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: about 5 years ago

10.14814/phy2.13376

Male apoE*3-Leiden.CETP mice on high-fat high-cholesterol diet exhibit a biphasic dyslipidemic response, mimicking the changes in plasma lipids observed through life in men
Cited by: 18
Author(s): Yared Paalvast, Albert Gerding, Yanan Wang, Vincent W. Bloks, Theo H. van Dijk, Rick Havinga, Ko Willems van Dijk, Patrick C.N. Rensen, Barbara M. Bakker, Jan Albert Kuivenhoven, Albert K. Groen
Software Mentions: 5
Published: almost 9 years ago

10.1111/pbi.13051

Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice
Cited by: 50
Author(s): Roslen Anacleto, Saurabh Badoni, Sabiha Parween, Vito M. Butardo, Gopal Misra, Rosa Paula Cuevas, Markus Kuhlmann, Trinidad P. Trinidad, Aida C. Mallillin, Cecilia Acuin, Anthony R. Bird, Matthew K. Morell, Nese Sreenivasulu
Software Mentions: 5
Published: over 7 years ago

10.1007/s11103-020-01041-8

Integrative transcriptomics reveals genotypic impact on sugar beet storability
Cited by: 7
Author(s): Silvia Madritsch, Svenja Bomers, Alexandra Posekany, Agnes Burg, Rebekka Birke, Florian Emerstorfer, Reinhard Turetschek, Sandra Otte, Herbert Eigner, Eva Maria Sehr
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pbio.1000335

The Sexually Antagonistic Genes of Drosophila melanogaster
Cited by: 294
Author(s): Paolo Innocenti, Edward H. Morrow
Software Mentions: 5
Published: over 16 years ago

10.1371/journal.pbio.3000170

The temporal profile of activity-dependent presynaptic phospho-signalling reveals long-lasting patterns of poststimulus regulation
Cited by: 24
Author(s): Kasper Engholm-Keller, Ashley J. Waardenberg, Johannes Alexander Müller, Jesse R. Wark, Rowena N Fernando, Jonathan W. Arthur, Phillip J. Robinson, Dirk Dietrich, Susanne Schoch, Mark E. Graham
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pbio.2002940

The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity
Cited by: 46
Author(s): Rukeia El-Athman, Nikolaï Genov, J Mazùch, Kaiyang Zhang, Yong A. Yu, Luise Fuhr, Marconi Abreu, Yin Li, Thomas Wallach, Achim Kramer, Clemens A. Schmitt, Angela Relógio
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pbio.3001166

Neural stem cells traffic functional mitochondria via extracellular vesicles
Cited by: 79
Author(s): Luca Peruzzotti-Jametti, Joshua D. Bernstock, Cory M. Willis, Giulia Manferrari, Rebecca Rogall, Erika Fernández-Vizarra, James C Williamson, Alice Braga, Aletta van den Bosch, Tommaso Leonardi, Grzegorz Krzak, Ágnes Kittel, Cristiane Benincá, Nunzio Vicario, Sisareuth Tan, Carlos Bastos, Iacopo Bicci, Nunzio Iraci, JA Smith, Ben Peacock, Karin H. Müller, Paul J. Lehner, Edit I. Buzás, Nuno Faria, Massimo Zeviani, Christian Frezza, Alain Brisson, Nicholas J Matheson, Carlo Viscomi, Stefano Pluchino
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pmed.1003229

Maternal dysglycaemia, changes in the infant’s epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial
Cited by: 52
Author(s): Elie Antoun, Negusse Tadesse Kitaba, Philip Titcombe, Kathryn V. Dalrymple, Emma Garratt, Sheila J. Barton, Robert Murray, Paul Seed, Joanna D. Holbrook, Michael S. Kobor, David T.S. Lin, Julia L. MacIsaac, Graham C. Burdge, Sara L. White, Lucilla Poston, Keith M. Godfrey, Karen A. Lillycrop
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pntd.0007361

Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya
Cited by: 3
Author(s): David P. Tchouassi, Ephantus J. Muturi, Samwel O. Arum, Chang‐Hyun Kim, Christopher J. Fields, Baldwyn Torto
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: almost 14 years ago

10.1371/journal.pone.0174602

Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data
Cited by: 1
Author(s): Yunfeng Li, Jarrett Morrow, Benjamin A. Raby, Kelan G. Tantisira, Scott T. Weiss, Wei Huang, Weiliang Qiu
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0179726

Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors
Cited by: 166
Author(s): Nathan O. Siemers, James L. Holloway, Chang Han, Scott D. Chasalow, Petra Ross‐Macdonald, Charles F. Voliva, Joseph D. Szustakowski
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0017388

Azacytidine and Decitabine Induce Gene-Specific and Non-Random DNA Demethylation in Human Cancer Cell Lines
Cited by: 129
Author(s): Sabine Hagemann, Oliver Heil, Frank Lyko, Bodo Brueckner
Software Mentions: 5
Published: over 15 years ago

10.1371/journal.pone.0042678

The Role of Master Regulators in the Metabolic/Transcriptional Coupling in Breast Carcinomas
Cited by: 19
Author(s): Karol Baca-López, M. Mayorga, Alfredo Hidalgo-Miranda, Nora Gutiérrez-Nájera, Enrique Hernández‐Lemus
Software Mentions: 5
Published: about 14 years ago

10.1371/journal.pone.0086299

Functional Module Connectivity Map (FMCM): A Framework for Searching Repurposed Drug Compounds for Systems Treatment of Cancer and an Application to Colorectal Adenocarcinoma
Cited by: 33
Author(s): Feng Hsiang Chung, Yun Ru Chiang, Ai Lun Tseng, Yung Chuan Sung, Jean Lu, Min Chang Huang, Nianhan Ma, Hoong Chien Lee
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0203672

Integrating the skin and blood transcriptomes and serum proteome in hidradenitis suppurativa reveals complement dysregulation and a plasma cell signature
Cited by: 65
Author(s): Lauren Hoffman, Lewis Tomalin, Gregory S. Schultz, Michael D. Howell, Niroshana Anandasabapathy, Afsáneh Alavi, Mayte Suárez‐Fariñas, Michelle A. Lowes
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0251800

Comparison of machine-learning methodologies for accurate diagnosis of sepsis using microarray gene expression data
Cited by: 5
Author(s): Dominik Schaack, Markus A. Weigand, Florian Uhle
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0065267

Zinc Finger Nuclease Mediated Knockout of ADP-Dependent Glucokinase in Cancer Cell Lines: Effects on Cell Survival and Mitochondrial Oxidative Metabolism
Cited by: 14
Author(s): Susan Richter, Shona Morrison, Timothy Connor, Jiechuang Su, Cristin G. Print, Ron S. Ronimus, Sean L. McGee, William R. Wilson
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pone.0004481

Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
Cited by: 17
Author(s): Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 5
Published: over 17 years ago

10.1371/journal.pone.0081167

Cytokeratin 15 Marks Basal Epithelia in Developing Ureters and Is Upregulated in a Subset of Urothelial Cell Carcinomas
Cited by: 21
Author(s): Guihua Tai, Parisa Ranjzad, Fiona Marriage, Samrina Rehman, Helen Denley, Jill Dixon, Karen S. Mitchell, Philip J. Day, Adrian S. Woolf
Software Mentions: 5
Published: almost 13 years ago

10.3390/cancers13123014

Upper Aerodigestive Tract Squamous Cell Carcinomas Show Distinct Overall DNA Methylation Profiles and Different Molecular Mechanisms behind WNT Signaling Disruption
Cited by: 6
Author(s): Sheila Coelho Soares-Lima, Hisham Mehanna, Diego Camuzi, Paulo Thiago de Souza-Santos, Tatiana de Almeida Simão, Pedro Nicolau-Neto, Monique de Souza Almeida Lopes, Cyrille Cuenin, Fazlur Rahman Talukdar, Nikolaos Batis, Izabella Costa, Fernando Luiz Dias, Davide Degli Esposti, Mariana Boroni, Zdenko Herceg, Luís Felipe Ribeiro Pinto
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12082261

MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer
Cited by: 12
Author(s): Alessandra Cataldo, Sandra Romero-Córdoba, Ilaria Plantamura, Giulia Cosentino, Alfredo Hidalgo‐Miranda, Elda Tagliabue, Marilena V. Iorio
Software Mentions: 5
Published: about 6 years ago

