10.3389/fmicb.2019.01843

Stable Redox-Cycling Nitroxide Tempol Has Antifungal and Immune-Modulatory Properties
Cited by: 4
Author(s): Ava Hosseinzadeh, Marinos Stylianou, José Pedro Lopes, Daniel Curvello de Mendonça Müller, André Häggman, Sandra Holmberg, Christian Grumaz, Anders Johansson, Kai Sohn, Christoph Dieterich, Constantin F. Urban
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pcbi.1007241

Unified feature association networks through integration of transcriptomic and proteomic data
Cited by: 6
Author(s): Ryan McClure, Jason P. Wendler, Joshua N. Adkins, Jesica Swanstrom, Ralph S. Baric, Brooke L. Deatherage Kaiser, Kristie Oxford, Katrina M. Waters, Jason McDermott
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pcbi.1005680

Interactions between the tumor and the blood systemic response of breast cancer patients
Cited by: 21
Author(s): Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjøsne, Jan Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael Hallett
Software Mentions: 3
Published: almost 9 years ago

10.3389/fphys.2020.565240

Identification of Pathways and Key Genes in Venous Remodeling After Arteriovenous Fistula by Bioinformatics Analysis
Cited by: 10
Author(s): Jie Kong, Zhen Wang, Bin Zhao, Maofeng Gong, Jianbin Zhang, Zhaoxuan Lu, Yangyi Zhou, Changhong Liang, Haobo Su, Wensheng Lou, Guoping Chen, Jianping Gu, Xu He, Jianyan Wen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0211430

Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics
Cited by: 36
Author(s): Anastasia H. Potts, Yinping Guo, Brian M. M. Ahmer, Tony Romeo
Software Mentions: 3
Published: over 7 years ago

10.1242/dmm.010975

Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice
Cited by: 105
Author(s): Benjamin I. Laufer, Katarzyna Mantha, Morgan L. Kleiber, Eric J. Diehl, Sean M. F. Addison, Shiva M. Singh
Software Mentions: 3
Published: over 13 years ago

10.3389/fmicb.2021.650567

The Evaluation and Validation of Blood-Derived Novel Biomarkers for Precise and Rapid Diagnosis of Tuberculosis in Areas With High-TB Burden
Cited by: 6
Author(s): Zhen Gong, Yinzhong Gu, Kunlong Xiong, Jinxia Niu, Ruijuan Zheng, Bo Su, Lin Fan, Jingwei Xie
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-020-0693-2

Potential role of genomic imprinted genes and brain developmental related genes in autism
Cited by: 8
Author(s): Jian Li, Xue Lü, Mingya Wang, Yunyun Hu, Kaiyu Xue, Shuanglin Gu, Lili Lv, Saijun Huang, Wei Xie
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.01757

PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin
Cited by: 63
Author(s): Patrick L. Apopa, Lisa Alley, Rosalind B. Penney, Konstantinos Arnaoutakis, Matthew A. Steliga, Susan Jeffus, Emine Bircan, Banu Gopalan, Jing Jin, Preecha Patumcharoenpol, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nishi Shah, Gunnar Boysen, David W. Ussery, Intawat Nookaew, Pebbles Fagan, Gürkan Bebek, Mohammed S. Orloff
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-018-2107-4

Watchdog – a workflow management system for the distributed analysis of large-scale experimental data
Cited by: 20
Author(s): Michael Kluge, Caroline C. Friedel
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.6678

Genetic deletion of osteopontin in TRAMP mice skews prostate carcinogenesis from adenocarcinoma to aggressive human-like neuroendocrine cancers
Cited by: 8
Author(s): Giorgio Mauri, Elena Jachetti, Barbara Comuzzi, Matteo Dugo, Ivano Arioli, Silvia Miotti, Sabina Sangaletti, Emma Di Carlo, Claudio Tripodo, Mario P. Colombo
Software Mentions: 3
Published: over 10 years ago

10.18632/aging.101738

A four-methylated mRNA signature-based risk score system predicts survival in patients with hepatocellular carcinoma
Cited by: 28
Author(s): Yu Wang, Zhiping Ruan, Sizhe Yu, Tao Tian, Xuan Liu, Jing Li, Wenyuan Li, Xiao Wang, Luochengling Xiang, François X. Claret, Nan Kang, Hui Guo
Software Mentions: 3
Published: over 7 years ago

