10.3390/ijms22010078

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts
Cited by: 10
Author(s): Paulina Kołodziej-Wojnar, Joanna Borkowska, Zofia Wicik, Anna Domaszewska-Szostek, Jacek Połosak, Marta Cąkała-Jakimowicz, Olga Bujanowska, Monika Puzianowska-Kuźnicka
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-81933-x

Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Cited by: 15
Author(s): Heleen H.T. Middelkamp, Anouk H.A. Verboven, Aisen Vivas, Chantal Schoenmaker, Teun Klein Gunnewiek, Robert Passier, Cornelis A. Albers, Peter-Bram A.C. ’t Hoen, Nael Nadif Kasri, Andries D. van der Meer
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22179337

Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients
Cited by: 3
Author(s): Alicja Pacholewska, Christina Grimm, Carmen D. Herling, Matthias Lienhard, Anja Königs, Bernd Timmermann, Janine Altmüller, Oliver Mücke, Hans Christian Reinhardt, Christoph Plass, Ralf Herwig, Michael Hallek, Michal R. Schweiger
Software Mentions: 6
Published: about 5 years ago

10.1016/j.cell.2021.07.018

TDP-43 condensation properties specify its RNA-binding and regulatory repertoire
Cited by: 99
Author(s): Martina Hallegger, Anob M. Chakrabarti, Flora Lee, Bo Lim Lee, Aram Gustav Amalietti, Hana M. Odeh, Katie E. Copley, Jack D. Rubien, Bede Portz, Klara Kuret, Ina Huppertz, Frédérique Rau, Rickie Patani, Nicolas L. Fawzi, James Shorter, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2019.00823

Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages
Cited by: 19
Author(s): Lucas F. Maciel, David A. Morales-Vicente, Gilbert O. Silveira, Raphael O. Ribeiro, Giovanna G. O. Olberg, David S. Pires, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pbio.2003903

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development
Cited by: 62
Author(s): Hong Zhang, Shengqian Dou, Feng He, Junjie Luo, Liping Wei, Jian Lü
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pbio.3001022

A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies
Cited by: 27
Author(s): Kathy Darragh, Anna Orteu, Daniella Black, Kelsey J. R. P. Byers, Daiane Szczerbowski, Ian A. Warren, Pasi Rastas, Ana Pinharanda, John W. Davey, Sylvia Fernanda Garza, Diana Abondano Almeida, Richard M. Merrill, W. Owen McMillan, Stefan Schulz, Chris D. Jiggins
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.3000741

Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei
Cited by: 32
Author(s): Eva Doleželová, Michaela Kunzová, Mario Dejung, Michal Levin, Brian Panicucci, Clément Regnault, Christian J. Janzen, Michael P. Barrett, Falk Butter, Alena Zı́ková
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1006279

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
Cited by: 43
Author(s): Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Šejla Šalic, Violeta Serra, Markus K. Muellner, Vassiliki Théodorou, Sebastian M. Nijman
Software Mentions: 6
Published: about 10 years ago

10.1038/s41598-021-82429-4

Molecular characterization of atherosclerosis in HIV positive persons
Cited by: 5
Author(s): Adam Cornwell, Rohith Palli, Meera V. Singh, Lauren Benoodt, Alicia Tyrell, Jun Abe, Giovanni Schifitto, Sanjay B. Maggirwar, Juilee Thakar
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-021-00939-2

Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes
Cited by: 17
Author(s): David Z. Pan, Min‐Hua Zong, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Marı́a Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Kirsi H. Pietiläinen, Jussi Pihlajamäki, Markku Laakso, Kristina M. Garske, Päivi Pajukanta
Software Mentions: 6
Published: about 5 years ago

10.3390/cancers12113311

Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers
Cited by: 2
Author(s): Denílson Bezerra Marques, Layse Raynara Ferreira-Costa, Lorenna Larissa Ferreira-Costa, Ana Beatriz Bezerra-Oliveira, Romualdo da Silva Corrêa, Carlos César de Oliveira Ramos, Tatiana Vinasco-Sandoval, Kátia de Paiva Lopes, Ricardo Assunção Vialle, Amanda Ferreira Vidal, Vivian Nogueira Silbiger, Ândrea Ribeiro-dos-Santos
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.cub.2018.09.026