10.3390/cancers11121951

Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia
Cited by: 17
Author(s): Antonella Padella, Giorgia Simonetti, Giulia Paciello, George Giotopoulos, Carmen Baldazzi, Simona Righi, Martina Ghetti, Anna Stengel, Viviana Guadagnuolo, Rossella De Tommaso, Cristina Papayannidis, Valentina Robustelli, Eugenia Franchini, Andrea Ghelli Luserna di Rorà, Anna Ferrari, Maria Chiara Fontana, Samantha Bruno, Emanuela Ottaviani, Simona Soverini, Clelia Tiziana Storlazzi, Claudia Haferlach, Elena Sabattini, Nicoletta Testoni, Ilaria Iacobucci, Brian J.P. Huntly, Elisa Ficarra, Giovanni Martinelli
Software Mentions: 5
Published: almost 7 years ago

10.3390/cancers11010041

Epilepsy Associates with Decreased HIF-1α/STAT5b Signaling in Glioblastoma
Cited by: 11
Author(s): Sharon Berendsen, Wim G.M. Spliet, Marjolein Geurts, Wim Van Hecke, Tatjana Seute, Tom J. Snijders, Vincent Bours, Erica H. Bell, Arnab Chakravarti, Pierre A. Robe
Software Mentions: 5
Published: over 7 years ago

10.3390/cancers13092115

Chromatin-Directed Proteomics Identifies ZNF84 as a p53-Independent Regulator of p21 in Genotoxic Stress Response
Cited by: 8
Author(s): Anna Strzeszewska-Potyrała, Karolina Staniak, Joanna Czarnecka‐Herok, Mahmoud-Reza Rafiee, Marcin Herok, Grażyna Mosieniak, Jeroen Krijgsveld, Ewa Sikora
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12040792

Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas and Paired Normal Mucosae Reveals Cyclin D1 Deregulation and Compensatory Effect of Cyclin D2
Cited by: 7
Author(s): Jiří Novotný, Veronika Bandúrová, Hynek Strnad, Martin Chovanec, Miluše Hradilová, Jana Šáchová, Martin Šteffl, Josipa Grušanović, Roman Kodet, Václav Pačes, Lukáš Lacina, Karel Smetana, Jan Plzák, Michal Kolář, Tomáš Vomastek
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers13051097

Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer
Cited by: 10
Author(s): Martina K. Zowada, Stephan M. Tirier, Sebastian M. Dieter, Teresa G Krieger, Ava Oberlack, Robert Lorenz Chua, Mario Huerta, Foo Wei Ten, Karin Laaber, Jeongbin Park, Katharina Jechow, Torsten Müller, Mathias Kalxdorf, Mark Kriegsmann, Katharina Kriegsmann, Friederike Herbst, Jeroen Krijgsveld, Martin Schneider, Roland Eils, Hanno Glimm, Christian Conrad, Claudia R. Ball
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2020.09.062

M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained Immunity
Cited by: 126
Author(s): Nargis Khan, Jeffrey Downey, Joaquín Sanz, Eva Kaufmann, Birte Blankenhaus, Alain Pacis, Erwan Pernet, Eisha Ahmed, Sílvia Cardoso, Anastasia Nijnik, Bruce Mazer, Christopher M. Sassetti, Marcel A. Behr, Miguel P. Soares, Luis B. Barreiro, Maziar Divangahi
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: over 7 years ago

10.1016/j.cels.2021.05.005

A time-resolved proteomic and prognostic map of COVID-19
Cited by: 106
Author(s): Vadim Demichev, Pinkus Tober‐Lau, Oliver Lemke, Tatiana Nazarenko, Charlotte Thibeault, Harry J. Whitwell, Annika Röhl, Anja Freiwald, Łukasz Szyrwiel, Daniela Ludwig, Clara Correia‐Melo, Simran Kaur Aulakh, Elisa T Helbig, Paula Stubbemann, Lena J Lippert, Nana‐Maria Grüning, Oleg Blyuss, Spyros Vernardis, Matthew White, Christoph B. Messner, Michael Joannidis, Thomas Sonnweber, Sebastian Klein, Alex Pizzini, Yvonne Wohlfarter, Sabina Sahanic, Richard Hilbe, Benedikt Schaefer, Sonja Wagner, Mirja Mittermaier, Felix Machleidt, Carmen García, Christoph Ruwwe‐Glösenkamp, Tilman Lingscheid, Laure Bosquillon de Jarcy, Miriam Stegemann, Moritz Pfeiffer, Linda Jürgens, Sophy Denker, Daniel Zickler, Philipp Enghard, Aleksej Zelezniak, Archie Campbell, Caroline Hayward, David J. Porteous, Riccardo E. Marioni, Alexander Uhrig, Holger Müller-Redetzky, Heinz Zoller, Judith Löffler‐Ragg
Software Mentions: 5
Published: about 5 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: about 6 years ago