10.1186/s12885-020-06719-2

Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval
Cited by: 2
Author(s): Yun-Yu Sun, Lishan Wang, Changkuan Li, Rui Gu, Weidong Zang, Wei Song, Peng Xia
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1007485

Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level
Cited by: 38
Author(s): Simon Mathis Kønig, Vendela Rissler, Thilde Terkelsen, Matteo Lambrughi, Elena Papaleo
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0177442

Analysis of global DNA methylation changes in primary human fibroblasts in the early phase following X-ray irradiation
Cited by: 20
Author(s): Anna Maierhofer, Julia Flunkert, Marcus Dittrich, Tobias Müller, Detlev Schindler, Indrajit Nanda, Thomas Haaf
Software Mentions: 3
Published: over 9 years ago

10.1155/2021/8849977

A Risk Signature with Autophagy-Related Long Noncoding RNAs for Predicting the Prognosis of Clear Cell Renal Cell Carcinoma: Based on the TCGA Database and Bioinformatics
Cited by: 14
Author(s): Yundong Xuan, Wei-Hao Chen, Kan Liu, Yu Tang Gao, Shidong Zuo, Baojun Wang, Xin Ma, Xu Zhang
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.00163

Synthesis, Regulation and Degradation of Carotenoids Under Low Level UV-B Radiation in the Filamentous Cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 26
Author(s): Carole A. Llewellyn, Ruth L. Airs, Garry Farnham, Carolyn Greig
Software Mentions: 3
Published: over 6 years ago

10.1155/2021/8839747

A 5-lncRNA Signature Associated with Smoking Predicts the Overall Survival of Patients with Muscle-Invasive Bladder Cancer
Cited by: 2
Author(s): Haoyue Sheng, Guiming Zhang, Yao Qi Huang, Lili Sun, Guohai Shi, Dingwei Ye
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/8886897

Integrated Analysis of lncRNA-Associated ceRNA Network Identifies Two lncRNA Signatures as a Prognostic Biomarker in Gastric Cancer
Cited by: 7
Author(s): Shuyan Zhang, Shanshan Li, Jiuxin Guo, Ningyi Li, Caining Zhang, Jie Liu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fnins.2018.00742

Transcriptomic Characterization of the Human Habenula Highlights Drug Metabolism and the Neuroimmune System
Cited by: 22
Author(s): Bernard Le Foll, Leon French
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1008263

A transcriptome-based classifier to determine molecular subtypes in medulloblastoma
Cited by: 5
Author(s): Komal S. Rathi, Sherjeel Arif, Mateusz Koptyra, Ammar S. Naqvi, Deanne Taylor, Phillip B. Storm, Adam Resnick, Jo Lynne Rokita, Pichai Raman
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2017.02306

Antibiotic-Induced Alterations in Gut Microbiota Are Associated with Changes in Glucose Metabolism in Healthy Mice
Cited by: 89
Author(s): Richard R. Rodrigues, Renee Greer, Xiaoxi Dong, Karen D’Souza, Manoj Gurung, Jia Wu, Andrey Morgun, Natalia Shulzhenko
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.cell.2021.07.038

Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations
Cited by: 151
Author(s): Cindy G. Boer, Konstantinos Hatzikotoulas, Lorraine Southam, Lilja Stefánsdóttir, Yanfei Zhang, Rodrigo Coutinho de Almeida, Tian Wu, Jie Zheng, April Hartley, Maris Teder‐Laving, Anne Heidi Skogholt, Chikashi Terao, Eleni Zengini, G Alexiadis, Andrei Barysenka, Gyða Björnsdóttir, Maiken Elvestad Gabrielsen, Arthur Gilly, Þorvaldur Ingvarsson, Marianne Bakke Johnsen, Helgi Jónsson, Margreet Kloppenburg, Almut Luetge, Sigrún H. Lund, Reedik Mägi, Massimo Mangino, Rob R.G.H.H. Nelissen, Manu Shivakumar, Julia Steinberg, Hiroshi Takuwa, Laurent F. Thomas, Margo Tuerlings, Hunt All-In Pain, George C. Babis, Jason Pui Yin Cheung, Jae H. Kang, Peter Kraft, Steven A. Lietman, Dino Samartzis, P. Eline Slagboom, Kāri Stefánsson, Unnur Þorsteinsdóttir, Jonathan H Tobias, André G. Uitterlinden, Bendik S. Winsvold, John‐Anker Zwart, George Davey Smith, Pak C. Sham, Guðmar Þorleifsson, Tom R. Gaunt, Andrew P. Morris, Ana M. Valdes, Aspasia Tsezou, Kathryn S.E. Cheah, Shiro Ikegawa, Kristian Hveem, Tõnu Esko, J. Mark Wilkinson, Ingrid Meulenbelt, Ming Ta Michael Lee, Joyce B. J. van Meurs, Unnur Styrkársdóttir, Eleftheria Zeggini
Software Mentions: 3
Published: about 5 years ago

10.1534/g3.120.401477

Network Analysis Prioritizes <i>DEWAX</i> and <i>ICE1</i> as the Candidate Genes for Major eQTL Hotspots in Seed Germination of <i>Arabidopsis thaliana</i>
Cited by: 5
Author(s): Margi Hartanto, Ronny V.L. Joosen, L. Basten Snoek, Leo A.J. Willems, Mark G. Sterken, Dick de Ridder, Henk W. M. Hilhorst, Wilco Ligterink, Harm Nijveen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0041541

Identification of Pathway Deregulation – Gene Expression Based Analysis of Consistent Signal Transduction
Cited by: 16
Author(s): Jakub Mieczkowski, Karolina Swiatek-Machado, Bożena Kamińska
Software Mentions: 3
Published: about 14 years ago

10.18632/oncotarget.16252

Niclosamide is a potential therapeutic for familial adenomatosis polyposis by disrupting Axin-GSK3 interaction
Cited by: 26
Author(s): Ahn Sk, Nam Hee Kim, Kyungro Lee, Yong Hoon, Ji Hye Yang, So Young, Eunae Sandra Cho, Yoonmi Lee, Jeong Ho Seok, Hyun Soo Cho, Yongseok Jeon, Young Su Yuk, Suebean Cho, Kyoung Tai No, Hyun Sil Kim, Ho Lee, Jiwon Choi, Jong In Yook
Software Mentions: 3
Published: over 9 years ago

10.3389/fonc.2021.626748

PD-L2 Is Constitutively Expressed in Normal and Malignant Urothelium
Cited by: 6
Author(s): Alexander C. Dowell, Haydn Munford, Ankit Goel, Naheema S. Gordon, Nicholas D. James, Kar Keung Cheng, Maurice P. Zeegers, Douglas G. Ward, Richard T. Bryan
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0226212

NKL homeobox gene activities in normal and malignant myeloid cells
Cited by: 12
Author(s): Stefan Nagel, Michaela Scherr, Roderick A.F. MacLeod, Claudia Pommerenke, Max Koeppel, Corinna Meyer, Maren Kaufmann, Iris Dallmann, Hans Drexler
Software Mentions: 3
Published: almost 7 years ago

10.1155/2020/8867019

Development of an Autophagy Score Signature for Predicting Overall Survival in Papillary Renal Cell Carcinoma
Cited by: 2
Author(s): Xiang Gu, Xiaojun Chen, Lei Zhu, Wenbo Song, Ali Wang, Junfeng Chu, Tao Wang, Peng Jiang, Yuxiang Ge
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1004015

Dual Regulation of Gene Expression Mediated by Extended MAPK Activation and Salicylic Acid Contributes to Robust Innate Immunity in Arabidopsis thaliana
Cited by: 198
Author(s): Kazuhiko Tsuda, Akira Mine, Gerit Bethke, Daisuke Igarashi, Christopher Botanga, Yayoi Tsuda, Jane Glazebrook, Mitsuru Sato, Fumiaki Katagiri
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-020-58709-w

