bioconductor: EnhancedVolcano | Projects

10.15252/msb.20199247

<scp>STAT</scp> 3 ‐dependent analysis reveals <scp>PDK</scp> 4 as independent predictor of recurrence in prostate cancer
Cited by: 34
Author(s): Monika Oberhuber, Matteo Pecoraro, Mate Rusz, Georg Oberhuber, Maritta Wieselberg, Peter Haslinger, Elisabeth Gurnhofer, Michaela Schlederer, Tanja Limberger, Sabine Lagger, Jan Pěnčík, Petra Kodajova, Sandra Högler, Georg Stockmaier, Sandra Grund-Gröschke, Fritz Aberger, Marco Bolis, Jean-Philippe Theurillat, Robert Wiebringhaus, Theresa R. Weiss, Andrea Haitel, Marc Brehme, Wolfgang Wadsak, Johannes Griss, Thomas Mohr, Alexandra Hofer, Anton Jäger, Jürgen Pollheimer, Gerda Egger, Gunda Koellensperger, Matthias Mann, Brigitte Hantusch, Lukas Kenner
Software Mentions: 21
Published: over 4 years ago

10.1084/jem.20201795

Diagnostic blood RNA profiles for human acute spinal cord injury
Cited by: 21
Author(s): Nikos Kyritsis, Abel Torres-Espín, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong Fernandez, Libby Thomas, Rachel Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M DiGiorgio, Philip Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 19
Published: almost 4 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.3389/fcell.2020.592490

Transcriptome Sequencing Reveals Potential Roles of ICOS in Primary Sjögren’s Syndrome
Cited by: 19
Author(s): Jing Luo, Xin Liao, Lihe Zhang, Xin Xu, Senhong Ying, Mengjiao Yu, Lixia Zhu, Suxian Lin, Xiaobing Wang
Software Mentions: 14
Published: almost 4 years ago

10.3390/ijms22073681

Circulating miRNAs as Biomarkers for Mitochondrial Neuro-Gastrointestinal Encephalomyopathy
Cited by: 4
Author(s): Mark Mencias, Michelle Levene, Kevin Blighe, Bridget E. Bax
Software Mentions: 14
Published: over 3 years ago

10.3390/cancers13081788

Analysis of Intra-Tumoral Macrophages and T Cells in Non-Small Cell Lung Cancer (NSCLC) Indicates a Role for Immune Checkpoint and CD200-CD200R Interactions
Cited by: 7
Author(s): Anders Tøndell, Yashwanth Subbannayya, Sissel Gyrid Freim Wahl, Arnar Flatberg, Sveinung Sørhaug, Magne Børset, Markus Haug
Software Mentions: 12
Published: over 3 years ago

10.7554/eLife.66738

Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave
Cited by: 15
Author(s): Lindsay A. Hohsfield, Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Joshua Crapser, Dario X. Figueroa Velez, Shan Jiang, Sarah E Royer, Sung Jin Kim, Caden M Henningfield, Aileen J. Anderson, Sunil Gandhi, A Mortazavi, Matthew A. Inlay, Kim N. Green
Software Mentions: 12
Published: over 3 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-020-03549-8

BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Cited by: 12
Author(s): Pirunthan Perampalam, Frederick A. Dick
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.62250

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells
Cited by: 11
Author(s): Helen M Tauc, Imilce A. Rodriguez‐Fernandez, Jason A. Hackney, Michał Pawlak, Tal Oron, Jerome Korzelius, Hagar F. Moussa, Subhra Chaudhuri, Zora Modrušan, Bruce A Edgar, Heinrich Jasper
Software Mentions: 10
Published: over 3 years ago

10.1126/sciadv.abc8492

Persistent epigenetic reprogramming of sweet taste by diet
Cited by: 29
Author(s): Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, Monica Dus
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pone.0249148

Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans
Cited by: 5
Author(s): Nicholas A. Kinney, Lin Kang, Harpal Bains, Elizabeth Lawson, Mesam Husain, Kumayl Husain, Inderjit Sandhu, Yongdeok Shin, Javan K. Carter, Ramu Anandakrishnan, Pawel Michalak, Harold R. Garner
Software Mentions: 8
Published: over 3 years ago

10.1007/s13365-020-00931-3

Transcriptional signatures of Zika virus infection in astrocytes
Cited by: 3
Author(s): Blake Schouest, Tiffany A. Peterson, Dawn Szeltner, Elizabeth A. Scheef, Melody Baddoo, Nathan Ungerleider, Erik K. Flemington, Andrew G. MacLean, Nicholas J. Maness
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12974-020-01931-0

Effects of long-term and brain-wide colonization of peripheral bone marrow-derived myeloid cells in the CNS
Cited by: 28
Author(s): Lindsay A. Hohsfield, Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Edna E. Hingco, Sung Jin Kim, Ayer Darling Jue, Vivek Swarup, Mathew A. Inlay, Kim N. Green
Software Mentions: 8
Published: about 4 years ago

