bioconductor: biomaRt | Projects | Ecosyste.ms: Papers

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: almost 11 years ago

10.1186/s13148-018-0510-3

Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception
Cited by: 25
Author(s): Davide Gentilini, Edgardo Somigliana, Luca Pagliardini, Elisa Rabellotti, Paolo Garagnani, Luisa Bernardinelli, Enrico Papaleo, Massimo Candiani, Anna Maria Di Blasio, Paola Viganò
Software Mentions: 7
Published: over 6 years ago

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: about 3 years ago

10.1186/gm509

Comparison of methods to identify aberrant expression patterns in individual patients: augmenting our toolkit for precision medicine
Cited by: 5
Author(s): Daniel Bottomly, Peter Ryabinin, Jeffrey W. Tyner, Bill H. Chang, Marc Loriaux, Brian J. Druker, Shannon K. McWeeney, Beth Wilmot
Software Mentions: 6
Published: almost 12 years ago

10.3390/jpm10040210

Association of UBE3C Variants with Reduced Kidney Function in Patients with Diabetic Kidney Disease
Cited by: 3
Author(s): Ying Chun Chen, Mei Yi Wu, Zhi Yu, Wan Hsuan Chou, Yi Ting Lai, Chih-Chin Kao, Imaniar Noor Faridah, Mai Szu Wu, Wei Chiao Chang
Software Mentions: 6
Published: about 4 years ago

10.1523/JNEUROSCI.1675-19.2019

Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1008749

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
Cited by: 29
Author(s): Heini M. Natri, Katalina Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, Georgi Hudjashov, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero
Software Mentions: 6
Published: over 4 years ago

10.1111/acel.13381

Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity
Cited by: 7
Author(s): Rebecca L. McIntyre, Simone Denis, Rashmi Kamble, Marte Molenaars, Michael Petr, Bauke V. Schomakers, Mizanur Rahman, Siddhartha Datta Gupta, Márton L. Tóth, Siva A. Vanapalli, Aldo Jongejan, Morten Scheibye‐Knudsen, Riekelt H. Houtkooper, Georges E. Janssens
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007162

Cross-species functional modules link proteostasis to human normal aging
Cited by: 10
Author(s): Andrea Komljenović, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson‐Rechavi
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-019-0644-8

Clinical utility of custom-designed NGS panel testing in pediatric tumors
Cited by: 77
Author(s): Lea F. Surrey, Suzanne P. MacFarland, Fengqi Chang, Ke Cao, Komal S. Rathi, Gozde Akgumus, Daniel Gallo, Fumin Lin, Adam Gleason, Pichai Raman, Richard Aplenc, Rochelle Bagatell, Jane E. Minturn, Yaël P. Mossé, Mariarita Santi, Sarah K. Tasian, Angela J. Waanders, Mahdi Sarmady, John M. Maris, Stephen P. Hunger, Marilyn M. Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s12915-018-0615-3

Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways
Cited by: 79
Author(s): Ziyun Wu, Megan M. Senchuk, Dylan J. Dues, Benjamin K. Johnson, Jason Cooper, Leira Lew, Emily Machiela, Claire E. Schaar, Heather DeJonge, T. Keith Blackwell, Jeremy M. Van Raamsdonk
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pbio.2006687

Quantitative assessment of cell population diversity in single-cell landscapes
Cited by: 40
Author(s): Qi Liu, Charles A. Herring, Quanhu Sheng, Jie Ping, Alan J. Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J. Coffey, Yu Shyr, Ken S. Lau
Software Mentions: 6
Published: about 6 years ago

10.1093/dnares/dsz015

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model
Cited by: 8
Author(s): Antônio Pedro Camargo, Thiago S. Nakahara, Luiz E R Firmino, Paulo H.M. Netto, João Batista Plácido do Nascimento, Elisa Donnard, Pedro A. F. Galante, Marcelo Falsarella Carazzolle, Bettina Malnic, Fábio Papes
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.8192

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Cited by: 21
Author(s): Gökhan Karakülah, Nazmiye Arslan, Cihangir Yandım, Aslı Süner
Software Mentions: 6
Published: almost 5 years ago