Nanocatalytic activity of clean-surfaced, faceted nanocrystalline gold enhances remyelination in animal models of multiple sclerosis
Cited by: 44
Author(s): Andrew P. Robinson, Joanne Zhongyan Zhang, Haley E. Titus, Molly Karl, Mikhail Merzliakov, Adam R. Dorfman, Stephen J. Karlik, Michael G. Stewart, Richard K. Watt, Benjin D. Facer, Jon D. Facer, Noah D. Christian, Karen S. Ho, Michael T. Hotchkin, Mark G. Mortenson, Robert H. Miller, Stephen D. Miller
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.01036

RNA-Seq Reveals Enhanced Sugar Metabolism in Streptococcus mutans Co-cultured with Candida albicans within Mixed-Species Biofilms
Cited by: 66
Author(s): Jinzhi He, Dongyeop Kim, Xuedong Zhou, Sang‐Joon Ahn, Robert A. Burne, Vincent P. Richards, Hyun Koo
Software Mentions: 3
Published: over 9 years ago

10.1186/s12920-021-00975-2

Identification and validation of signal recognition particle 14 as a prognostic biomarker predicting overall survival in patients with acute myeloid leukemia
Cited by: 3
Author(s): Lingling Shi, Rui Huang, Yongrong Lai
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-9-390

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Cited by: 100
Author(s): Alexandra B. Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán Leparc, Thomas Tüchler, David P. Kreil, Diethard Mattanovich
Software Mentions: 3
Published: about 18 years ago

10.3390/diagnostics10090689

The Prognostic Significance of Immune-Related Metabolic Enzyme MTHFD2 in Head and Neck Squamous Cell Carcinoma
Cited by: 7
Author(s): Li Cui, Huan Chen, Xinyuan Zhao
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2407-13-585

The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts
Cited by: 10
Author(s): Pratiti Bandopadhayay, Anissa Jabbour, Christopher D. Riffkin, Marika Salmanidis, Lavinia Gordon, Dean Popovski, Lin Rigby, David M. Ashley, D. Neil Watkins, David M. Thomas, Elizabeth Algar, Paul G. Ekert
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13000-014-0210-z

Unveiling transcription factor regulation and differential co-expression genes in Duchenne muscular dystrophy
Cited by: 7
Author(s): Lijun Tian, Junhua Cao, Xingqiang Deng, Chuanling Zhang, Tong Qian, Xianxiang Song, Baoshan Huang
Software Mentions: 3
Published: almost 12 years ago

10.3389/fmicb.2020.00476

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth
Cited by: 40
Author(s): Idit Kosti, Svetlana Lyalina, Katherine S. Pollard, Atul J. Butte, Marina Sirota
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1001027

Reconstruction of the Core and Extended Regulons of Global Transcription Factors
Cited by: 65
Author(s): Y. Dufour, Patricia J. Kiley, Timothy J. Donohue
Software Mentions: 3
Published: about 16 years ago

10.7554/eLife.65331

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast
Cited by: 2
Author(s): Rachael Emily Turner, Paul F. Harrison, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Belinda J. Goldie, Michael See, Amanda L. Peterson, Ralf B. Schittenhelm, David Powell, Darren J. Creek, Bernhard Dichtl, Traude H. Beilharz
Software Mentions: 3
Published: about 5 years ago

10.1186/s12967-020-02366-0

Development and validation of a hypoxia-immune-based microenvironment gene signature for risk stratification in gastric cancer
Cited by: 59
Author(s): Yifan Liu, Jianhua Wu, Weiwei Huang, Shao‐Wen Weng, Baochun Wang, Yiming Chen, Hao Wang
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-62076-x

Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism
Cited by: 61
Author(s): Nathan J. Schauer, Xiaoxi Liu, Robert S. Magin, Laura M. Doherty, Wai Cheung Chan, Scott B. Ficarro, Wanyi Hu, Rebekka M. Roberts, Roxana E. Iacob, Björn Stolte, Andrew O. Giacomelli, Sumner Perera, Kyle T. McKay, Sarah A. Boswell, Ellen Weisberg, Arghya Ray, Dharminder Chauhan, Sirano Dhe‐Paganon, KS Anderson, James D. Griffin, Jianing Li, William C. Hahn, Peter K. Sorger, John R. Engen, Kimberly Stegmaier, Jarrod A. Marto, Sara J. Buhrlage
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-852

Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models
Cited by: 10
Author(s): Sophie Rodius, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Céline Jeanty, Juan Manuel González‐Rosa, Mark Ibberson, Ricardo Costa, Ioannis Xénarios, Nadia Mercader, Francisco Azuaje
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-020-68437-w

Injection of seminal fluid into the hemocoel of honey bee queens (Apis mellifera) can stimulate post-mating changes
Cited by: 9
Author(s): W. Cameron Jasper, Laura M. Brutscher, Christina M. Grozinger, Elina L. Niño
Software Mentions: 3
Published: about 6 years ago

10.1186/s12916-021-01917-6

Serum transferrin as a biomarker of hepatocyte nuclear factor 4 alpha activity and hepatocyte function in liver diseases
Cited by: 6
Author(s): Nurdan Güldiken, Josepmaría Argemi, Berivan Gurbuz, Stephen R. Atkinson, Martin Oliverius, Petr Fila, Karim Hamesch, Tony Bruns, Joaquín Cabezas, Juan José Lozano, Jelena Mann, Sheng Cao, Philippe Maury, Vijay H. Shah, Christian Trautwein, Mark Thursz, R. Bataller, Pavel Strnad
Software Mentions: 3
Published: over 5 years ago

10.1186/s13073-019-0674-2

Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis
Cited by: 52
Author(s): Clara Lorente-Sorolla, Antonio García-Gómez, Francesc Català-Moll, Víctor Toledano, Laura Ciudad, José Avendaño-Ortíz, Charbel Maroun Eid, Alejandro Martín-Quirós, Mónica Martínez-Gallo, Adolfo Ruiz-Sanmartín, Álvaro García del Campo, Ricard Ferrer, Juan Carlos Ruiz‐Rodríguez, Damiana Álvarez-Errico, Eduardo López-Collazo, Esteban Ballestar
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-86230-1

Ionizing radiation exposure of stem cell-derived chondrocytes affects their gene and microRNA expression profiles and cytokine production
Cited by: 2
Author(s): Ewelina Stelcer, Katarzyna Kulcenty, Marcin Ruciński, Marta Kruszyna-Mochalska, A. Skrobała, Agnieszka Sobecka, Karol Jopek, Wiktoria Suchorska
Software Mentions: 3
Published: over 5 years ago

10.1186/s13073-018-0557-y

Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells
Cited by: 27
Author(s): Ksenia S. Anufrieva, Victoria О. Shender, Georgij Arapidi, Marat S. Pavlyukov, M. I. Shakhparonov, Polina V. Shnaider, Ivan Butenko, Maria A. Lagarkova, Vadim M. Govorun
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0181926

Whole blood microRNA expression may not be useful for screening non-small cell lung cancer
Cited by: 20
Author(s): Santosh K. Patnaik, Eric Kannisto, Reema Mallick, Anil Vachani, Sai Yendamuri
Software Mentions: 3
Published: about 9 years ago

10.1186/s12967-016-0886-9

Serum microRNA-1233 is a specific biomarker for diagnosing acute pulmonary embolism
Cited by: 33
Author(s): Thorsten Kessler, Jeanette Erdmann, Baiba Vilne, Petra Bruse, Volkhard Kurowski, Patrick Diemert, Heribert Schunkert, Hendrik B. Sager
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1003868

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
Cited by: 71
Author(s): Nicholas J. Croucher, Andrea M. Mitchell, Katherine A. Gould, Donald Inverarity, Lars Barquist, Theresa Feltwell, María Fookes, Simon R. Harris, Janina Dordel, Susannah J. Salter, Sarah Browall, Helena Žemličková, Julian Parkhill, Staffan Normark, Birgitta Henriques‐Normark, Jason Hinds, Tim Mitchell, Stephen D. Bentley
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pgen.1009446

Critical role of the BAF chromatin remodeling complex during murine neural crest development
Cited by: 13
Author(s): Kathleen Wung Bi-Lin, Pratap Veerabrahma Seshachalam, Tran Tuoc, Anastassia Stoykova, Sujoy Ghosh, Manvendra K. Singh
Software Mentions: 3
Published: over 5 years ago

