verena Nadin Fritsch, Vu Van Loi, Tobias Busche, Quach Ngoc Tung, Roland Lill, Petra Horvatek, Christiane Wolz, Jörn Kalinowski, Haike Antelmann
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00024-16

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre
Cited by: 283
Author(s): Jessica A. Bryant, Tara M. Clemente, Donn A. Viviani, Allison A. Fong, Kimberley Anh Thomas, Paul F. Kemp, David M. Karl, Angelicque E. White, Edward F. DeLong
Software Mentions: 1
Published: about 9 years ago

10.1093/molbev/msab107

Population Bottlenecks Strongly Affect the Evolutionary Dynamics of Antibiotic Persistence
Cited by: 21
Author(s): Etthel Windels, Richard J. Fox, Krishna Yerramsetty, Katherine Krouse, Tom Wenseleers, Janne Swinnen, Paul Matthay, Laure Verstraete, Dorien Wilmaerts, Bram Van den Bergh, Jan Michiels
Software Mentions: 1
Published: over 4 years ago

10.1080/20961790.2017.1349639

RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion: a pilot study
Cited by: 17
Author(s): Jian Xu, Rui Zhao, Ye Xue, Huan-Qin Xiao, Yanliang Sheng, Dong Zhao, Jie-Tao He, Hongyan Huang, Qi Wang, Huijun Wang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0222954

Impact of the severity of negative energy balance on gene expression in the subcutaneous adipose tissue of periparturient primiparous Holstein dairy cows: Identification of potential novel metabolic signals for the reproductive system
Cited by: 13
Author(s): Namya Mellouk, Christelle Ramé, Delphine Naquin, Yan Jaszczyszyn, Jean-Luc Touzé, Eric Briant, Daniel Guillaume, Theodoros Ntallaris, P. Humblot, Joëlle Dupont
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2015.00703

The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly
Cited by: 12
Author(s): Charles Pepe-Ranney, Edward K. Hall
Software Mentions: 1
Published: about 10 years ago

10.1093/bioinformatics/bty553

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
Cited by: 10
Author(s): Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz
Software Mentions: 1
Published: almost 7 years ago

10.1038/s42003-021-01829-4

IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection
Cited by: 62
Author(s): Bruce A. Rosa, Mushtaq Ahmed, Dhiraj Kumar Singh, José Alberto Choreño-Parra, Journey Cole, Luis Armando Jiménez-Álvarez, Tatiana Sofia Rodrı́guez-Reyna, Bindu Singh, Olga González, Ricardo Carrión, Larry S. Schlesinger, John Martin, Joaquı́n Zúñiga, Makedonka Mitreva, Deepak Kaushal, Shabaana A. Khader
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.03287

Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH in Corynebacterium glutamicum ATCC 13032
Cited by: 12
Author(s): Hana Dostálová, Tobias Busche, Jiří Holátko, Lenka Rucká, Václav Štěpánek, Ivan Barvı́k, Jan Nešvera, Jörn Kalinowski, Miroslav Pátek
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2018.00629

Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra
Cited by: 22
Author(s): Benedikt M Mortzfeld, Jan Taubenheim, Sebastian Fraune, Alexander Klimovich, Thomas C. G. Bosch
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22010079

Ordinary Gasoline Emissions Induce a Toxic Response in Bronchial Cells Grown at Air-Liquid Interface
Cited by: 7
Author(s): Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Michal Šíma, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka, Pavel Rőssner
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00083-18

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria
Cited by: 52
Author(s): Egle Cekanaviciute, Anne-Katrin Pröbstel, Anna Thomann, Tessel F. Runia, Patrizia Casaccia, Ilana Katz Sand, Elizabeth Crabtree, Sneha Singh, John Morrissey, Patrick Barba, Refujia Gomez, Rob Knight, Sarkis K. Mazmanian, Jennifer Graves, Bruce A.C. Cree, Scott S. Zamvil, Sergio E. Baranzini
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers13184528

Surfaceome Profiling of Rhabdomyosarcoma Reveals B7-H3 as a Mediator of Immune Evasion
Cited by: 11
Author(s): Roxane R. Lavoie, Patricio C. Gargollo, Mohamed E. Ahmed, Young S. Kim, Emily Baer, Doris A. Phelps, Cristine Charlesworth, Benjamin J. Madden, Liguo Wang, Peter J. Houghton, John C. Cheville, Haidong Dong, Candace F. Granberg, Fabrice Lucien
Software Mentions: 1
Published: almost 4 years ago

10.1242/bio.049684

Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation
Cited by: 13
Author(s): Tamsin J Samuels, Yoav Arava, Aino I Järvelin, Francesca Robertson, Young Seok Lee, Yang Lu, Ching-Po Yang, Tzumin Lee, David Ish‐Horowicz, Ilan Davis
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.01339

Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs
Cited by: 9
Author(s): Brittney N Keel, W. M. Snelling, A. K. Lindholm‐Perry, W. T. Oliver, L. A. Kuehn, G. A. Rohrer
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2021.618476