10.3390/ijms22073618

Transcriptome Analyses of Myometrium from Fibroid Patients Reveals Phenotypic Differences Compared to Non-Diseased Myometrium
Cited by: 9
Author(s): Emmanuel N. Paul, Gregory W. Burns, Tyler J. Carpenter, Joshua Grey, Asgerally T. Fazleabas, Jose M. Teixeira
Software Mentions: 8
Published: over 3 years ago

10.3389/fgene.2020.00396

Single-Cell Transcriptomic Analysis Reveals Mitochondrial Dynamics in Oocytes of Patients With Polycystic Ovary Syndrome
Cited by: 34
Author(s): Lingbin Qi, Boxuan Liu, Xian Chen, Qiwei Liu, Wanqiong Li, Bo Lv, Xiaoyu Xu, Lu Wang, Qiao Zeng, Jinfeng Xue, Zhigang Xue
Software Mentions: 7
Published: over 4 years ago

10.3389/fmolb.2020.565530

Cross-Sectional Transcriptional Analysis of the Aging Murine Heart
Cited by: 4
Author(s): Matthew Greenig, Andrew Melville, Derek Huntley, Mark Isalan, Michał Mielcarek
Software Mentions: 7
Published: about 4 years ago

10.3390/genes11101165

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
Cited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: about 4 years ago

10.3390/ijms21134727

Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies
Cited by: 16
Author(s): Maximilian Fuchs, Fabian Philipp Kreutzer, Lorenz A. Kapsner, Saskia Mitzka, Annette Just, Filippo Perbellini, Cesare M. Terracciano, Xiaoyan Ke, Robert Geffers, Christian Bogdan, Hans‐Ulrich Prokosch, Jan Fiedler, Thomas Thum, Meik Kunz
Software Mentions: 7
Published: over 4 years ago

10.1016/j.celrep.2020.107930

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Cited by: 17
Author(s): Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Paweł Masiewicz, Tanit Guitart, Bernd Simon, Jan Provazník, Frank Stein, Per Haberkant, Lara Sweetapple, Laura Villacorta, Dylan Mooijman, Vladimı́r Beneš, Mikhail M. Savitski, Fátima Gebauer, Janosch Hennig
Software Mentions: 7
Published: over 4 years ago

10.3390/cancers13092126

Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential
Cited by: 7
Author(s): Syuzo Kaneko, Toutai Mitsuyama, Kouya Shiraishi, Noriko Ikawa, Kanto Shozu, Ai Dozen, Hidenori Machino, Ken Asada, Masaaki Komatsu, Asako Kukita, Kenbun Sone, Hiroshi Yoshida, Noriko Motoi, Shinya Hayami, Yutaka Yoneoka, Tomoyasu Kato, Takashi Kohno, Toru Natsume, Gottfried von Keudell, Vassiliki Saloura, Hiroki Yamaue, Ryuji Hamamoto
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-81103-z

Cysteine: an overlooked energy and carbon source
Cited by: 19
Author(s): Luise Göbbels, Anja Poehlein, Albert Dumnitch, Richard Egelkamp, Cathrin Kröger, Johanna Haerdter, Thomas Hackl, Artur Feld, H. Weller, Rolf Daniel, Wolfgang R. Streit, Marie Charlotte Schoelmerich
Software Mentions: 6
Published: almost 4 years ago

10.3390/genes11060623

Computational Analysis of Transcriptomic and Proteomic Data for Deciphering Molecular Heterogeneity and Drug Responsiveness in Model Human Hepatocellular Carcinoma Cell Lines
Cited by: 3
Author(s): Panagiotis Agioutantis, Heleni Loutrari, Fragiskos N. Kolisis
Software Mentions: 6
Published: over 4 years ago

10.3389/fimmu.2021.676173

Interleukin-17A Causes Osteoarthritis-Like Transcriptional Changes in Human Osteoarthritis-Derived Chondrocytes and Synovial Fibroblasts In Vitro
Cited by: 20
Author(s): Jolet Y Mimpen, Mathew Baldwin, Adam P. Cribbs, Martin Philpott, Andrew Carr, Stephanie G. Dakin, Sarah Snelling
Software Mentions: 6
Published: over 3 years ago

10.1093/g3journal/jkaa043

Global translational landscape of the Candida albicans morphological transition
Cited by: 8
Author(s): Vasanthakrishna Mundodi, Saket Choudhary, Andrew D. Smith, David Kadosh
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms22115814

Genomic Characterization of Cisplatin Response Uncovers Priming of Cisplatin-Induced Genes in a Resistant Cell Line
Cited by: 7
Author(s): Hadar Golan Berman, Pooja Chauhan, Shira Shalev, Hiba Hassanain, Avital Parnas, Sheera Adar
Software Mentions: 6
Published: over 3 years ago