10.1186/s13040-016-0122-4

Elevated transcriptional levels of aldolase A (ALDOA) associates with cell cycle-related genes in patients with NSCLC and several solid tumors
Cited by: 25
Author(s): Fan Zhang, Jiediao Lin, Xiaoyu Zuo, Yingping Zhuang, Chao‐Qun Hong, Guojun Zhang, Xiaojiang Cui, Yukun Cui
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2019.02709

Label-Free Proteomic Approach to Study the Non-lethal Effects of Silver Nanoparticles on a Gut Bacterium
Cited by: 4
Author(s): Guido Domingo, Federica Villa, Candida Vannini, Elisa Garuglieri, Elisabetta Onelli, Marcella Bracale, Francesca Cappitelli
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: over 8 years ago

10.3389/fnins.2012.00156

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs
Cited by: 13
Author(s): Sergei A. Manakov, Andrew Morton, Anton J. Enright, Seth G. N. Grant
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0112102

Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling
Cited by: 84
Author(s): W. Clay Spencer, Rebecca McWhirter, Tyne Miller, Pnina Strasbourger, Owen Thompson, LaDeana W. Hillier, Robert H. Waterston, David M. Miller
Software Mentions: 3
Published: almost 12 years ago

10.18632/aging.102365

Association of a novel seven-gene expression signature with the disease prognosis in colon cancer patients
Cited by: 21
Author(s): Haojie Yang, Lun Hua, Hong-Cheng Lin, Dan Gan, Wei Jin, Can Cui, Yixin Yan, Yiming Qian, Changpeng Han, Zhenyi Wang
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2020.01179

Analysis of Virus and Host Proteomes During Productive HSV-1 and VZV Infection in Human Epithelial Cells
Cited by: 14
Author(s): Werner J. D. Ouwendijk, Lennard J. M. Dekker, Henk-Jan van den Ham, Tihana Lenac Roviš, Erik Haefner, Stipan Jonjić, Jürgen Haas, Theo M. Luider, Georges M. G. M. Verjans
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.577530

GPR115 Contributes to Lung Adenocarcinoma Metastasis Associated With LAMC2 and Predicts a Poor Prognosis
Cited by: 13
Author(s): Yingjing Wang, Muqi Shi, Nan Yang, Xiaoyu Zhou, Liqin Xu
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13073-016-0310-3

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis
Cited by: 18
Author(s): Valeriya Malysheva, Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Hinrich Gronemeyer
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1006620

Mutations in mitochondrial DNA causing tubulointerstitial kidney disease
Cited by: 47
Author(s): Thomas M. Connor, Simon Hoer, Andrew Mallett, Daniel P. Gale, Aurora Gómez-Durán, Viktor Posse, Robin Antrobus, Pablo Moreno, Marco Sciacovelli, Christian Frezza, Jennifer Duff, Neil Sheerin, John A. Sayer, Margaret Ashcroft, Michael S. Wiesener, Gavin Hudson, Claes M. Gustafsson, Patrick F. Chinnery, Patrick H. Maxwell
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0006646

Genome-Wide mRNA Expression Analysis of Hepatic Adaptation to High-Fat Diets Reveals Switch from an Inflammatory to Steatotic Transcriptional Program
Cited by: 55
Author(s): Marijana Radonjić, Jorn R. de Haan, Marjan J. van Erk, Ko Willems van Dijk, Sjoerd A.A. van den Berg, Philip J. de Groot, Michael Müller, Ben van Ommen
Software Mentions: 3
Published: about 17 years ago

10.1242/dev.146910

In the fetal thymus, Gli3 in thymic epithelial cells promotes thymocyte positive selection and differentiation by repression of<i>Shh</i>
Cited by: 17
Author(s): Anisha Solanki, Diana C. Yánez, Scott R. Ross, Ching‐In Lau, Eleftheria Papaioannou, Jiawei Li, José Ignacio Saldaña, Tessa Crompton
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-018-2513-7

Capturing context-specific regulation in molecular interaction networks
Cited by: 5
Author(s): Stephen Rush, Dirk Repsilber
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1005969

Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators
Cited by: 49
Author(s): So Yeon Kwon, Valentina Grisan, Boyun Jang, John Herbert, Paul Badenhorst
Software Mentions: 3
Published: over 10 years ago