10.1002/1878-0261.12161

Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis
Cited by: 19
Author(s): Martín Del Castillo Velasco-Herrera, Louise van der Weyden, Jérémie Nsengimana, Anneliese O. Speak, Marcela Sjöberg, D. Timothy Bishop, Göran Jönsson, Julia Newton-Bishop, David J. Adams
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12859-016-1298-9

Evaluating tools for transcription factor binding site prediction
Cited by: 75
Author(s): Narayan Jayaram, Daniel Usvyat, Andrew C.R. Martin
Software Mentions: 6
Published: about 8 years ago

10.7554/eLife.53618

Combined deletion of Glut1 and Glut3 impairs lung adenocarcinoma growth
Cited by: 15
Author(s): Caroline Contat, Pierre‐Benoit Ancey, Nadine Zangger, Silvia Sabatino, Justine Pascual, Stéphane Escrig, Linda Jensen, Christine Goepfert, Bernard Lanz, Mario Lepore, Rolf Gruetter, A. Rossier, Sabina Berezowska, Christina Neppl, Inti Zlobec, Stéphanie Clerc-Rosset, Graham Knott, Jeffrey C. Rathmell, E. Dale Abel, A. Meibom, Etienne Meylan
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0128854

ONION: Functional Approach for Integration of Lipidomics and Transcriptomics Data
Cited by: 5
Author(s): Monika Piwowar, Wiktor Jurkowski
Software Mentions: 6
Published: over 9 years ago

10.3390/genes11070802

Convergence of Prognostic Gene Signatures Suggests Underlying Mechanisms of Human Prostate Cancer Progression
Cited by: 6
Author(s): Bogdan A. Luca, Vincent Moulton, Christopher Ellis, Shea P. Connell, Daniel Brewer, Christopher S. Cooper
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1009737

Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver
Cited by: 9
Author(s): Benjamin P. Flynn, Matthew T. Birnie, Yvonne M. Kershaw, Audrys G Pauža, Sohyoung Kim, Songjoon Baek, Mark F. Rogers, Alex Paterson, Diana A. Stavreva, David Murphy, Gordon L. Hager, Stafford Lightman, Becky Conway-Campbell
Software Mentions: 6
Published: over 3 years ago

10.3390/cancers13010143

Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies
Cited by: 17
Author(s): Irene Pérez-Díez, Marta R. Hidalgo, Pablo Malmierca-Merlo, Zoraida Andreu, Sergio Romera-Giner, Rosa Farràs, María de la Iglesia-Vayá, Mariano Provencio, Atocha Romero, Francisco García‐García
Software Mentions: 6
Published: almost 4 years ago

10.1093/g3journal/jkab274

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland
Cited by: 1
Author(s): S. Eryn McFarlane, Josephine M. Pemberton
Software Mentions: 6
Published: over 3 years ago

10.1016/j.stemcr.2017.09.018

Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos
Cited by: 33
Author(s): Rachel Jennings, Andrew Berry, Dave T. Gerrard, Stephen J. Wearne, James Strutt, Sarah Withey, Mariya Chhatriwala, Karen Piper Hanley, Ludovic Vallier, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0066826

A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development
Cited by: 31
Author(s): Alicia N. Schep, Boris Adryan
Software Mentions: 6
Published: over 11 years ago

10.1016/j.ebiom.2021.103383

Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Cited by: 4
Author(s): Kevin A. Roth, Louis Coussement, Elena V. Knatko, Maureen Higgins, Sandra Steyaert, Charlotte M. Proby, Tim De Meyer, Albena T. Dinkova‐Kostova
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-77055-5

Identification of transcription factor co-regulators that drive prostate cancer progression
Cited by: 11
Author(s): Manjunath Siddappa, Sajad A. Wani, Mark D. Long, Damien A. Leach, Ewy A. Mathé, Charlotte Bevan, Moray J. Campbell
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0068414

NanoMiner — Integrative Human Transcriptomics Data Resource for Nanoparticle Research
Cited by: 20
Author(s): Lingjia Kong, Soile Tuomela, Lauri Hahne, Helena Ahlfors, Olli Yli‐Harja, Bengt Fadeel, Riitta Lahesmaa, Reija Autio
Software Mentions: 6
Published: over 11 years ago

10.12688/f1000research.25713.2

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
Cited by: 1
Author(s): Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0155802

Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis
Cited by: 6
Author(s): Bernard Fongang, Andrzej Kudlicki
Software Mentions: 6
Published: over 8 years ago