10.1017/S0031182021000111

Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella
Cited by: 5
Author(s): Arnar K. S. Sandholt, Feifei Xu, Robert Söderlund, Anna Lundén, Karin Troell, Staffan G. Svärd, Eva Wattrang
Software Mentions: 6
Published: almost 4 years ago

10.1128/mBio.01849-21

Hofbauer Cells Spread Listeria monocytogenes among Placental Cells and Undergo Pro-Inflammatory Reprogramming while Retaining Production of Tolerogenic Factors
Cited by: 7
Author(s): Siavash Azari, Lauren J. Johnson, Amy Webb, Sophia M Kozlowski, Xiaoli Zhang, Kara M. Rood, Amal O. Amer, Stéphanie Seveau
Software Mentions: 6
Published: about 3 years ago

10.3390/cancers13081817

USP22 Suppresses SPARC Expression in Acute Colitis and Inflammation-Associated Colorectal Cancer
Cited by: 8
Author(s): Robyn Laura Kosinsky, Dominik Saul, Christoph Ammer‐Herrmenau, William A. Faubion, Albrecht Neeße, Steven A. Johnsen
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-020-06987-z

Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit
Cited by: 6
Author(s): Franz J. Lichtner, Verneta L. Gaskins, Kerik D. Cox, Wayne M. Jurick
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-021-92439-x

The amniotic fluid cell-free transcriptome in spontaneous preterm labor
Cited by: 11
Author(s): Gaurav Bhatti, Roberto Romero, Nardhy Gómez-López, Roger Piqué-Regi, Percy Pacora, Eun-Jung Jung, Lami Yeo, Chaur‐Dong Hsu, Mahendra Kavdia, Adi L. Tarca
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-021-07443-2

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing
Cited by: 12
Author(s): Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutiérrez, Jorge Del‐Pozo, José M. Yáñez, Ross D. Houston
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-80240-1

Ethanol exposure drives colon location specific cell composition changes in a normal colon crypt 3D organoid model
Cited by: 11
Author(s): Matthew Devall, Sarah J. Plummer, Jennifer Bryant, Lucas T. Jennelle, Stephen Eaton, Christopher H. Dampier, Jeroen R. Huyghe, Ulrike Peters, Steven M. Powell, Graham Casey
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.ppat.1009304

Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Cited by: 39
Author(s): Anna Both, Jia-Bin Huang, Minyue Qi, Christian Lausmann, Samira Weißelberg, Henning Büttner, Susanne Lezius, Antonio Virgilio Failla, Coralie Martin, Marc Stegger, Thorsten Gehrke, Sharmin Baig, Mustafa Citak, Malik Alawi, Martin Aepfelbacher, Holger Rohde
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.immuni.2020.03.011

Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants
Cited by: 47
Author(s): Lucy H. Jackson-Jones, Peter Smith, Jordan Raymond Portman, Marlene S Magalhaes, Katie J. Mylonas, Matthieu Vermeren, Mark Nixon, Beth E. P. Henderson, Ross Dobie, Sonja Vermeren, Laura Denby, Neil C. Henderson, Damian J. Mole, C Benezech
Software Mentions: 6
Published: over 4 years ago

10.3390/genes12040549

Clinical Identification of Dysregulated Circulating microRNAs and Their Implication in Drug Response in Triple Negative Breast Cancer (TNBC) by Target Gene Network and Meta-Analysis
Cited by: 15
Author(s): Amal Qattan, Taher Al‐Tweigeri, Wafa Alkhayal, Kausar Suleman, Asma Tulbah, Suad Bin Amer
Software Mentions: 6
Published: over 3 years ago

10.3390/genes11121487

RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
Cited by: 13
Author(s): Marie Lataretu, Martin Hölzer
Software Mentions: 6
Published: almost 4 years ago

10.3389/fimmu.2020.00715

Hepatic Transcriptome Analysis Identifies Divergent Pathogen-Specific Targeting-Strategies to Modulate the Innate Immune System in Response to Intramammary Infection
Cited by: 15
Author(s): A. Heimes, J. Brodhagen, Rosemarie Weikard, Hans‐Martin Seyfert, Doreen Becker, M. Meyerholz, Wolfram Petzl, Holm Zerbe, Martina Hoedemaker, L. Rohmeier, Hans‐Joachim Schuberth, Marion Schmicke, Susanne Engelmann, Christa Kühn
Software Mentions: 6
Published: over 4 years ago

10.3390/biology10060502

Characterization of Tumor-Associated Macrophages and the Immune Microenvironment in Limited-Stage Neuroendocrine-High and -Low Small Cell Lung Cancer
Cited by: 22
Author(s): Dávid Dóra, Christopher J. Rivard, Hui Yu, Shivaun Lueke Pickard, Viktória László, Tünde Harkó, Zsolt Megyesfalvi, Elek Dinya, Csongor Gerdán, Gábor Szegvári, Fred R. Hirsch, Balázs Döme, Zoltán Lohinai
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-020-07002-1