10.18632/aging.102943

Genetic networks in Parkinson’s and Alzheimer’s disease
Cited by: 23
Author(s): Jack Kelly, Rana Moyeed, Camille Carroll, Shouqing Luo, Xinzhong Li
Software Mentions: 3
Published: over 6 years ago

10.1523/ENEURO.0287-18.2018

Overweight Mice Show Coordinated Homeostatic and Hedonic Transcriptional Response across Brain
Cited by: 0
Author(s): Ilario De Toma, Ilona Grabowicz, Marta Fructuoso, Daniel Trujillano, Bartek Wilczyński, Mara Dierssen
Software Mentions: 3
Published: almost 8 years ago

10.1534/g3.112.004127

Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor
Cited by: 19
Author(s): Jeffrey A. Lewis, Audrey P. Gasch
Software Mentions: 3
Published: almost 14 years ago

10.1186/1471-2334-10-176

Tracking the transcriptional host response from the acute to the regenerative phase of experimental pneumococcal meningitis
Cited by: 16
Author(s): Matthias Wittwer, Denis Grandgirard, Janine Rohrbach, Stephen L. Leib
Software Mentions: 3
Published: over 16 years ago

10.1186/s12916-016-0617-3

Human newborn bacille Calmette–Guérin vaccination and risk of tuberculosis disease: a case-control study
Cited by: 47
Author(s): Helen A. Fletcher, Ali Filali‐Mouhim, Elisa Nemes, Anthony Hawkridge, Alana Keyser, Samuel Njikan, Mark Hatherill, Thomas J. Scriba, Brian Abel, Benjamin M. Kagina, Ashley Veldsman, Nancy Marín Agudelo, Gilla Kaplan, Gregory Hussey, Rafick‐Pierre Sékaly, Willem A. Hanekom
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0240250

Multicenter analysis of sputum microbiota in tuberculosis patients
Cited by: 7
Author(s): Claudia Sala, Andrej Benjak, Delia Goletti, Sayera Banu, Jesica Mazza-Stadler, Katia Jaton, Philippe Busso, Sille Remm, Marion Leleu, Jacques Rougemont, Fabrizio Palmieri, Gilda Cuzzi, Ornella Butera, Valentina Vanini, Shahjahan Kabir, S. M. Mazidur Rahman, Laurent Nicod, Stewart T. Cole
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1000574

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities
Cited by: 53
Author(s): So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst
Software Mentions: 3
Published: about 17 years ago

10.1080/21623945.2021.1910154

Cleavage of the vaspin N-terminus releases cell-penetrating peptides that affect early stages of adipogenesis and inhibit lipolysis in mature adipocytes
Cited by: 4
Author(s): Catherine A Tindall, Estelle Erkner, Jan Stichel, Annette G. Beck‐Sickinger, Anne Hoffmann, Juliane Weiner, John T. Heiker
Software Mentions: 3
Published: over 5 years ago

10.1016/j.bbrep.2015.08.012

Xanthophylls lutein and zeaxanthin modify gene expression and induce synthesis of hyaluronan in keratinocyte model of human skin
Cited by: 9
Author(s): Rasia Li, Stephen D. Turner, David L. Brautigan
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1006477

Gene Expression Differences in Prostate Cancers between Young and Old Men
Cited by: 26
Author(s): Yuan-Chun Ding, Huiqing Wu, Charles Warden, Linda Steele, Xueli Liu, Maarten van Iterson, Xiwei Wu, Rebecca A. Nelson, Zheng Liu, Yate-Ching Yuan, Susan L. Neuhausen
Software Mentions: 3
Published: over 9 years ago

10.3389/fpsyt.2021.628361

A Potential Autophagy-Related Competing Endogenous RNA Network and Corresponding Diagnostic Efficacy in Schizophrenia
Cited by: 12
Author(s): Rongjie Li, Qiaoye Wang, Yufen Qiu, Youshi Meng, Lei Wei, Hao Wang, Ruikang Mo, Donghua Zou, Chunbin Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-11-280

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
Cited by: 4
Author(s): Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panos Deloukas, Simon Tavaré
Software Mentions: 3
Published: over 16 years ago