10.18632/aging.203448

Effects of Siberian fir terpenes extract Abisil on antioxidant activity, autophagy, transcriptome and proteome of human fibroblasts
Cited by: 1
Author(s): Anastasiya V. Lipatova, George S. Krasnov, Pavel Vorobyov, Pavel Melnikov, Olga N. Alekseeva, Yulia S. Vershinina, Alexander G. Brzhozovskiy, Daria Goliusova, Faniya Maganova, Natalia F. Zakirova, Anna V. Kudryavtseva, Alexey Moskalev
Software Mentions: 6
Published: about 3 years ago

10.3390/genes9080392

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
Cited by: 16
Author(s): Bernhard C. Thiel, Roman Ochsenreiter, Veerendra P. Gadekar, Andrea Tanzer, Ivo L. Hofacker
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0092111

Transcriptome Analysis Reveals Differential Splicing Events in IPF Lung Tissue
Cited by: 69
Author(s): Tracy Nance, Kevin S. Smith, Vanessa Anaya, Rhea Richardson, Lawrence Ho, Mauro Pala, Sara Mostafavi, Alexis Battle, Carol Feghali‐Bostwick, Glenn D. Rosen, Stephen B. Montgomery
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0252365

Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence
Cited by: 19
Author(s): B. Werner, Aline Koch, Ena Šečić, Jonas Engelhardt, Lukas Jelonek, Jens Steinbrenner, Karl‐Heinz Kogel
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0239495

Sources of variation in cell-type RNA-Seq profiles
Cited by: 16
Author(s): Johan Gustafsson, Felix Held, Jonathan L. Robinson, Elias Björnson, Rebecka Jörnsten, Jens Nielsen
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0227258

Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2
Cited by: 29
Author(s): Nhi Hin, Morgan Newman, Jan Kaslin, Alon M. Douek, Amanda L. Lumsden, Seyyed Hani Moussavi Nik, Yang Dong, Xin Zhou, Noralyn B. Mañucat-Tan, Alastair J. Ludington, David L. Adelson, Stephen Pederson, Michael Lardelli
Software Mentions: 6
Published: almost 5 years ago

10.1186/1752-0509-8-17

Identification of core T cell network based on immunome interactome
Cited by: 4
Author(s): Gabriel Teku, Csaba Ortutay, Mauno Vihinen
Software Mentions: 6
Published: almost 11 years ago

10.1186/s12918-018-0620-8

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
Cited by: 11
Author(s): Theresia Conrad, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger, Derek J. Mattern, Vito Valiante, Reinhard Guthke, Ilse D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde
Software Mentions: 6
Published: about 6 years ago

10.12688/f1000research.14541.1

drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics
Cited by: 37
Author(s): Paul Brennan
Software Mentions: 6
Published: over 6 years ago

10.1016/j.jaut.2019.06.009

Predicting drug-free remission in rheumatoid arthritis: A prospective interventional cohort study
Cited by: 28
Author(s): Kenneth F. Baker, Andrew Skelton, Dennis Lendrem, Adam Scadeng, Ben Thompson, Arthur G. Pratt, John D. Isaacs
Software Mentions: 6
Published: almost 5 years ago

10.3389/fimmu.2020.628804

Transcriptomic Analysis of Long-Term Protective Immunity Induced by Vaccination With Mycoplasma gallisepticum Strain ts-304
Cited by: 5
Author(s): Sathya N Kulappu Arachchige, Neil D. Young, Anna Kanci Condello, Oluwadamilola S Omotainse, Amir H. Noormohammadi, Nadeeka K. Wawegama, Glenn F. Browning
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12920-018-0358-6

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability
Cited by: 5
Author(s): Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Abou Jamra, Fulvia Ferrazzi
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1007633

Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion
Cited by: 45
Author(s): Yasmine J. Liu, Georges E. Janssens, Rebecca L. McIntyre, Marte Molenaars, Rashmi Kamble, Arwen W. Gao, Aldo Jongejan, Michel van Weeghel, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 6
Published: over 5 years ago

10.1186/s13148-020-00881-x

Gene–methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk
Cited by: 7
Author(s): Julia Romanowska, Øystein Ariansen Haaland, Astanand Jugessur, Miriam Gjerdevik, Zongli Xu, Jack A. Taylor, Allen J. Wilcox, Inge Jonassen, Rolv Terje Lie, Håkon K. Gjessing
Software Mentions: 6
Published: over 4 years ago