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking
Cited by: 13
Author(s): Clemens Falker‐Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, W. Bessei, Jörn Bennewitz, Jens Tetens
Software Mentions: 5
Published: about 4 years ago

10.1186/s12916-020-01806-4

ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis
Cited by: 7
Author(s): Sara Charmsaz, Ben Doherty, Sinéad Cocchiglia, Damir Varešlija, Attilio Marino, Nicola Cosgrove, Ricardo Marques, Nolan Priedigkeit, Siobhan Purcell, Fiona T. Bane, Jarlath Bolger, Christopher Byrne, Philip J. O’Halloran, Francesca Brett, Katherine M. Sheehan, Kieran Brennan, Ann M. Hopkins, Stephen Keelan, Petra Jagušt, Stephen F. Madden, Chiara Martinelli, Matteo Battaglini, Steffi Oesterreich, Adrian V. Lee, Gianni Ciofani, Arnold D. Hill, Leonie S. Young
Software Mentions: 5
Published: about 4 years ago

10.3390/jof7070562

mRNA Inventory of Extracellular Vesicles from Ustilago maydis
Cited by: 21
Author(s): Seomun Kwon, Oliver Rupp, Andreas Brachmann, Christopher Blum, Anton Kraege, Alexander Goesmann, Michael Feldbrügge
Software Mentions: 5
Published: over 3 years ago

10.3390/ani11092606

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens
Cited by: 2
Author(s): Panpradub Sinpru, Cindy Riou, Shin Kubota, Chotima Poompramun, Wittawat Molee, Amonrat Molee
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.68603

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair
Cited by: 49
Author(s): Shintaro Ide, Yoshihiko Kobayashi, Kana Ide, Sarah A. Strausser, Koki Abe, Savannah Herbek, Lori L. O’Brien, Steven D. Crowley, Laura Barisoni, Aleksandra Tata, Purushothama Rao Tata, Tomokazu Souma
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.ppat.1009441

Viral infection of human neurons triggers strain-specific differences in host neuronal and viral transcriptomes
Cited by: 8
Author(s): Colleen A. Mangold, Molly M. Rathbun, Daniel W. Renner, Chad V. Kuny, Moriah L. Szpara
Software Mentions: 5
Published: over 3 years ago

10.3389/fnmol.2021.712609

NMDARs Drive the Expression of Neuropsychiatric Disorder Risk Genes Within GABAergic Interneuron Subtypes in the Juvenile Brain
Cited by: 7
Author(s): Vivek Mahadevan, Apratim Mitra, Yajun Zhang, Xitong Yuan, Areg Peltekian, Ramesh Chittajallu, Caroline Esnault, Dragan Maric, C. T. Rhodes, Kenneth A. Pelkey, Ryan Dale, Timothy J. Petros, Chris J. McBain
Software Mentions: 5
Published: about 3 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: about 3 years ago

10.1128/mBio.02500-19

A Conserved Streptococcal Virulence Regulator Controls the Expression of a Distinct Class of M-Like Proteins
Cited by: 7
Author(s): Jonathan D. D’Gama, Zhe Ma, Hailong Zhang, Li Xu, Hongjie Fan, Ellen Ruth A. Morris, Noah D. Cohen, Colette Cywes‐Bentley, Gerald B. Pier, Matthew K. Waldor
Software Mentions: 5
Published: about 5 years ago

10.1016/j.tranon.2021.101107

3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Xinyuan Liu, Beate Gündel, Xidan Li, Jianping Liu, Andrew N. Wright, Matthias Löhr, Gustav Arvidsson, Rainer Heuchel
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-93845-x

Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
Cited by: 12
Author(s): Priyanka Banerjee, Premanand Balraj, Nilesh Sudhakar Ambhore, S.A. Wicher, Rodney D. Britt, Christina M. Pabelick, Y. S. Prakash, Venkatachalem Sathish
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2020.02129

Transcriptome Profiling of Human Monocyte-Derived Macrophages Upon CCL2 Neutralization Reveals an Association Between Activation of Innate Immune Pathways and Restriction of HIV-1 Gene Expression
Cited by: 7
Author(s): Daniela Angela Covino, Karolina Elżbieta Kaczor‐Urbanowicz, Jing Lü, Maria Vincenza Chiantore, Gianna Fiorucci, Maria Fenicia Vescio, Laura Catapano, Cristina Purificato, Clementina Maria Galluzzo, Roberta Amici, Mauro Andreotti, Maria Cristina Gauzzi, Matteo Pellegrini, Laura Fantuzzi
Software Mentions: 5
Published: about 4 years ago

10.3390/cancers13092000

Lipidomics as a Diagnostic Tool for Prostate Cancer
Cited by: 21
Author(s): Magdalena Buszewska-Forajta, Paweł Pomastowski, Fernanda Monedeiro, Justyna Walczak-Skierska, Marcin Markuszewski, Marcin Matuszewski, Michał J. Markuszewski
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pbio.3000710