10.1186/s41016-021-00235-3

The increasing expression of GPX7 related to the malignant clinical features leading to poor prognosis of glioma patients
Cited by: 5
Author(s): Jiawei Yao, Xin Chen, Zhendong Liu, Ruotian Zhang, Cheng Zhang, Quan Yang, Penglei Yao, Qiuyi Jiang, Jianing Wu, Shen Zhao
Software Mentions: 5
Published: over 5 years ago

10.1186/s13148-016-0266-6

DNA methylation and smoking in Korean adults: epigenome-wide association study
Cited by: 48
Author(s): Mi Kyeong Lee, Yoonki Hong, Sun‐Young Kim, Stephanie J. London, Woo Jin Kim
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13148-018-0580-2

Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis
Cited by: 26
Author(s): Youdinghuan Chen, David A. Armstrong, Lucas A. Salas, Haley F. Hazlett, Amanda B. Nymon, John A. Dessaint, Daniel Aridgides, Diane Mellinger, Xiaoying Li, Brock C. Christensen, Alix Ashare
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13148-019-0769-z

DNA methylation associated with postpartum depressive symptoms overlaps findings from a genome-wide association meta-analysis of depression
Cited by: 6
Author(s): Dana M. Lapato, Roxann Roberson‐Nay, Robert M. Kirkpatrick, Bradley T. Webb, Timothy P. York, Patricia A. Kinser
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13148-021-01149-8

Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer
Cited by: 7
Author(s): Javier Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban‐Rodríguez, María Dolores Diestro, Javier Benı́tez, Fátima Sánchez-Cabo, Rafael Álvarez, Javier de Castro
Software Mentions: 5
Published: about 5 years ago

10.1186/s13148-021-01083-9

Estimands in epigenome-wide association studies
Cited by: 9
Author(s): Jochen Kruppa, Miriam Sieg, Gregor Richter, Anne Pohrt
Software Mentions: 5
Published: over 5 years ago

10.1186/s13148-019-0637-x

Association of leukocyte DNA methylation changes with dietary folate and alcohol intake in the EPIC study
Cited by: 20
Author(s): Flavie Perrier, Vivian Viallon, Srikant Ambatipudi, Akram Ghantous, Cyrille Cuenin, Héctor Hernández-Vargas, Véronique Chajès, Laura Baglietto, Marco Matejcic, Hortensia Moreno-Macías, Tilman Kühn, Heiner Boeing, Anna Karakatsani, Αναστασία Κοτανίδου, Antonia Trichopoulou, Sabina Sieri, Salvatore Panico, Francesca Fasanelli, Martijn E.T. Dollé, N. Charlotte Onland‐Moret, Ivonne Sluijs, Elisabete Weiderpass, J. Ramón Quiŕos, Antonio Agudo, José María Huerta, Eva Ardanaz, Miren Dorronsoro, Tammy Y.N. Tong, Konstantinos K. Tsilidis, Elio Riboli, Marc J. Gunter, Zdenko Herceg, Pietro Ferrari, Isabelle Romieu
Software Mentions: 5
Published: over 7 years ago

10.1093/femsyr/foab011

Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production
Cited by: 2
Author(s): Leonie Baumann, Tyler W. Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Software Mentions: 5
Published: over 5 years ago

10.3389/fnagi.2021.686066

Significant Difference of Immune Cell Fractions and Their Correlations With Differential Expression Genes in Parkinson’s Disease
Cited by: 13
Author(s): Yilin Huang, Huisheng Liu, Jiaqi Hu, Chongyin Han, Zhenggang Zhong, Wei Luo, Yuhu Zhang, Fei Ling
Software Mentions: 5
Published: about 5 years ago

10.3389/fcvm.2021.631650

Integrated DNA Methylation and Gene Expression Analysis Identified S100A8 and S100A9 in the Pathogenesis of Obesity
Cited by: 7
Author(s): Ningyuan Chen, Miao Liu, Wei Lin, Donghua Zou, Ling Huang, Jian Huang, Wei Shi, Li-Lin Li, Yu-Xing Luo, Hao Liang, Shang‐Ling Pan, Junhua Peng
Software Mentions: 5
Published: over 5 years ago