10.1534/g3.117.300489

DrosophilaLarval Brain Neoplasms Present Tumour-Type Dependent Genome Instability
Cited by: 4
Author(s): Fabrizio Rossi, Camille Stephan‐Otto Attolini, José Luis Mosquera, Cayetano González
Software Mentions: 6
Published: over 6 years ago

10.1016/j.immuni.2020.07.003

Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans
Cited by: 130
Author(s): Urszula Cytlak, Anastasia Resteu, Sarah Pagan, Kile Green, Paul Milne, Sheetal Maisuria, David McDonald, Gillian Hulme, Andrew Filby, Benjamin Carpenter, Rachel Queen, Sophie Hambleton, Rosie Hague, Hana Lango Allen, James Thaventhiran, Gina M. Doody, Matthew Collin, Venetia Bigley
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1006840

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Cited by: 54
Author(s): Syed Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles K. Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
Software Mentions: 6
Published: over 7 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: over 7 years ago

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 11 years ago

10.18632/oncotarget.24907

Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas
Cited by: 34
Author(s): David S. Guttery, Kevin Blighe, Konstantinos Polymeros, R. Paul Symonds, Salvador Macip, Esther L. Moss
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2020.01095

Peptidylarginine Deiminase 4 Promotes the Renal Infiltration of Neutrophils and Exacerbates the TLR7 Agonist-Induced Lupus Mice
Cited by: 14
Author(s): Norio Hanata, Hirofumi Shoda, Hiroaki Hatano, Yasuo Nagafuchi, Takashi Komai, Tomohisa Okamura, Akari Suzuki, I Ketut Gunarta, Katsuji Yoshioka, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2019.00527

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome
Cited by: 37
Author(s): Fergal J. Duffy, January Weiner, Scott G. Hansen, David L. Tabb, Sara Suliman, Ethan Thompson, Jeroen Maertzdorf, Steven G. Smith, Gerard Tromp, Shreemanta K. Parida, Drew Dover, Michael K. Axthelm, Jayne S. Sutherland, Hazel M. Dockrell, Tom H. M. Ottenhoff, Thomas J. Scriba, Louis J. Picker, Gerhard Walzl, Stefan H. E. Kaufmann, Daniel E. Zak
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02386-z

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Cited by: 4
Author(s): Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Lior Pachter
Software Mentions: 5
Published: over 3 years ago

10.1186/s11689-020-09316-3

Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Bonnie Alberry, Christina A Castellani, Shiva M. Singh
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2164-10-22

BioMart – biological queries made easy
Cited by: 718
Author(s): Damian Smedley, Syed Haider, Benoît Ballester, Richard Holland, Darin London, Guðmundur Á. Þórisson, Arek Kasprzyk
Software Mentions: 5
Published: almost 16 years ago

10.3389/fimmu.2018.01868

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development
Cited by: 11
Author(s): Friederike Ebner, Mathias Kuhring, Aleksandar Radonić, Ankur Midha, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 5
Published: over 6 years ago

10.3390/pharmaceutics13081105

Evaluation of an Intravitreal Rho-Associated Kinase Inhibitor Depot Formulation in a Rat Model of Diabetic Retinopathy
Cited by: 2
Author(s): Cécile Lebon, Heike Neubauer, Marianne Berdugo, Kimberley Delaunay, Elke Markert, Kolja Becker, Katja S. Baum-Kroker, J. Prestle, Holger Fuchs, Remko A. Bakker, Francine Behar‐Cohen
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-016-3075-6

Non-linear interactions between candidate genes of myocardial infarction revealed in mRNA expression profiles
Cited by: 17
Author(s): Katherine E. Hartmann, Michał Seweryn, Samuel K. Handelman, Grzegorz A. Rempała, Wolfgang Sadée
Software Mentions: 5
Published: about 8 years ago

10.18632/aging.103935

Increased expression of myelin-associated genes in frontal cortex of SNCA overexpressing rats and Parkinson&#x2019;s disease patients
Cited by: 7
Author(s): Thomas Hentrich, Zinah Wassouf, Christine Ehrhardt, Eva Haas, James D. Mills, Eleonora Aronica, Tiago F. Outeiro, Jeannette Hübener‐Schmid, Olaf Rieß, Nicolas Casadei, Julia M. Schulze‐Hentrich
Software Mentions: 5
Published: about 4 years ago