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice
Cited by: 18
Author(s): Virlana M. Shchuka, Luis E. Abatti, Huayun Hou, Nawrah Khader, Anna Dorogin, Michael D. Wilson, Oksana Shynlova, Jennifer A. Mitchell
Software Mentions: 5
Published: over 4 years ago

10.3390/genes11040415

Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep
Cited by: 14
Author(s): Kisun Pokharel, Jaana Peippo, Melak Weldenegodguad, Mervi Honkatukia, Menghua Li, Juha Kantanen
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-82067-w

Calcium calmodulin kinase II activity is required for cartilage homeostasis in osteoarthritis
Cited by: 11
Author(s): Giovanna Nalesso, Anne‐Sophie Thorup, S. Eldridge, Armando M. De Palma, Amanpreet Kaur, Kiran Peddireddi, Kevin Blighe, Sharmila Rana, B. Stott, Tonia L. Vincent, B.L. Thomas, Jessica Bertrand, J. Sherwood, Antonella Fioravanti, Costantino Pitzalis, Francesco Dell’Accio
Software Mentions: 5
Published: over 3 years ago

10.3390/pathogens9120997

A Paradox in Bacterial Pathogenesis: Activation of the Local Macrophage Inflammasome Is Required for Virulence of Streptococcus uberis
Cited by: 10
Author(s): Nathan Archer, Sharon A. Egan, Tracey J. Coffey, Richard D. Emes, Maria Filippa Addis, Philip N. Ward, Adam Blanchard, James A. Leigh
Software Mentions: 5
Published: almost 4 years ago

10.3389/fimmu.2021.701273

Immune Signature Linked to COVID-19 Severity: A SARS-Score for Personalized Medicine
Cited by: 5
Author(s): Jules Russick, Pierre-Emmanuel Foy, Nathalie Josseaume, Maxime Meylan, Nadine Benhamouda, Amos Kirilovsky, Carine El Sissy, Éric Tartour, David Smadja, Alexandre Karras, Jean‐Sébastien Hulot, Marine Livrozet, Antoine Fayol, Jean‐Benoît Arlet, Jean‐Luc Diehl, Marie-Agnès Dragon-Durey, Franck Pagès, Isabelle Cremer
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1009734

Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans
Cited by: 10
Author(s): Delaney C Pagliuso, Devavrat M Bodas, Amy E. Pasquinelli
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers13184518

The Tumor Microenvironment-Dependent Transcription Factors AHR and HIF-1α Are Dispensable for Leukemogenesis in the Eµ-TCL1 Mouse Model of Chronic Lymphocytic Leukemia
Cited by: 3
Author(s): Susanne Gonder, Anne Largeot, Ernesto Gargiulo, Sandrine Pierson, Iria Fernandez Botana, Giulia Pagano, Jérôme Paggetti, Etienne Moussay
Software Mentions: 4
Published: about 3 years ago

10.3390/cancers13030527

Radiosensitizing Pancreatic Cancer with PARP Inhibitor and Gemcitabine: An In Vivo and a Whole-Transcriptome Analysis after Proton or Photon Irradiation
Cited by: 7
Author(s): Waisse Waissi, Anaïs Nicol, Matthieu Jung, M. Rousseau, D. Jarnet, Georges Noël, Hélène Burckel
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.stem.2020.08.004

Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development
Cited by: 43
Author(s): Edie I. Crosse, Sabrina Gordon-Keylock, Stanislav Rybtsov, Anahí Binagui-Casas, Hannah Felchle, Nneka C. Nnadi, Kristina Kirschner, Tamir Chandra, Sara Tamagno, David J. Webb, Fiona Rossi, Richard A. Anderson, Alexander Medvinsky
Software Mentions: 4
Published: about 4 years ago

10.3390/cells10051008

Transcriptome Analysis of Hypoxic Lymphatic Endothelial Cells Indicates Their Potential to Contribute to Extracellular Matrix Rearrangement
Cited by: 18
Author(s): Jürgen Becker, Sonja Schwoch, Christina Zelent, Maren Sitte, Gabriela Salinas, Jörg Wilting
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.700489

Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds
Cited by: 4
Author(s): Sofia Michailidou, Athanasios Ι. Gelasakis, Georgios Banos, G. Arsenos, Anagnostis Argiriou
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.630988

Transcriptomic Profiling of Fibropapillomatosis in Green Sea Turtles (Chelonia mydas) From South Texas
Cited by: 9
Author(s): Nicholas B. Blackburn, Ana C Leandro, Nina Nahvi, Mariana A. Devlin, Marcelo Leandro, Ignacio Martinez Escobedo, Juan M. Peralta, Jeff George, Brian A. Stacy, Thomas W. deMaar, John Blangero, Megan Keniry, Joanne E. Curran
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.691725