10.3389/fcvm.2021.663509

Development and Validation of a Random Forest Diagnostic Model of Acute Myocardial Infarction Based on Ferroptosis-Related Genes in Circulating Endothelial Cells
Cited by: 14
Author(s): Yifan Chen, Jianfeng Shi, Jun Pu
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2021.723103

A Calcium-Related Immune Signature in Prognosis Prediction of Patients With Glioma
Cited by: 1
Author(s): Cha Lin, Jian Chen, Zhaoying Su, Pei Liu, Zheyu Liu, Chenchen Zhu, Dakang Xu, Lin Zhang, Xu Pei, Ganqiang Liu, Xinjian Liu
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.690542

Predicting Panel of Metabolism and Immune-Related Genes for the Prognosis of Human Ovarian Cancer
Cited by: 7
Author(s): Lingyun Zhang, Wenwen Sun, Weimin Ren, Jinguo Zhang, Guoxiong Xu
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2020.00552

Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1
Cited by: 15
Author(s): Wee Siang Teo, Holly Holliday, N. Karthikeyan, Aurélie Cazet, Daniel Roden, Kate Harvey, Christina Valbirk Konrad, Reshma Murali, Binitha Anu Varghese, Archana P. Thankamony, Chia-Ling Chan, Andrea McFarland, Simon Junankar, Sunny Ye, Jessica Yang, Iva Nikolić, Jaynish S. Shah, Laura A. Baker, Ewan K.A. Millar, Matthew J. Naylor, Christopher J. Ormandy, Sunil R. Lakhani, Warren Kaplan, Albert S. Mellick, Sandra A. O’Toole, Alexander Swarbrick, Radhika Nair
Software Mentions: 5
Published: about 6 years ago

10.3389/fcell.2020.588041

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy
Cited by: 3
Author(s): Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.570336

A Novel Immune-Related Prognostic Signature in Head and Neck Squamous Cell Carcinoma
Cited by: 10
Author(s): Yi Zhang, Ping Chen, Qiang Zhou, Hongyan Wang, Qingquan Hua, Jie Wang, Hongliang Zhong
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.672674

Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer
Cited by: 10
Author(s): Jianfeng Zheng, Jialu Guo, Huizhi Zhang, Benben Cao, XU Guomin, Zhifen Zhang, Jinyi Tong
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.670746

P2RY14 Is a Potential Biomarker of Tumor Microenvironment Immunomodulation and Favorable Prognosis in Patients With Head and Neck Cancer
Cited by: 8
Author(s): Qingxiang Li, Le Xu, Yuke Li, Rong Yang, Qiao Qiao, Yifei Wang, Lin Wang, Yuxing Guo, Chuanbin Guo
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.00863

N6-Methyladenosine RNA Methylation Regulators Have Clinical Prognostic Values in Hepatocellular Carcinoma
Cited by: 4
Author(s): Wei Liu, Cuiqing Zhong, Deguan Lv, Mengjie Tang, Feng Xie
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2021.617133

Weighted Correlation Gene Network Analysis Reveals New Potential Mechanisms and Biomarkers in Non-obstructive Azoospermia
Cited by: 10
Author(s): Meng Dong, Hao Li, Xue Zhang, Jichun Tan
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.00505

Analysis of Circular RNA-Related Competing Endogenous RNA Identifies the Immune-Related Risk Signature for Colorectal Cancer
Cited by: 16
Author(s): Wei Song, Jun Ren, Chuntao Wang, Yuhang Ge, Tao Fu
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2020.595361

Identification of Hub Prognosis-Associated Oxidative Stress Genes in Pancreatic Cancer Using Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Xin Qiu, Qin-Han Hou, Qiuyue Shi, Haixing Jiang, Shanyu Qin
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.653209

Exploring the Imbalance of Periodontitis Immune System From the Cellular to Molecular Level
Cited by: 11
Author(s): Long-Fei He, Lijuan Liu, Ti Li, Deshu Zhuang, Jiayin Dai, Bo Wang, Liangjia Bi
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.707713

Identification of Candidate Blood mRNA Biomarkers in Intracerebral Hemorrhage Using Integrated Microarray and Weighted Gene Co-expression Network Analysis
Cited by: 3
Author(s): Feng Jin, Lei Li, Yuehan Hao, Ling Tang, Yuye Wang, Zhiyi He
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2015.00169