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis
Cited by: 35
Author(s): Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E. M. Furlong
Software Mentions: 6
Published: almost 8 years ago

10.3389/fgene.2021.675260

Aluminum or Low pH – Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress
Cited by: 16
Author(s): Miriam Szurman-Zubrzycka, Karolina Chwiałkowska, Magdalena Niemira, Mirosław Kwaśniewski, M. Nawrot, Monika Gajecka, Paul B. Larsen, Iwona Szarejko
Software Mentions: 6
Published: over 5 years ago

10.3389/fvets.2019.00214

Transcriptomic Profiling of Duodenal Epithelium Reveals Temporally Dynamic Impacts of Direct Duodenal Starch-Infusion During Dry Period of Dairy Cattle
Cited by: 2
Author(s): Congjun Li, Shudai Lin, María Jose Ranilla-García, VI Ransom L. Baldwin
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-021-85256-9

Creation and validation of models to predict response to primary treatment in serous ovarian cancer
Cited by: 11
Author(s): Jesús González Bosquet, Eric J. Devor, A.M. Newtson, Brian J. Smith, David Bender, Michael J. Goodheart, Megan McDonald, Terry A. Braun, Kristina W. Thiel, Kimberly K. Leslie
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22126319

Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome
Cited by: 6
Author(s): Sulev Kõks, Abigail L Pfaff, Vivien J. Bubb, John P. Quinn
Software Mentions: 6
Published: over 5 years ago

10.1186/s13148-020-00944-z

Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
Cited by: 38
Author(s): Qingqin Li, Yu Sun, Tania Wang
Software Mentions: 6
Published: almost 6 years ago

10.3390/biomedicines9091192

Self-Organization Provides Cell Fate Commitment in MSC Sheet Condensed Areas via ROCK-Dependent Mechanism
Cited by: 3
Author(s): Peter Nimiritsky, Ekaterina Novoseletskaya, Roman Eremichev, Natalya Alexandrushkina, Maxim Karagyaur, O. V. Vetrovoy, Nataliya Basalova, А. М. Хрусталева, Alexander Tyakht, Anastasia Efimenko, В. А. Ткачук
Software Mentions: 6
Published: about 5 years ago

10.1186/s13148-018-0593-x

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13059-020-02081-5

The Tug1 lncRNA locus is essential for male fertility
Cited by: 59
Author(s): Jordan P. Lewandowski, Gabrijela Dumbović, Audrey Watson, Tae-Young Hwang, Emily Jacobs-Palmer, Nydia P Chang, Christian Much, Kyle M. Turner, Christopher Kirby, Nimrod D. Rubinstein, Abigail F. Groff, Steve C. Liapis, Chiara Gerhardinger, Assaf C. Bester, Pier Paolo Pandolfi, John G. Clohessy, Hopi E. Hoekstra, Martin Sauvageau, John L. Rinn
Software Mentions: 6
Published: about 6 years ago

10.20892/j.issn.2095-3941.2020.0073

Single-cell RNA-seq reveals the immune escape and drug resistance mechanisms of mantle cell lymphoma
Cited by: 23
Author(s): Liang Wang, Steven Mo, Xin Li, Yuanyuan He, Jing Yang
Software Mentions: 6
Published: almost 7 years ago

10.3390/nu12041042

Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model
Cited by: 33
Author(s): Ping Xu, Feng Yan, Yuhai Zhao, Xiangbo Chen, Shili Sun, Yuefei Wang, Le Ying
Software Mentions: 6
Published: over 6 years ago