Severe COVID-19 Recovery Is Associated with Timely Acquisition of a Myeloid Cell Immune-Regulatory Phenotype
Cited by: 29
Author(s): A.C. Trombetta, Guilherme B. Farias, André M. C. Gomes, Ana Godinho‐Santos, Pedro Rosmaninho, Carolina M. Conceição, Joel Laia, Diana Santos, Afonso R. M. Almeida, Catarina Mota, Andréia Gomes, María Luisa Madueño Serrano, Marc Veldhoen, Ana E. Sousa, S. Fernandes
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.676980

Integrative Multi-Omics Reveals Serum Markers of Tuberculosis in Advanced HIV
Cited by: 9
Author(s): Sonya Krishnan, Artur T. L. Queiroz, Amita Gupta, Nikhil Gupte, Gregory P. Bisson, Johnstone Kumwenda, Kogieleum Naidoo, Lerato Mohapi, Vidya Mave, Rosie Mngqibisa, Javier R. Lama, Mina C. Hosseinipour, Bruno B. Andrade, Petros C. Karakousis
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2021.643137

Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs
Cited by: 4
Author(s): А. В. Щенникова, Alexey V. Beletsky, M. A. Filyushin, М. А. Слугина, Eugeny V. Gruzdev, Andrey V. Mardanov, Е. З. Кочиева, Н. В. Равин
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-78983-y

Local injections of β-NGF accelerates endochondral fracture repair by promoting cartilage to bone conversion
Cited by: 13
Author(s): Kevin O. Rivera, Fabrizio Russo, Ryan M. Boileau, Ryan E. Tomlinson, Theodore Miclau, Ralph Marcucio, Tejal A. Desai, Chelsea S. Bahney
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.stemcr.2020.06.003

Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome
Cited by: 118
Author(s): Jessica Cinkornpumin, Sin Young Kwon, Yixin Guo, Ishtiaque Hossain, Jacinthe Sirois, Colleen S. Russett, Hsin Wei Tseng, Hiroaki Okae, Takahiro Arima, Thomas F. Duchaîne, Wanlu Liu, William A. Pastor
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2020.01775

Cultivation of Clear Cell Renal Cell Carcinoma Patient-Derived Organoids in an Air-Liquid Interface System as a Tool for Studying Individualized Therapy
Cited by: 23
Author(s): Laura Kristin Esser, Vittorio Branchi, Sonia Leonardelli, Natalie Pelusi, Adolfo Simón, Niklas Klümper, Jörg Ellinger, Stefan Hauser, Maria A. Gonzalez‐Carmona, Manuel Ritter, Glen Kristiansen, Hubert Schorle, Michael Hölzel, Marieta Toma
Software Mentions: 3
Published: about 4 years ago

10.3389/fonc.2021.693353

Identification of Key Genes Related to CD8+ T-Cell Infiltration as Prognostic Biomarkers for Lung Adenocarcinoma
Cited by: 6
Author(s): Minjun Du, Yicheng Liang, Zixu Liu, Xingkai Li, Mei Liang, Boxuan Zhou, Yushun Gao
Software Mentions: 3
Published: about 3 years ago

10.3390/biology10040266

PER2 Circadian Oscillation Sensitizes Esophageal Cancer Cells to Chemotherapy
Cited by: 6
Author(s): Juan Alfonso Redondo, Romain Bibes, Alizée Vercauteren Drubbel, Benjamin Dassy, Xavier Bisteau, Eléonore Maury, Benjamin Beck
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.01624

Activation of the DR3-TL1A Axis in Donor Mice Leads to Regulatory T Cell Expansion and Activation With Reduction in Graft-Versus-Host Disease
Cited by: 13
Author(s): Melissa Mavers, Federico Simonetta, Hidekazu Nishikii, Jessica V. Ribado, Kristina Maas‐Bauer, Maite Álvarez, Toshihito Hirai, Mustafa Turkoz, Jeanette Baker, Robert S. Negrin
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2020.607175

Mobilized Multipotent Hematopoietic Progenitors Stabilize and Expand Regulatory T Cells to Protect Against Autoimmune Encephalomyelitis
Cited by: 3
Author(s): Sarantis Korniotis, Maud d’Aveni, Sébastien Hergalant, Hélène Letscher, Emmanuel Tejerina, Pauline Gastineau, Viviane A Agbogan, Christophe Gras, Guillemette Fouquet, Julien Rossignol, Jean-Claude Chèvre, Nicolas Cagnard, Marie‐Thérèse Rubio, Olivier Hermine, Flora Zavala
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2020.00850

Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts
Cited by: 5
Author(s): Waritta Sawaengdee, Kairong Cui, Keji Zhao, Suradej Hongeng, Suthat Fucharoen, Patompon Wongtrakoongate
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.661243

Ligand–Receptor Interactions Elucidate Sex-Specific Pathways in the Trajectory From Primordial Germ Cells to Gonia During Human Development
Cited by: 11
Author(s): Arend W. Overeem, Yolanda W. Chang, Jeroen Spruit, Celine M. Roelse, Susana M. Chuva de Sousa Lopes
Software Mentions: 3
Published: over 3 years ago