Identifying differential transcription factor binding in ChIP-seq
Cited by: 21
Author(s): Dai-Ying Wu, Danielle Bittencourt, Michael R. Stallcup, Kimberly D. Siegmund
Software Mentions: 5
Published: over 11 years ago

10.3389/fgene.2021.707299

Esophageal Cancer Associated Immune Genes as Biomarkers for Predicting Outcome in Upper Gastrointestinal Tumors
Cited by: 9
Author(s): Chuanhui Zhu, Qianqian Xia, Bin Gu, Mengjing Cui, Xing Zhang, Wenjing Yan, Dan Meng, Siyuan Shen, Shuqian Xie, Xueliang Li, Hua Jin, Shizhi Wang
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.722803

Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets
Cited by: 9
Author(s): Yong Liu, Shengnan Cui, Jiayi Sun, Xin Yan, Dongran Han
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.579709

Potential of Immune-Related Genes as Biomarkers for Diagnosis and Subtype Classification of Preeclampsia
Cited by: 8
Author(s): Ying Wang, Zhen Li, Guanhua Song, Jun Wang
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.622683

Bioinformatics Analysis Identifies Molecular Markers Regulating Development and Progression of Endometriosis and Potential Therapeutic Drugs
Cited by: 7
Author(s): Ying Peng, Cheng Peng, Fang Zheng, Gang Chen
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.619821

Comprehensive Profiling Reveals Distinct Microenvironment and Metabolism Characterization of Lung Adenocarcinoma
Cited by: 3
Author(s): Li Chang, Chen Tian, Yangyang Liu, Jinyan Liang, Yue Zeng, Qifan Yang, Yuting Liu, Di Wu, Jingjing Wu, Juanjuan Wang, Kai Zhang, Fei Gu, Yue Hu, Li Liu
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2019.01716

Enhanced Immunomodulation in Inflammatory Environments Favors Human Cardiac Mesenchymal Stromal-Like Cells for Allogeneic Cell Therapies
Cited by: 3
Author(s): Falk Diedrichs, Meaghan Stolk, Karsten Jürchott, Marion Haag, Michael Sittinger, Martina Seifert
Software Mentions: 5
Published: about 7 years ago

10.3389/fimmu.2019.01629

Sonic Hedgehog Is a Determinant of γδ T-Cell Differentiation in the Thymus
Cited by: 12
Author(s): Konstantinos Mengrelis, Ching‐In Lau, Jasmine Rowell, Anisha Solanki, S. Norris, Scott R. Ross, M. Ono, Susan V. Outram, Tessa Crompton
Software Mentions: 5
Published: about 7 years ago

10.3389/fimmu.2018.02406

Molecular Signature of Aluminum Hydroxide Adjuvant in Ovine PBMCs by Integrated mRNA and microRNA Transcriptome Sequencing
Cited by: 15
Author(s): Endika Varela-Martínez, Naiara Abendaño, Javier Asín, Maialen Sistiaga-Poveda, Marta Pérez, Ramsés Reina, D. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 5
Published: almost 8 years ago

10.3389/fmed.2021.637885

Acid pH Increases SARS-CoV-2 Infection and the Risk of Death by COVID-19
Cited by: 19
Author(s): Leandro Jimenez, Ana Campos Codo, Vanderson de Souza Sampaio, Antônio Edson Rocha Oliveira, Lucas Kaoru Kobo Ferreira, Gustavo Gastão Davanzo, Lauar de Brito Monteiro, João Victor Virgílio-da-Silva, Mayla Gabriela Silva Borba, Gabriela Fabiano de Souza, Nathalia Zini, F Gandolfi, Stéfanie Primon Muraro, José Luiz Proença-Módena, Fernando Almeida Val, Gisely Cardoso de Melo, Wuelton Marcelo Monteiro, Maurício Lacerda Nogueira, Marcus Vinícius Guimarães Lacerda, Pedro M. Moraes‐Vieira, Helder I. Nakaya
Software Mentions: 5
Published: about 5 years ago

10.3389/fphar.2020.577150

Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer
Cited by: 4
Author(s): Shengnan Bao, Yi Chen, Fan Yang, Chunxiao Sun, Mingli Yang, Li Wei, Xiang Huang, Jun Li, Hao Wu, Yongmei Yin
Software Mentions: 5
Published: about 6 years ago