10.3389/fpls.2021.642828

Natural Genetic Diversity in Tomato Flavor Genes
Cited by: 12
Author(s): Lara Pereira, Manoj Sapkota, Michael Alonge, Yi Zheng, Youjun Zhang, Hamid Razifard, Nathan K Taitano, Michael C. Schatz, Alisdair R. Fernie, Ying Wang, Zhangjun Fei, Ana L. Caicedo, Denise M. Tieman, Esther van der Knaap
Software Mentions: 6
Published: over 5 years ago

10.1002/ctm2.253

Multiregion single‐cell sequencing reveals the transcriptional landscape of the immune microenvironment of colorectal cancer
Cited by: 34
Author(s): Wei Wang, Yu Zhong, Zhenkun Zhuang, Junping Xie, Yueer Lu, Chengzhi Huang, Yan Sun, Liang Wu, Jianhua Yin, Hang Yu, Zhiqiang Jiang, Shanshan Wang, Chunqing Wang, Yuanhang Zhang, Yilin Huang, Chongyin Han, Zhenggang Zhong, Jialin Hu, Ying Ouyang, Huisheng Liu, Mengya Yu, Xiaochan Wei, Dandan Chen, Lizhen Huang, Yong Hou, Zhanglin Lin, Shiping Liu, Fei Ling, Xueqing Yao
Software Mentions: 6
Published: almost 6 years ago

10.1161/CIRCULATIONAHA.119.039596

Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins
Cited by: 74
Author(s): Sonia Chothani, Sebastian Schäfer, Eleonora Adami, V. Sivakumar, Anissa A. Widjaja, Sarah R. Langley, Jessie Tan, Mao Wang, Nicholas M Quaife, Chee Jian Pua, G. D’Agostino, Shamini Guna Shekeran, Benjamin L. George, Si Ching Lim, Elaine Yiqun Cao, Sebastiaan van Heesch, Franziska Witte, Leanne E. Felkin, Eleni G. Christodoulou, Jinqiao Dong, Susanne Blachut, Giannino Patone, Paul J.R. Barton, Norbert Hübner, Stuart A. Cook, Owen J. L. Rackham
Software Mentions: 6
Published: about 7 years ago

10.1161/CIRCULATIONAHA.120.046464

Hyperglycemia Induces Trained Immunity in Macrophages and Their Precursors and Promotes Atherosclerosis
Cited by: 75
Author(s): Laurienne Edgar, Naveed Akbar, Adam Braithwaite, Thomas Krausgruber, Héctor Gallart-Ayala, Jade Bailey, Alastair Corbin, Tariq E. Khoyratty, Joshua T Chai, Mohammad Alkhalil, André F. Rendeiro, Klemen Žiberna, Ritu Arya, Thomas J. Cahill, Christoph Bock, Jurga Laurencikiene, Mark J. Crabtree, Madeleine E. Lemieux, Niels P. Riksen, Mihai G. Netea, Craig E. Wheelock, Keith M. Channon, Mikael Rydén, Irina A. Udalova, Ricardo Carnicer, Robin P. Choudhury
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2020.00404

Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization
Cited by: 20
Author(s): Hrant Hovhannisyan, Ester Saus, Ewa Księżopolska, Alex J Hinks Roberts, Edward J. Louis, Toni Gabaldón
Software Mentions: 6
Published: over 6 years ago

10.1186/s13578-021-00691-5

A single-cell interactome of human tooth germ from growing third molar elucidates signaling networks regulating dental development
Cited by: 7
Author(s): Yueqi Shi, Yinglan Yu, Yuqiong Zhou, Jing Zhao, Wenjie Zhang, Duohong Zou, Weichen Song, Shaoyi Wang
Software Mentions: 6
Published: about 5 years ago

10.5808/gi.20074

Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing
Cited by: 2
Author(s): Jiyeon Han, Yeonjoo Jung, Yukyung Jun, Sungsu Park, Sanghyuk Lee
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2021.665153

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species
Cited by: 9
Author(s): Annie Robic, Chloé Cerutti, Christa Kühn, Thomas Faraut
Software Mentions: 6
Published: over 5 years ago