10.3389/fcell.2020.00461

Expression of ncRNAs on the DLK1-DIO3 Locus Is Associated With Basal and Mesenchymal Phenotype in Breast Epithelial Progenitor Cells
Cited by: 13
Author(s): Zuzana Budková, Anna Karen Sigurdardottir, Eiríkur Briem, Jón Þór Bergþórsson, Snaevar Sigurðsson, Magnús K. Magnússon, Gunnhildur Ásta Traustadóttir, Thorarinn Gudjonsson, Bylgja Hilmarsdóttir
Software Mentions: 3
Published: over 4 years ago

10.1096/fj.201902664

The TGF‐b/SOX4 axis and ROS‐driven autophagy co‐mediate CD39 expression in regulatory T‐cells
Cited by: 24
Author(s): Marlene C. Gerner, Liesa S. Ziegler, Ralf Schmidt, Martin Krenn, Fritz Zimprich, Keziban Uyanik‐Ünal, Vassiliki Konstantopoulou, Sophia Derdak, Giorgia Del Favero, Ilse Schwarzinger, Kaan Boztuğ, Klaus G. Schmetterer
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-64761-3

Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing
Cited by: 31
Author(s): Nihal Bandara, David Wood, Inka Vanwonterghem, Philip Hugenholtz, Bmy Cheung, LP Samaranayake
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-73747-0

A role for the immune system in advanced laryngeal cancer
Cited by: 9
Author(s): Marta Tagliabue, Fausto Maffini, Caterina Fumagalli, Sara Gandini, Daniela Lepanto, Federica Corso, Salvatore Cacciola, Alberto Ranghiero, Alessandra Rappa, Davide Vacirca, Maria Cossu Rocca, Daniela Alterio, Elena Guerini-Rocco, Augusto Cattaneo, Francesco Chu, Stefano Zorzi, Giuseppe Curigliano, Susanna Chiocca, Massimo Barberis, Giuseppe Viale, Mohssen Ansarin
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-78669-5

Long non-coding RNA levels can be modulated by 5-azacytidine in Schistosoma mansoni
Cited by: 10
Author(s): Murilo Sena Amaral, Lucas F. Maciel, Gilbert O. Silveira, Giovanna G. O. Olberg, João V. P. Leite, Lucas K. Imamura, Adriana S. A. Pereira, Patrícia A. Miyasato, Eliana Nakano, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-021-07540-2

Functional genomics of a Spiroplasma associated with the carmine cochineals Dactylopius coccus and Dactylopius opuntiae
Cited by: 7
Author(s): Arturo Vera‐Ponce de León, Marian Dominguez-Mirazo, Rafael Bustamante-Brito, Victor M. Higareda‐Alvear, Mónica Rosenblueth, Esperanza Martı́nez-Romero
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-02562-8

Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma
Cited by: 13
Author(s): Alexander Bondoc, Kathryn Glaser, Kang Jin, Charissa Lake, Stefano Cairo, James I. Geller, Gregory M. Tiao, Bruce J. Aronow
Software Mentions: 3
Published: about 3 years ago

10.3390/cancers13020189

The Caspase-1/IL-18 Axis of the Inflammasome in Tumor Cells: A Modulator of the Th1/Tc1 Response of Tumor-Infiltrating T Lymphocytes in Colorectal Cancer
Cited by: 8
Author(s): Linda Bilonda Mutala, Cécile Deleine, Matilde Karakachoff, Delphine Dansette, Kathleen Ducoin, Romain Oger, Olivia Rousseau, J. Podevin, Emilie Duchalais, P Fourquier, Wassila El Alami Thomas, Pierre‐Antoine Gourraud, Jaafar Bennouna, Camille Brochier, Nadine Gervois, Céline Bossard, Anne Jarry
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers13051170

ANO1 Expression Orchestrates p27Kip1/MCL1-Mediated Signaling in Head and Neck Squamous Cell Carcinoma
Cited by: 7
Author(s): Artemis Filippou, Henna Pehkonen, Piia-Riitta Karhemo, Juho Väänänen, Anni I. Nieminen, Juha Klefström, Reidar Grénman, Antti Mäkitie, Heikki Joensuu, Outi Monni
Software Mentions: 3
Published: over 3 years ago

10.1128/JVI.01010-21

Kinetic Multi-omic Analysis of Responses to SARS-CoV-2 Infection in a Model of Severe COVID-19
Cited by: 19
Author(s): Angelene M. Cantwell, Harinder Singh, Maryann P. Platt, Yonghao Yu, Yi‐Han Lin, Yuji Ikeno, Gene B. Hubbard, Yan Xiang, Norberto González-Juarbe, Peter H. Dube
Software Mentions: 3
Published: about 3 years ago