Transcriptomic, Biochemical, and Morphological Study Reveals the Mechanism of Inhibition of Pseudopestalotiopsis camelliae-sinensis by Phenazine-1-Carboxylic Acid
Cited by: 7
Author(s): Qiaoxiu Yin, Rui Yang, Yafeng Ren, Zhao Yang, Tao Li, Haoliang Huang, Qin Tang, Dongxue Li, Shilong Jiang, Xian Wu, Delu Wang, Zhuo Chen
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00161-19

A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei
Cited by: 20
Author(s): Amanda Cristina Campos Antoniêto, Karoline Maria Vieira Nogueira, Renato Graciano de Paula, Luísa Czamanski Nora, Murilo Henrique Anzolini Cassiano, María‐Eugenia Guazzaroni, Fausto Almeida, Thiago Aparecido da Silva, Laure Nicolas Annick Ries, Leandro José de Assis, Gustavo H. Goldman, Roberto Nascimento Silva, Rafael Silva‐Rocha
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2018.03059

Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching
Cited by: 31
Author(s): Stephan Christel, Malte Herold, Sören Bellenberg, Antoine Buetti‐Dinh, Mohamed El Hajjami, Igor V. Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mario Vera, Mark Dopson
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0254985

Interleukin-22 mitigates acute respiratory distress syndrome (ARDS)
Cited by: 7
Author(s): Sharven Taghavi, Olan Jackson‐Weaver, Sarah Abdullah, Alanna Wanek, Robert Drury, Jacob Packer, Aaron Cotton-Betteridge, Juan Duchesne, Derek Pociask, Jay K. Kolls
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12987-021-00255-2

Reduction in pericyte coverage leads to blood–brain barrier dysfunction via endothelial transcytosis following chronic cerebral hypoperfusion
Cited by: 32
Author(s): Zhengyu Sun, Chenhao Gao, Dandan Gao, Ruihua Sun, Wei Li, Feng‐Yu Wang, Yanliang Wang, Huixia Cao, Guoyu Zhou, Jiewen Zhang, Junkui Shang
Software Mentions: 1
Published: about 4 years ago

10.1051/bmdcn/2019090427

The RNA degradation pathway is involved in PPARα-modulated anti-oral tumorigenesis
Cited by: 13
Author(s): Nen Chung Chang, Yiping Huang
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.41930

HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses
Cited by: 53
Author(s): Simon Langer, Christian Hammer, Kristina Hopfensperger, Lukas Klein, Dominik Hotter, Paul D. De Jesus, Kristina M. Herbert, Lars Pache, Nikaïa Smith, Johannes A. van der Merwe, Sumit K. Chanda, Jacques Fellay, Frank Kirchhoff, Daniel Sauter
Software Mentions: 1
Published: over 6 years ago

10.1128/mSystems.00289-19

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples
Cited by: 54
Author(s): Sonia Tarallo, Giulio Ferrero, Gaetano Gallo, A. Francavilla, Giuseppe Clerico, A. Realis Luc, Paolo Manghi, Andrew Maltez Thomas, Paolo Víneis, Nicola Segata, Barbara Pardini, Alessio Naccarati, Francesca Cordero
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.01154

A Novel Regulator Modulates Glucan Production, Cell Aggregation and Biofilm Formation in Streptococcus sanguinis SK36
Cited by: 12
Author(s): Bin Zhu, Lei Song, Xiangzhen Kong, Lorna MacLeod, Ping Xu
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0250977

Peptide 1018 inhibits swarming and influences Anr-regulated gene expression downstream of the stringent stress response in Pseudomonas aeruginosa
Cited by: 3
Author(s): Lauren Wilkinson, Morgan A. Alford, Shannon R. Coleman, Bing Wu, Ahwon Lee, Travis M. Blimkie, Manjeet Bains, Reza Falsafi, Daniel Pletzer, Robert E. W. Hancock
Software Mentions: 1
Published: about 4 years ago

10.1128/mSystems.00584-19

Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community
Cited by: 10
Author(s): Diego Rivera Gelsinger, Gherman Uritskiy, Rahul Reddy, Adam Munn, Katie Farney, Jocelyne DiRuggiero
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21218106

A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice (Oryza sativa L.)
Cited by: 4
Author(s): Prasanta K. Subudhi, Richard Garcia, Sapphire Coronejo, Teresa B. De Leon
Software Mentions: 1
Published: over 4 years ago

10.1155/2019/7149296

miRNA and mRNA Integration Network Construction Reveals Novel Key Regulators in Left-Sided and Right-Sided Colon Adenocarcinoma
Cited by: 15
Author(s): Likun Yang, Li Lin, Jing Ma, Shimin Yang, Chao Zou, Xiaozhou Yu
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0248996

Reduction of fibrosis and immune suppressive cells in ErbB2-dependent tumorigenesis by an LXR agonist
Cited by: 3
Author(s): Sheng Gao, Hongyan Yuan, Lü Jin, Suman Ranjit, Julia Panov, Xun Lu, Moshe Levi, Robert I. Glazer
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0205067