10.1093/gigascience/giy059

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: over 8 years ago

10.3389/fimmu.2021.651254

High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells
Cited by: 5
Author(s): Kensei Kishimoto, Catera L. Wilder, Justin Buchanan, Minh Anh Nguyen, Chidera Okeke, Alexander Hoffmann, Quen J. Cheng
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22168482

Multicellular Human Cardiac Organoids Transcriptomically Model Distinct Tissue-Level Features of Adult Myocardium
Cited by: 17
Author(s): Charles M. Kerr, Dylan Richards, Donald R. Menick, Kristine Y. DeLeon‐Pennell, Ying Mei
Software Mentions: 6
Published: about 5 years ago

10.1186/s13059-020-02147-4

CSS: cluster similarity spectrum integration of single-cell genomics data
Cited by: 29
Author(s): Zhisong He, Agnieska Brazovskaja, Sebastian Ebert, J. Gray Camp, Barbara Treutlein
Software Mentions: 6
Published: about 6 years ago

10.1016/j.ccell.2017.07.004

Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets
Cited by: 212
Author(s): Myron G. Best, Nik Sol, Sjors G J G In ‘t Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N. Niemeijer, Aniko V. Fejes, Lee Ann Tjon Kon Fat, Anna Egberdina Huis In 't Veld, Cyra E. Leurs, Tessa Y. Le Large, Laura L. Meijer, Irsan Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward P. Post, Laurine E. Wedekind, Jillian Wilhelmina Paulina Bracht, Michelle Esenkbrink, Leon J. Wils, Francesca Favaro, Jilian D. Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C. Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C.A. de Jager, Rolf T. Urbanus, Imo E. Hoefer, Gérard Pasterkamp, Christine Mannhalter, José Gomez-Arroyo, Harm Jan Bogaard, David P. Noske, W. Peter Vandertop, Daan van den Broek, Bauke Ylstra, R. Jonas A. Nilsson, Jelle Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent Lewandrowski, Bakhos A. Tannous, Adrianus J. de Langen, Egbert F. Smit, Michel M. van den Heuvel, Thomas Würdinger
Software Mentions: 6
Published: about 9 years ago

10.3389/fpls.2021.613059

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)
Cited by: 24
Author(s): Vicent Arbona, Miguel González-Guzmán, Zara Pitarch, José Tomás Matus, Héctor Candela, José L. Rambla, Antonio Granell, Aurelio Gómez‐Cadenas
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2019.02568

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level
Cited by: 22
Author(s): Yannick F. Fuchs, Virag Sharma, Anne Eugster, Gloria Kraus, Robert Morgenstern, Andreas Dahl, Susanne Reinhardt, A. Petzold, Annett Lindner, Doreen Löbel, Ezio Bonifacio
Software Mentions: 6
Published: almost 7 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: over 5 years ago

10.1002/JLB.5MA0120-209R

Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells
Cited by: 28
Author(s): Giuseppe Ercolano, Tania Wyss, Bérengère Salomé, Pedro Romero, Sara Trabanelli, Camilla Jandus
Software Mentions: 6
Published: over 6 years ago

10.1016/j.csbj.2019.04.012

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts
Cited by: 23
Author(s): Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pgen.1009574

Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets
Cited by: 13
Author(s): Matthew R. Hass, Daniel Brissette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
Software Mentions: 6
Published: over 5 years ago

10.1038/s42003-021-02320-w

A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels
Cited by: 13
Author(s): Guste Urbonaite, Jimmy Tsz Hang Lee, Ping Liu, Guillermo E. Parada, Martin Hemberg, Murat Açar
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-018-0122-7

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish
Cited by: 44
Author(s): Marianna Pauletto, Tereza Manousaki, Serena Ferraresso, Massimiliano Babbucci, Alexandros Tsakogiannis, Bruno Louro, Nicola Vitulo, Viet Ha Quoc, R. Carraro, Daniela Bertotto, Rafaella Franch, Francesco Maroso, Muhammad Aslam, Anna K. Sonesson, Barbara Simionati, G Malacrida, Alessandro Cestaro, Stefano Caberlotto, Elena Sarropoulou, C. C. Mylonas, Deborah M. Power, Tomaso Patarnello, Adelino V.M. Canário, Costas S. Tsigenopoulos, Luca Bargelloni
Software Mentions: 5
Published: about 8 years ago