10.3389/fpls.2018.01256

Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicagotruncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms
Cited by: 14
Author(s): Kai Battenberg, Daniel Potter, Christine A. Tabuloc, Joanna C. Chiu, Alison M. Berry
Software Mentions: 5
Published: almost 8 years ago

10.3389/fpls.2017.00367

Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding
Cited by: 14
Author(s): Jan Ištvánek, Jana Dluhošová, Petr Dluhoš, Lenka Pátková, J. Nedĕlník, Jana Řepková
Software Mentions: 5
Published: over 9 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 7 years ago

10.1534/g3.113.007849

Opposing Activities of DRM and MES-4 Tune Gene Expression and X-Chromosome Repression in<i>Caenorhabditis elegans</i>Germ Cells
Cited by: 8
Author(s): Tomoko M. Tabuchi, Andreas Rechtsteiner, Susan Strome, Kirsten Hagstrom
Software Mentions: 5
Published: over 12 years ago

10.1186/s13059-018-1490-5

A comparative study of endoderm differentiation in humans and chimpanzees
Cited by: 31
Author(s): Lauren E. Blake, Samantha M. Thomas, John Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad, Bryan J. Pavlovic
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13059-019-1674-7

Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list
Cited by: 38
Author(s): Paul F. Harrison, Andrew Pattison, David Powell, Traude H. Beilharz
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-019-1764-6

BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
Cited by: 94
Author(s): Tongxin Wang, Travis Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang, Kun Huang
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-019-1878-x

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
Cited by: 24
Author(s): Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A.C. ’t Hoen, B.T. Heijmans, Joyce B. J. van Meurs
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-020-01960-1

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons
Cited by: 35
Author(s): Peipei Li, Elizabeth Ensink, Sean Lang, Lee Marshall, Meghan Schilthuis, Jared Lamp, Irving E. Vega, Viviane Labrie
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-020-02050-y

Dynamic rewiring of the human interactome by interferon signaling
Cited by: 21
Author(s): Craig H. Kerr, Michael A. Skinnider, Daniel D. T. Andrews, Angel M. Madero, Queenie Chan, R. Greg Stacey, Nikolay Stoynov, Eric Jan, Leonard J. Foster
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-021-02334-x

The impact of cell type and context-dependent regulatory variants on human immune traits
Cited by: 27
Author(s): Zepeng Mu, Wei Wei, Benjamin Jung Fair, Jinlin Miao, Ping Zhu, Yang Li
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02401-3

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
Cited by: 18
Author(s): Enrique Zozaya‐Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson, Sarah‐Jane Dawson
Software Mentions: 5
Published: about 5 years ago

10.1186/gm377

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
Cited by: 47
Author(s): Pär G. Engström, Diva Tommei, Stefan H. Stricker, Christine Ender, Steven M. Pollard, Paul Bertone
Software Mentions: 5
Published: over 14 years ago

10.1186/gm500

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy
Cited by: 105
Author(s): Mark N Cruickshank, Alicia Oshlack, Christiane Theda, Peter G Davis, David Martino, Penelope M. Sheehan, Yun Dai, Richard Saffery, Lex W. Doyle, Jeffrey M Craig
Software Mentions: 5
Published: over 13 years ago

10.1186/s13073-016-0315-y

The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p
Cited by: 34
Author(s): Zsolt Czimmerer, Tamás Varga, Máté Kiss, Cesaré Ovando Vázquez, Quang Minh Doan‐Xuan, Dominik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna Nagy, Bence Dániel, Szilárd Póliska, Attila Horváth, Gergely Nagy, Éva Várallyay, Matthew N. Poy, Judith E. Allen, Zsolt Bacsó, Cei Abreu‐Goodger, László Nagy
Software Mentions: 5
Published: over 10 years ago

10.1186/s13073-016-0319-7

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer
Cited by: 20
Author(s): Safiye Çelik, Benjamin A. Logsdon, Stephanie L. Battle, Charles W. Drescher, Mara H. Rendi, R. David Hawkins, Su-In Lee
Software Mentions: 5
Published: over 10 years ago

10.1186/s13073-017-0432-2

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
Cited by: 33
Author(s): Leif Väremo, Tora Ida Henriksen, Camilla Schéele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
Software Mentions: 5
Published: over 9 years ago