Hypoxia/reperfusion predisposes to atherosclerosis
Cited by: 6
Author(s): Richard Finsterwalder, Minu Karthika Ganesan, Heide Leb, Andreas Habertheuer, José Basílio, Irene M. Lang, Milica Krunic, Dominik Wiedemann, Peter Petzelbauer
Software Mentions: 1
Published: almost 7 years ago

10.1128/mSystems.00070-20

Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii
Cited by: 19
Author(s): Lauren E. Manck, Josh L. Espinoza, Christopher L. Dupont, Katherine A. Barbeau
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0189608

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium
Cited by: 4
Author(s): Robbie M. Martin, Stephen P. Dearth, Gary R. LeCleir, Shawn R. Campagna, Elizabeth Fozo, Erik R. Zinser, Steven W. Wilhelm
Software Mentions: 1
Published: over 7 years ago

10.1155/2017/4585213

MicroRNA Mediating Networks in Granulosa Cells Associated with Ovarian Follicular Development
Cited by: 9
Author(s): Bao-Yun Zhang, Long Chen, Guangde Feng, Xu Wei, Ke Zhang, Mingxing Chu, Pingqing Wang
Software Mentions: 1
Published: over 8 years ago

10.1093/femsec/fiy095

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage
Cited by: 25
Author(s): Ciara Keating, Dermot Hughes, Thérèse Mahony, Denise Cysneiros, Umer Zeeshan Ijaz, Colette Smith, Vincent O'Flaherty
Software Mentions: 1
Published: about 7 years ago

10.1186/s13578-021-00655-9

rpoS-mutation variants are selected in Pseudomonas aeruginosa biofilms under imipenem pressure
Cited by: 13
Author(s): Xiangke Duan, Yanrong Pan, Zhao Cai, Yumei Liu, Yingdan Zhang, Moxiao Liu, Yang Liu, Ke Wang, Lian-Hui Zhang, Liang Yang
Software Mentions: 1
Published: about 4 years ago

10.3389/fmicb.2020.00726

Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis
Cited by: 13
Author(s): Victor Jayeola, Michael McClelland, Steffen Porwollik, Chu Wu, Jeffrey M. Farber, Sophia Kathariou
Software Mentions: 1
Published: about 5 years ago

10.1155/2021/6681925

Identification of Critical Genes and lncRNAs in Osteolysis after Total Hip Arthroplasty and Osteoarthritis by RNA Sequencing
Cited by: 2
Author(s): Guang Yang, Kai Tang, Qiao Li, Yixin Li, Shui Sun
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.666277

Transcriptional Responses of Herbaspirillum seropedicae to Environmental Phosphate Concentration
Cited by: 3
Author(s): Mariana Grillo-Puertas, Josefina M. Villegas, Vânia C. S. Pankievicz, Michelle Z. Tadra-Sfeir, Francisco José Teles Mota, Elvira María Hébert, Liziane Cristina Campos Brusamarello-Santos, Raúl O. Pedraza, Fábio O. Pedrosa, Viviana Andrea Rapisarda, Emanuel Maltempi de Souza
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers13122873

A Novel Signature of CCNF-Associated E3 Ligases Collaborate and Counter Each Other in Breast Cancer
Cited by: 15
Author(s): Shu Chun Chang, Chin Sheng Hung, Bo Xiang Zhang, Tsung Han Hsieh, Wei‐Hsiu Hsu, Jeak Ling Ding
Software Mentions: 1
Published: about 4 years ago

10.1155/2021/8890176

Transcriptomic Analyses Reveal Gene Expression Profiles and Networks in Nasopharyngeal Carcinoma
Cited by: 3
Author(s): Yuwen Zhou, Weiqiang Yang, Xueshuang Mei, Hongyi Hu
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2020.00310

A Primer for Microbiome Time-Series Analysis
Cited by: 39
Author(s): Ashley R. Coenen, Sarah K. Hu, Elaine Luo, Daniel Muratore, Joshua S. Weitz
Software Mentions: 1
Published: over 5 years ago

10.1186/s13578-021-00536-1

Neuregulin 1/ErbB4 signaling contributes to the anti-epileptic effects of the ketogenic diet
Cited by: 6
Author(s): Jin Wang, Jie Huang, Yuanquan Li, Shan Yao, Chunqing Wu, Ying Wáng, Feng Gao, Min-Dong Xu, Guobin Huang, Changqin Zhao, Jiahui Wu, Yun-Long Zhang, Renjie Jiao, Zihao Deng, Wei Jie, Huibin Li, Aiguo Xuan, Xiangdong Sun
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers11020164

MEK Inhibition Induces Canonical WNT Signaling through YAP in KRAS Mutated HCT-15 Cells, and a Cancer Preventive FOXO3/FOXM1 Ratio in Combination with TNKS Inhibition
Cited by: 9
Author(s): Nina Solberg, Maria Melheim, Martin Frank Strand, Petter Angell Olsen, Stefan Krauß
Software Mentions: 1
Published: over 6 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583