10.3389/fpls.2020.597589

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves
Cited by: 3
Author(s): Sophie Moreau, Géraldine van Aubel, Rekin’s Janky, Pierre Van Cutsem
Software Mentions: 5
Published: almost 6 years ago

10.3389/fpls.2019.00223

Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage
Cited by: 56
Author(s): Stefan Petrasch, Christian J. Silva, Saskia D Mesquida-Pesci, Karina Gallegos, Casper van den Abeele, Victor Papin, Francisco Javier Fernández-Acero, Steven J. Knapp, Bárbara Blanco-Ulate
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2020.00132

Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes
Cited by: 9
Author(s): Miguel A. Flores‐Vergara, Elen Oneal, Mário Costa, Gonzalo H. Villarino, Caitlyn Roberts, María Angels de Luis Balaguer, Sı́lvia Coimbra, John H. Willis, Robert G. Franks
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2019.00689

Transcription Profiling of Monocyte-Derived Macrophages Infected In Vitro With Two Strains of Streptococcus agalactiae Reveals Candidate Pathways Affecting Subclinical Mastitis in Cattle
Cited by: 6
Author(s): Anna Lewandowska-Sabat, Е. В. Кирсанова, Christophe Klopp, T. R. Solberg, B. Heringstad, Olav Østerås, Preben Boysen, I. Olsaker
Software Mentions: 5
Published: about 7 years ago

10.3389/fpls.2019.00156

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens
Cited by: 12
Author(s): Anne L. Sternberger, Megan J. Bowman, Colin Kruse, Kevin L. Childs, Harvey E. Ballard, Sarah E. Wyatt
Software Mentions: 5
Published: over 7 years ago

10.1093/bib/bbaa339

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test
Cited by: 9
Author(s): Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed Lein, Richard H. Scheuermann
Software Mentions: 5
Published: almost 6 years ago

10.3389/fpls.2021.695439

Genome-Wide Identification and Characterization of Small Peptides in Maize
Cited by: 15
Author(s): Yan Liang, Wanchao Zhu, Sijia Chen, Qidong Jia, Li Lin
Software Mentions: 5
Published: over 5 years ago

10.3389/fphys.2019.00278

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
Cited by: 14
Author(s): Jianbin Zhang, Qiangqiang Nie, Chaozeng Si, Wang Cheng, Yang Chen, Weiliang Sun, Pei Lin, Jing Guo, Jie Kong, Yiyao Cui, Feng Wang, Xueqiang Fan, Zhidong Ye, Jianyan Wen, Peng Liu
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2020.567812

Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line
Cited by: 13
Author(s): Ganrea Chanthavixay, Colin Kern, Ying Wang, Perot Saelao, Susan J. Lamont, Rodrigo A. Gallardo, Gonzalo Rincón, Huaijun Zhou
Software Mentions: 5
Published: about 6 years ago

10.3389/fphys.2021.637924

A Subpopulation of Schwann Cell-Like Cells With Nerve Regeneration Signatures Is Identified Through Single-Cell RNA Sequencing
Cited by: 4
Author(s): Zairong Wei, Shenyou Shu, Mingjun Zhang, Sitian Xie, Shijie Tang, Kaiyu Nie, Haihong Li
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.625466

Zebrafish Chromosome 14 Gene Differential Expression in the fmr1hu2787 Model of Fragile X Syndrome
Cited by: 1
Author(s): Karissa Barthelson, Lachlan Baer, Yang Dong, Melanie L. Hand, Zac Pujic, Morgan Newman, Geoffrey J. Goodhill, Robert I. Richards, Stephen Pederson, Michael Lardelli
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2018.00026

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse
Cited by: 26
Author(s): Barbora Kuntová, Romana Stopková, Pavel Stopka
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2019.01126

Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation
Cited by: 29
Author(s): Yuan Tian, Haishen Wen, Xin Qi, Xiaoyan Zhang, Shikai Liu, Bingyu Li, Yalong Sun, Jifang Li, Feng He, Wenzhao Yang, Yun Li
Software Mentions: 5
Published: almost 7 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 6 years ago

10.3389/fimmu.2018.02055

Molecular and Cellular Response to Experimental Anisakis pegreffii (Nematoda, Anisakidae) Third-Stage Larval Infection in Rats
Cited by: 19
Author(s): Ivana Bušelić, Željka Trumbić, Jerko Hrabar, Anamarija Vrbatović, Ivana Bočina, Ivona Mladineo
Software Mentions: 5
Published: about 8 years ago

10.3389/fgene.2021.649619

Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer
Cited by: 21
Author(s): Anshika Chowdhary, Venkata Satagopam, Reinhard Schneider
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2021.643298

Immunomodulation of T Helper Cells by Tumor Microenvironment in Oral Cancer Is Associated With CCR8 Expression and Rapid Membrane Vitamin D Signaling Pathway
Cited by: 14
Author(s): Marco Fraga, Milly Yáñez, Macarena Sherman, Faryd Llerena, Mauricio Hernández, Guillermo Nourdin, Francisco Álvarez, Joaquín Urrizola, César Rivera, Liliana Lamperti, Lorena Nova, S Rojas Castro, Olga Zambrano, Alejandro Cifuentes, León Campos, Sergio Moya, J. Pastor, Marcelo Nuñez, Jorge Gatica, Jorge Figueroa, Felipe Zúñiga, Carlos Salomón, Gustavo Cerda, Ricardo Puentes, Gonzalo Labarca, Mabel Vidal, Reuben McGregor, Estefanía Nova-Lamperti
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.663091

Identification of a Potentially Functional circRNA-miRNA-mRNA Regulatory Network in Melanocytes for Investigating Pathogenesis of Vitiligo
Cited by: 4
Author(s): Lili Li, Zhi Xie, Xiliang Qian, Tai Wang, Minmin Jiang, Jinglin Qin, Chen Wang, Rongqun Wu, Canling Song
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.607314

Genetic Dissection of the Regulatory Mechanisms of Ace2 in the Infected Mouse Lung
Cited by: 11
Author(s): Fuyi Xu, Jun Gao, Silke Bergmann, Amy C. Sims, David G. Ashbrook, Ralph S. Baric, Yan Cui, Colleen B. Jonsson, Kui Li, Robert W. Williams, Klaus Schughart, Lu Lu
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2021.705848

Brg1 Supports B Cell Proliferation and Germinal Center Formation Through Enhancer Activation
Cited by: 6
Author(s): Dominik Schmiedel, Hadas Hezroni, Amit Hamburg, Ziv Shulman
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2018.01286

seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data
Cited by: 61
Author(s): Ziyi Chen, Lijun Quan, Anfei Huang, Qiang Zhao, Yuan Yao, Xuye Yuan, Qin Shen, Jingzhe Shang, Yinyin Ben, F. Xiao-Feng Qin, Aiping Wu
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2017.00168

A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics
Cited by: 44
Author(s): John S. House, Fabian A. Grimm, Dereje D. Jima, Yifeng Zhou, Ivan Rusyn, Fred A. Wright
Software Mentions: 5
Published: almost 9 years ago

10.3389/fimmu.2021.716661

The Metabolic Landscape of Thymic T Cell Development In Vivo and In Vitro
Cited by: 10
Author(s): Victoria Sun, Mark S. Sharpley, Karolina Elżbieta Kaczor‐Urbanowicz, Peter Chang, Amélie Montel‐Hagen, S. R. Lopez, Alexandre Zampieri, Yuhua Zhu, Stéphanie C. de Barros, Chintan Parekh, David Casero, Utpal Banerjee, Gay M. Crooks
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2020.558036