10.3390/ijms22115858

Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development
Cited by: 4
Author(s): Nazli Serin, Gry H. Dihazi, Asima Tayyeb, Christof Lenz, Gerhard A. Müller, Michael Zeisberg, Hassan Dihazi
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2021.637832

Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation
Cited by: 3
Author(s): Paula Díez, Martín Pérez‐Andrés, Martin Bøgsted, Mikel Azkargorta, Rodrigo García-Valiente, Rosa Ma Dégano, E Blanco, Sheila Mateos-Gomez, Paloma Bárcena, Santiago Cruz, Rafael Góngora, Félix Elortza, Alicia Landeira-Viñuela, Pablo Juanes-Velasco, Víctor Segura, Raúl Manzano-Román, Júlia Almeida, Karen Dybkær, Alberto Órfão, Manuel Fuentes
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22168451

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data
Cited by: 8
Author(s): Christian Vahlensieck, Cora S. Thiel, Jan Andreas Adelmann, Béatrice Lauber, Jennifer Polzer, Oliver Ullrich
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2019.02474

Multi-Parameter Analysis of Biobanked Human Bone Marrow Stromal Cells Shows Little Influence for Donor Age and Mild Comorbidities on Phenotypic and Functional Properties
Cited by: 55
Author(s): Anastazja Andrzejewska, Rusan Catar, Janosch Schoon, Taimoor H. Qazi, F. Andrea Sass, Dorit Jacobi, Antje Blankenstein, Simon Reinke, D. H. Krüger, Mathias Streitz, Stephan Schlickeiser, Sarina Richter, Naima Souidi, Christien Madlen Beez, Julian Kamhieh-Milz, Ulrike Krüger, Tomasz Żemojtel, Karsten Jürchott, Dirk Strunk, Petra Reinke, Georg N. Duda, Guido Moll, Sven Geißler
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2019.01863

Molecular Characterization of Human Lymph Node Stromal Cells During the Earliest Phases of Rheumatoid Arthritis
Cited by: 13
Author(s): Emmanuel Karouzakis, J Hähnlein, Cristoforo Grasso, Johanna F. Semmelink, Paul P. Tak, Daniëlle M. Gerlag, Caroline Ospelt, Lisa G. M. van Baarsen
Software Mentions: 5
Published: over 5 years ago

10.3390/cells10061371

Single-Cell Transcriptional Heterogeneity of Lymphatic Endothelial Cells in Normal and Inflamed Murine Lymph Nodes
Cited by: 18
Author(s): Eliane Sibler, Yuliang He, Luca Ducoli, Nadja Keller, Noriki Fujimoto, Lothar C. Dieterich, Michael Detmar
Software Mentions: 5
Published: over 3 years ago

10.1093/molbev/msab140

De Novo Mutation Rate Variation and Its Determinants in Chlamydomonas
Cited by: 16
Author(s): Eugenio López‐Cortegano, Rory J. Craig, Jobran Chebib, Toby Samuels, Andrew D. Morgan, Susanne A. Kraemer, Katharina B. Böndel, Rob W. Ness, Nick Colegrave, Peter D. Keightley
Software Mentions: 5
Published: over 3 years ago

10.3390/mi12080865

Bioprinting of Adult Dorsal Root Ganglion (DRG) Neurons Using Laser-Induced Side Transfer (LIST)
Cited by: 7
Author(s): Katiane Roversi, Hamid Ebrahimi Orimi, Marcelo Falchetti, Edroaldo Lummertz da Rocha, Sébastien Talbot, Christos Boutopoulos
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22179146

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-015-1820-x

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications
Cited by: 19
Author(s): Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James, Jean Yee Hwa Yang
Software Mentions: 5
Published: over 9 years ago

10.3390/genes12060824

Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data
Cited by: 4
Author(s): Sunghyun Cho, Prabuddha Manjula, Minjun Kim, Eunjin Cho, Dooho Lee, Seung Hwan Lee, Jun Heon Lee, Dongwon Seo
Software Mentions: 5
Published: over 3 years ago