10.7150/thno.46642

Precise and efficient silencing of mutant KrasG12D by CRISPR-CasRx controls pancreatic cancer progression
Cited by: 26
Author(s): Wang Jiang, Hao Li, Xiyu Liu, Jianping Zhang, Wuhu Zhang, Tianjiao Li, Liang Liu, Xianjun Yu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0233980

iPSCs from people with MS can differentiate into oligodendrocytes in a homeostatic but not an inflammatory milieu
Cited by: 24
Author(s): Itzy E. Morales Pantoja, Matthew D. Smith, Labchan Rajbhandari, Linzhao Cheng, Yongxing Gao, Vasiliki Mahairaki, Arun Venkatesan, Peter A. Calabresi, Kathryn C. Fitzgerald, Katharine A. Whartenby
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9030656

Cranberry Proanthocyanidins and Dietary Oligosaccharides Synergistically Modulate Lactobacillus plantarum Physiology
Cited by: 7
Author(s): Ezgi Özcan, Michelle R Rozycki, David A. Sela
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8071068

In vitro Edwardsiella piscicida CK108 Transcriptome Profiles with Subinhibitory Concentrations of Phenol and Formalin Reveal New Insights into Bacterial Pathogenesis Mechanisms
Cited by: 8
Author(s): Ju Bin Yoon, Sungmin Hwang, Se-Won Baek, Seung-Ki Lee, Woo Young Bang, Ki Hwan Moon
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-021-01137-3

Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis
Cited by: 44
Author(s): Sage E. Foley, Christine Tuohy, Merran Dunford, Michael J. Grey, Heidi De Luca, Caitlin Cawley, Rose L. Szabady, Ana Maldonado‐Contreras, Jean Marie Houghton, Doyle V. Ward, Randall J. Mrsny, Beth A. McCormick
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms20030641

Placental CX3CL1 is Deregulated by Angiotensin II and Contributes to a Pro-Inflammatory Trophoblast-Monocyte Interaction
Cited by: 18
Author(s): Olivia Nonn, Jacqueline Guettler, Désirée Forstner, Sabine Maninger, Julianna Zadora, András Balogh, Alina Frolova, Andreas Glasner, Florian Herse, Martin Gauster
Software Mentions: 3
Published: almost 6 years ago

10.3390/metabo11080525

Metabolomic Profiling of Adults with Congenital Heart Disease
Cited by: 8
Author(s): Ari Cedars, Cedric Manlhiot, Jong Mi Ko, Teodoro Bottiglieri, Erland Arning, Angela Weingarten, Alexander R. Opotowsky, Shelby Kutty
Software Mentions: 3
Published: over 3 years ago

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22179432

Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts
Cited by: 0
Author(s): Laurent Winckers, Chris T. Evelo, Egon Willighagen, Martina Kutmon
Software Mentions: 3
Published: about 3 years ago

10.3389/fnmol.2021.718241

Single-Cell RNA-Seq of Cisplatin-Treated Adult Stria Vascularis Identifies Cell Type-Specific Regulatory Networks and Novel Therapeutic Gene Targets
Cited by: 13
Author(s): Ian Taukulis, Rafal T. Olszewski, Soumya Korrapati, Katharine A. Fernandez, Erich T. Boger, Tracy S. Fitzgerald, Robert J. Morell, Lisa L. Cunningham, Michael Hoa
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22147537

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula
Cited by: 4
Author(s): Yuanyuan Zhao, Junchao Zhang, Zhanmin Sun, Yixiong Tang, Yihan Wu
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-88924-y

Metastasis is altered through multiple processes regulated by the E2F1 transcription factor
Cited by: 3
Author(s): Matthew Swiatnicki, Eran R. Andrechek
Software Mentions: 2
Published: over 3 years ago

10.1186/s40168-020-00932-8

Microbial function and genital inflammation in young South African women at high risk of HIV infection
Cited by: 20
Author(s): Arghavan Alisoltani, Monalisa T. Manhanzva, Matthys Potgieter, Christina Balle, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Morné Du Plessis, Nina Radzey, Zac McDonald, Bridget Calder, Imane Allali, Nicola Mulder, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien, Adam Godzik, Jonathan M. Blackburn, David L. Tabb, Linda‐Gail Bekker, Heather B. Jaspan, Jo‐Ann S. Passmore, Lindi Masson
Software Mentions: 2
Published: about 4 years ago

10.3389/fmed.2020.568096

Circulating miRNAs Associated With ER Stress and Organ Damage in a Preclinical Model of Trauma Hemorrhagic Shock
Cited by: 6
Author(s): Ana Teresa Luís, Matthias Hackl, Mohammad Jafarmadar, Claudia Keibl, Julia M. Jilge, Johannes Grillari, Soheyl Bahrami, Andrey V. Kozlov
Software Mentions: 2
Published: about 4 years ago

Projects: bioconductor: EnhancedVolcano

Papers Mentioning EnhancedVolcano 123