The Novel Omega-6 Fatty Acid Docosapentaenoic Acid Positively Modulates Brain Innate Immune Response for Resolving Neuroinflammation at Early and Late Stages of Humanized APOE-Based Alzheimer's Disease Models
Cited by: 14
Author(s): Qiu-Lan Ma, Cansheng Zhu, Marco Morselli, Trent Su, Matteo Pelligrini, Zhengqi Lu, Mychica Jones, Paul Denver, Daniel Castro, Xiaohong Gu, Frances Relampagos, Kaitlin Caoili, Bruce Teter, Sally A. Frautschy, Gregory M. Cole
Software Mentions: 5
Published: almost 6 years ago

10.3389/fimmu.2021.669920

Myeloid ATP Citrate Lyase Regulates Macrophage Inflammatory Responses In Vitro Without Altering Inflammatory Disease Outcomes
Cited by: 6
Author(s): Sanne G.S. Verberk, Hendrik J. P. van der Zande, Jeroen Baardman, Kyra E. de Goede, Karl J. Harber, Eelco D. Keuning, Joost M. Lambooij, Frank Otto, Anna Zawistowska-Deniziak, Helga E. de Vries, Menno P.J. de Winther, Bruno Guigas, Jan Van den Bossche
Software Mentions: 5
Published: over 5 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 5 years ago

10.3390/plants10071465

Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max
Cited by: 11
Author(s): Ramon de Koning, Raphaël Kiekens, Mary Esther Muyoka Toili, Geert Angenon
Software Mentions: 5
Published: about 5 years ago

10.7150/ijbs.45693

Cancer stem cell property and gene signature in bone-metastatic Breast Cancer cells
Cited by: 7
Author(s): An Luo, Yue Xu, Shujun Li, Jinxia Bao, Jianrong Lu, Nan Ding, Qian Zhao, Yuting Fu, Fei Liu, William C. Cho, Xunbin Wei, Haiyun Wang, Zuoren Yu
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41396-020-0606-6

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava
Cited by: 12
Author(s): Romain Savary, Cindy Dupuis, Frédéric G. Masclaux, Ivan D. Mateus, Edward C. Rojas, Ian R. Sanders
Software Mentions: 5
Published: over 6 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 6 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: about 6 years ago

10.1371/journal.pbio.3000434

GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors
Cited by: 55
Author(s): Krishna Sriram, Kevin Moyung, Ross Corriden, Hannah Carter, Paul A. Insel
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-021-86070-z

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Cited by: 7
Author(s): Karen Davey, Daniel Wong, Filip A. Konopacki, Eugene Kwa, Tony Ly, Heike Fiegler, Christopher R. Sibley
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-86002-x

Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway
Cited by: 102
Author(s): Andrea R. Daamen, Prathyusha Bachali, Katherine A. Owen, Kathryn M. Kingsmore, Erika L. Hubbard, Adam C. Labonte, Robert Robl, Sneha Shrotri, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-85669-6

Transcriptome of rhesus macaque (Macaca mulatta) exposed to total-body irradiation
Cited by: 12
Author(s): Yaoxiang Li, Jatinder Singh, Rency S. Varghese, Yubo Zhang, Oluseyi O. Fatanmi, Amrita K. Cheema, Vijay K. Singh
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms22052738

Identification of Overexpressed Genes in Malignant Pleural Mesothelioma
Cited by: 11
Author(s): Federica Morani, Luisa Bisceglia, Giulia Rosini, Luciano Mutti, Ombretta Melaiu, Stefano Landi, Federica Gemignani
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pbio.3000704

Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
Cited by: 83
Author(s): Noriki Fujimoto, Yuliang He, Marco D’Addio, Carlotta Tacconi, Michael Detmar, Lothar C. Dieterich
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms221910297

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development
Cited by: 10
Author(s): Saeid Babaei, Mohan B. Singh, Prem L. Bhalla
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-85061-4

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Cited by: 12
Author(s): Jerry C. Wang, Gokul Ramaswami, Daniel H. Geschwind
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-84667-y