10.1186/s13073-020-00779-6

Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci
Cited by: 24
Author(s): Tianlu Li, Lourdes Ortiz-Fernández, Eduardo Andrés-León, Laura Ciudad, Biola M. Javierre, Elena López‐Isac, Alfredo Guillén‐Del‐Castillo, Carmen Pilar Simeón-Aznar, Esteban Ballestar, Javier Martín
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13073-021-00924-9

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Cited by: 8
Author(s): Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander, Micah T. McClain
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-021-00956-1

De novo transcriptomic subtyping of colorectal cancer liver metastases in the context of tumor heterogeneity
Cited by: 8
Author(s): Seyed H. Moosavi, Peter W. Eide, Ina A. Eilertsen, Tuva H. Brunsell, Kaja Christine Graue Berg, Bård I. Røsok, Kristoffer Watten Brudvik, Bjørn Atle Bjørnbeth, Marianne Grønlie Guren, Arild Nesbakken, Ragnhild A. Lothe, Anita Sveen
Software Mentions: 5
Published: about 5 years ago

10.1002/glia.23615

Genetic control of cellular morphogenesis in Müller glia
Cited by: 18
Author(s): Mark Charlton‐Perkins, Alexandra D. Almeida, R. Macdonald, William A. Harris
Software Mentions: 5
Published: over 7 years ago

10.1186/s41065-021-00181-1

Prognostic biomarkers and therapeutic targets in oral squamous cell carcinoma: a study based on cross-database analysis
Cited by: 10
Author(s): Wanli Yang, Wei Zhou, Xinhui Zhao, Xiaoqian Wang, Lili Duan, Yiding Li, Liaoran Niu, Junfeng Chen, Yujie Zhang, Yu Han, Daiming Fan, Liu Hong
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.ppat.1008477

Immunosuppressive FK506 treatment leads to more frequent EBV-associated lymphoproliferative disease in humanized mice
Cited by: 15
Author(s): Nicole Caduff, Donal McHugh, Anita Murer, Patrick C. Rämer, Ana Raykova, Vanessa Landtwing, Lisa Rieble, Christian W. Keller, Michael Prummer, Laurent Hoffmann, Janice K. P. Lam, Aks Chiang, Friedrich Raulf, Tarik Azzi, Christoph Berger, Tina Rubic-Schneider, Elisabetta Traggiai, Jan D. Lünemann, Michael Kammüller, Christian Münz
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1008869

Macrophage maturation from blood monocytes is altered in people with HIV, and is linked to serum lipid profiles and activation indices: A model for studying atherogenic mechanisms
Cited by: 16
Author(s): Emily Bowman, Cheryl M. Cameron, Brian Richardson, Milind V. Kulkarni, Janelle Gabriel, Morgan J. Cichon, Ken M. Riedl, Yousef Mustafa, Michael Cartwright, Brandon Snyder, Subha V. Raman, David A. Zidar, Susan L. Koletar, Martin P. Playford, Nehal N. Mehta, Scott F. Sieg, Michael L. Freeman, Michael M. Lederman, Mark J. Cameron, Nicholas T. Funderburg
Software Mentions: 5
Published: almost 6 years ago

10.1155/2020/6937475

A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma
Cited by: 18
Author(s): Yingkun Xu, Xiunan Li, Yaling Han, Zilong Wang, Chenglin Han, Ningke Ruan, Jianyi Li, Xiao Yu, Qinghua Xia, Guangzhen Wu
Software Mentions: 5
Published: almost 6 years ago

10.1073/pnas.1822046116

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: about 7 years ago

10.3390/proteomes8030015

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
Cited by: 9
Author(s): Subina Mehta, Caleb Easterly, Ray Sajulga, Robert Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 5
Published: about 6 years ago

10.1186/s12931-019-1085-z

Airway host-microbiome interactions in chronic obstructive pulmonary disease
Cited by: 82
Author(s): Zhang Wang, Barbara Maschera, Simon Lea, Umme Kolsum, David Michalovich, Stephanie Van Horn, Christopher Traini, James R. Brown, Edith M. Hessel, Dave Singh
Software Mentions: 5
Published: over 7 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: about 8 years ago

10.1038/s41597-020-0527-2

Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain
Cited by: 6
Author(s): Kimberly A. Aldinger, Andrew E. Timms, James W. MacDonald, Hanna K. McNamara, Jennifer Herstein, Theo K. Bammler, Oleg V. Evgrafov, James A. Knowles, Pat Levitt
Software Mentions: 5
Published: over 6 years ago