10.1093/hmg/ddaa140

Motor neuron translatome reveals deregulation of SYNGR4 and PLEKHB1 in mutant TDP-43 amyotrophic lateral sclerosis models
Cited by: 13
Author(s): Rita F Marques, Jan Broder Engler, Katrin Küchler, Ross A. Jones, Thomas Lingner, Gabriela Salinas, Thomas H. Gillingwater, Manuel A. Friese, Kent E. Duncan
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.66904

Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology
Cited by: 14
Author(s): Markus Terrey, Scott I. Adamson, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 5
Published: over 3 years ago

10.1038/s41398-019-0666-4

Hepatic gene expression explains primary drug toxicity in bipolar disorder
Cited by: 0
Author(s): Anna Maria Birkl-Toeglhofer, Christoph Birkl, Ida C. Llenos, Serge Weis, Johannes Haybaeck
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-018-1489-y

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells
Cited by: 25
Author(s): Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jérémy Denizot, Raquel Manzano García, Steven Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip T. Hawkins, Len R. Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick Varga‐Weisz
Software Mentions: 5
Published: about 6 years ago

10.1038/s41398-021-01358-y

Zbtb16 regulates social cognitive behaviors and neocortical development
Cited by: 23
Author(s): Noriyoshi Usui, Stefano Berto, Ami Konishi, Makoto Kondo, Genevieve Konopka, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.21049

Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13072-020-00346-8

DAMEfinder: a method to detect differential allele-specific methylation
Cited by: 8
Author(s): Stephany Orjuela, Dania Machlab, Mirco Menigatti, Giancarlo Marra, Mark D. Robinson
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-018-5396-0

s·nr: a visual analytics framework for contextual analyses of private and public RNA-seq data
Cited by: 0
Author(s): Paul Klemm, Peter Frommolt, Jan-Wilhelm Kornfeld
Software Mentions: 5
Published: almost 6 years ago

10.1093/g3journal/jkab146

The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes
Cited by: 3
Author(s): Astra S. Bryant, Elissa A. Hallem
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0038365

Detection of Simultaneous Group Effects in MicroRNA Expression and Related Target Gene Sets
Cited by: 21
Author(s): Stephan Artmann, Klaus Jung, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 5
Published: over 12 years ago

10.1038/s41598-021-87779-7

Identification of genes associated with altered gene expression and m6A profiles during hypoxia using tensor decomposition based unsupervised feature extraction
Cited by: 10
Author(s): Sanjiban Sekhar Roy, Y-h. Taguchi
Software Mentions: 5
Published: over 3 years ago

10.7150/thno.47137

USP7 targeting modulates anti-tumor immune response by reprogramming Tumor-associated Macrophages in Lung Cancer
Cited by: 87
Author(s): Xiaomeng Dai, Lisen Lu, Suke Deng, Jingshu Meng, Chao Wan, Jing Huang, Yajie Sun, Yan Hu, Bian Wu, Gang Wu, Jonathan F. Lovell, Jin Huang, Kunyu Yang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-019-6127-x

Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake
Cited by: 9
Author(s): Haibo Li, Kristina M. Feye, Yet Nguyen, Anoosh Rakhshandeh, Crystal L. Loving, Jack C. M. Dekkers, Nicholas K. Gabler, Christopher K. Tuggle
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-021-04112-9

NoRCE: non-coding RNA sets cis enrichment tool
Cited by: 4
Author(s): Gülden Olgun, Afshan Nabi, Öznur Taştan
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2021.626187

Dysregulation of Transcription Factor Networks Unveils Different Pathways in Human Papillomavirus 16-Positive Squamous Cell Carcinoma and Adenocarcinoma of the Uterine Cervix
Cited by: 9
Author(s): Saloê Bispo, Ticiana Della Justina Farias, Patrícia Savio de Araujo-Souza, Ricardo Cintra, Hellen Geremias dos Santos, Natasha Andressa Nogueira Jorge, Mauro A. A. Castro, Gabriel Wajnberg, Nicole de Miranda Scherer, Maria Luiza Nogueira Dias Genta, Jesus Paula Carvalho, Luísa Lina Villa, Laura Sichero, Fábio Passetti
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-51379-3

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium
Cited by: 9
Author(s): Les Kallestad, Seth Blackshaw, Ahmad M. Khalil, Krzysztof Palczewski
Software Mentions: 5
Published: about 5 years ago