Neuron-specific spinal cord translatomes reveal a neuropeptide code for mouse dorsal horn excitatory neurons
Cited by: 15
Author(s): Rebecca R Das Gupta, Louis Scheurer, Paweł Pelczar, Hendrik Wildner, Hanns Ulrich Zeilhofer
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-84270-1

Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model
Cited by: 4
Author(s): Valentin Baloche, Julie Rivière, Thi Bao Tram Tran, Aurore Gelin, Olivia Bawa, Nicolas Signolle, Mouhamadou Diop, Philippe Dessen, Stéphanie Beq, Muriel D. David, P. Busson
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1004105

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
Cited by: 173
Author(s): Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Z. Rassenti, Christian Barrett, Kristen Jepsen, Catriona Jamieson, Dennis A. Carson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pcbi.1008195

VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution
Cited by: 9
Author(s): Wei Wen, Adam J. Mead, Supat Thongjuea
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-021-81472-5

Drosophila Hox genes induce melanized pseudo-tumors when misexpressed in hemocytes
Cited by: 6
Author(s): Titus Ponrathnam, Ravina Saini, Sofia Banu, Rakesh Mishra
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008770

Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone
Cited by: 19
Author(s): Stine M. Præstholm, Majken Siersbæk, Ronni Nielsen, Xuguang Zhu, Anthony N. Hollenberg, Sheue-yann Cheng, Lars Grøntved
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1005952

Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade
Cited by: 46
Author(s): Antonia Klein, Eva Schultner, Helena Lowak, Lukas Schrader, Juergen Heinze, Luke Holman, Jan Oettler
Software Mentions: 5
Published: over 10 years ago

10.3390/ijms22179228

SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues
Cited by: 13
Author(s): Guoshuai Cai, Mulong Du, Yohan Bossé, Helmut Albrecht, Fei Qin, Xizhi Luo, X Michelle Androulakis, Chao Cheng, Mitzi Nagarkatti, Mitzi Nagarkatti, David C. Christiani, Michael L. Whitfield, Christopher I. Amos, Feifei Xiao
Software Mentions: 5
Published: about 5 years ago

10.1242/bio.040683

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Cited by: 4
Author(s): Isabel Reuter, Jana Jäckels, Susanne Kneitz, Jochen Kuper, Klaus–Peter Lesch, Christina Lillesaar
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pgen.1006017

Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes
Cited by: 42
Author(s): Kévin Lebrigand, Le He, Nishant Thakur, Marie-Jeanne Arguel, Jolanta Polanowska, Bernard Henrissat, Éric Record, Ghislaine Magdelenat, Valérie Barbe, Sylvain Raffaele, Pascal Barbry, Jonathan J. Ewbank
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pgen.1007631

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic
Cited by: 16
Author(s): Peter A. Combs, Hunter B. Fraser
Software Mentions: 5
Published: almost 8 years ago

10.3390/biom11020291

Determination of Genotoxicity Attributed to Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line
Cited by: 4
Author(s): Joong Won Lee, Hee Jae Lee, Young Joo Lee, Yong Beom Lim, Woo Jong Sim, Ji Hye Jang, Hye Ryeon Heo, Hyunwoo Lim, Ji Won Jung, Jin Sik Kim
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-75128-z

Novel genomic targets of valosin-containing protein in protecting pathological cardiac hypertrophy
Cited by: 5
Author(s): Ning Zhou, Xin Chen, Jing Xi, Ben Ma, Christiana Leimena, Shaunrick Stoll, Gangjian Qin, Charles Wang, Hongyu Qiu
Software Mentions: 5
Published: almost 6 years ago

10.3390/cancers12010037

Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 158
Author(s): Magdalena Niemira, François Collin, Anna Szałkowska, Agnieszka Bielska, Karolina Chwiałkowska, Joanna Reszeć, Jacek Nikliński, Mirosław Kwaśniewski, Adam Krętowski
Software Mentions: 5
Published: almost 7 years ago

10.3390/ijms21186488

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

10.1038/s41598-017-14942-4

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