10.1126/sciadv.abd7819

High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 5
Published: almost 4 years ago

10.3389/fnmol.2019.00272

DYRK1A Overexpression Alters Cognition and Neural-Related Proteomic Pathways in the Hippocampus That Are Rescued by Green Tea Extract and/or Environmental Enrichment
Cited by: 18
Author(s): Ilario De Toma, Mireia Ortega, Patrick Aloy, Eduard Sabidó, Mara Dierssen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0220934

Profiling DNA methylation patterns of zebrafish liver associated with parental high dietary arachidonic acid
Cited by: 18
Author(s): Anne‐Catrin Adam, Kai Kristoffer Lie, Paul Whatmore, Lars Martin Jakt, Mari Moren, Kaja H. Skjærven
Software Mentions: 5
Published: over 5 years ago

10.1186/s12863-020-00852-4

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2019.01535

A Bioinformatics Approach to Explore MicroRNAs as Tools to Bridge Pathways Between Plants and Animals. Is DNA Damage Response (DDR) a Potential Target Process?
Cited by: 9
Author(s): Massimo Bellato, Davide De Marchi, Carla Gualtieri, Elisabetta Sauta, Paolo Magni, Anca Macovei, Lorenzo Pasotti
Software Mentions: 5
Published: almost 5 years ago

10.3389/fnins.2019.00002

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
Cited by: 51
Author(s): Shradha Mukherjee, Christine Klaus, Mihaela Pricop-Jeckstadt, Jeremy A. Miller, Felix L Struebing
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0123609

Mapsnp: An R Package to Plot a Genomic Map for Single Nucleotide Polymorphisms
Cited by: 5
Author(s): Fuquan Zhang, Yong Xu, Hongbao Cao, Chunhui Jin, Cheng Zhang, Guoqiang Wang, Yin Yao Shugart
Software Mentions: 5
Published: over 9 years ago

10.1186/s12860-020-00295-w

Molecular docking and machine learning analysis of Abemaciclib in colon cancer
Cited by: 14
Author(s): José Liñares-Blanco, Cristian R. Munteanu, Alejandro Pazos, Carlos Fernández-Lozano
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2105-11-221

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
Cited by: 77
Author(s): Alberto Risueño, Celia Fontanillo, Marcel E. Dinger, Javier De Las Rivas
Software Mentions: 5
Published: over 14 years ago

10.1172/JCI91363

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes
Cited by: 70
Author(s): Bon Ham Yip, Violetta Steeples, Emmanouela Repapi, Richard N. Armstrong, Miriam Llorian, S. Roy, Jacqueline Shaw, Hamid Dolatshad, Stephen Taylor, Amit Verma, Matthias Bartenstein, Paresh Vyas, Nicholas C. P. Cross, Luca Malcovati, Mario Cazzola, Eva Hellström‐Lindberg, Seishi Ogawa, Christopher W.J. Smith, Andrea Pellagatti, Jacqueline Boultwood
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2021.662239

Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution
Cited by: 5
Author(s): Vladimir Jovanović, Melanie Sarfert, Carlos S. Reyna-Blanco, Henrike Indrischek, Dulce I. Valdivia, Ekaterina Shelest, Katja Nowick
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1007268

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans
Cited by: 106
Author(s): Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2020.550769

HDAC3 Mediates the Inflammatory Response and LPS Tolerance in Human Monocytes and Macrophages
Cited by: 26
Author(s): Mohammed Ghiboub, Jing Zhao, Andrew Y. Li Yim, Ronald Schilderink, Caroline Verseijden, Patricia H. P. van Hamersveld, José Duarte, Theodorus B. M. Hakvoort, Iris Admiraal, Nicola Harker, David F. Tough, Peter Henneman, Menno P.J. de Winther, Wouter J. de Jonge
Software Mentions: 5
Published: about 4 years ago

10.3389/fcell.2021.688855

Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells
Cited by: 7
Author(s): Dilek Cansu Gürer, İpek Erdoğan, Ulvi Ahmadov, Merve Başol, Osama Sweef, Gulcin Cakan-Akdogan, Bünyamin Akgül
Software Mentions: 4
Published: about 3 years ago

Projects: bioconductor: biomaRt

Papers Mentioning biomaRt 446