10.1155/2019/6469420

Integrated Analysis of Oncogenic Networks in Colorectal Cancer Identifies GUCA2A as a Molecular Marker
Cited by: 24
Author(s): Hui Zhang, Yuanyuan Du, Zhuo Wang, Rui Lou, Jianzhong Wu, Jifeng Feng
Software Mentions: 3
Published: about 7 years ago

10.1155/2021/8357585

Comprehensive Analysis of CD163 as a Prognostic Biomarker and Associated with Immune Infiltration in Glioblastoma Multiforme
Cited by: 3
Author(s): Hao Li, Di Wang, Bolong Yi, Heng Cai, Zhuo Xi, Xin Lou, Zhen Li
Software Mentions: 3
Published: about 5 years ago

10.1155/2020/8571932

AHNAK2 Is Associated with Poor Prognosis and Cell Migration in Lung Adenocarcinoma
Cited by: 9
Author(s): Shusen Zhang, Yuanyuan Lu, Ling Qi, Hongyan Wang, Zhihua Wang, Zhigang Cai
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1008513

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1
Cited by: 34
Author(s): Zhejun Ji, Marianthi Kiparaki, Virginia Folgado, Amit Kumar, Jorge Polo Blanco, Gerard Rimesso, Jacky Chuen, Yang Liu, Deyou Zheng, Nicholas E. Baker
Software Mentions: 3
Published: almost 7 years ago

10.18632/aging.202958

Identification of a novel glycolysis-related gene signature for predicting the prognosis of osteosarcoma patients
Cited by: 16
Author(s): Mengkai Yang, Xiao‐Jun Ma, Zhuoying Wang, Tao Zhang, Yingqi Hua, Zhengdong Cai
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2407-14-64

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: over 12 years ago

10.7554/eLife.51406

Proteome profile of peripheral myelin in healthy mice and in a neuropathy model
Cited by: 52
Author(s): Sophie B Siems, Olaf Jahn, Maria A Eichel, Nirmal Kannaiyan, Lai Man Natalie Wu, Diane L. Sherman, Kathrin Kusch, Dörte Hesse, Ramona B. Jung, Robert Fledrich, Michael W. Sereda, Moritz J. Rossner, Peter Brophy, Hauke Werner
Software Mentions: 3
Published: over 6 years ago

10.1186/s13073-015-0227-2

Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritis
Cited by: 12
Author(s): Nan Du, Kaiyu Jiang, Ashley Sawle, Mark Barton Frank, Carol A. Wallace, Aidong Zhang, James N. Jarvis
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0006735

Identification of Genes Responsive to Solar Simulated UV Radiation in Human Monocyte-Derived Dendritic Cells
Cited by: 18
Author(s): Hortensia de la Fuente, Amalia Lamana, Marı́a Mittelbrunn, S. Pérez‐Gala, Salvador González, Amaro García‐Díez, Miguel A. Vega, Francisco Sánchez-Madrid
Software Mentions: 3
Published: about 17 years ago

10.1038/s41598-020-57723-2

The FGF, TGFβ and WNT axis Modulate Self-renewal of Human SIX2+ Urine Derived Renal Progenitor Cells
Cited by: 28
Author(s): Shaifur Rahman, Wasco Wruck, Lucas‐Sebastian Spitzhorn, Lisa Nguyen, Martina Bohndorf, Soraia Martins, Fatima Asar, Audrey Ncube, Lars Erichsen, Nina Graffmann, James Adjaye
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0052493

Anti-Inflammatory Lactobacillus rhamnosus CNCM I-3690 Strain Protects against Oxidative Stress and Increases Lifespan in Caenorhabditis elegans
Cited by: 134
Author(s): Gianfranco Grompone, Patricia Martorell, Silvia Llopis, Núria González, Salvador Genovés, Ana Paula Mulet, Tamara Fernández-Calero, Inés Tiscornia, Mariela Bollati-Fogolín, Isabelle Chambaud, Benoît Foligné, Agustín Montserrat, Daniel Ramón
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-015-2237-2

Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions
Cited by: 76
Author(s): Laura A. L. Dillon, Rahul Suresh, Kwame Okrah, Héctor Corrada Bravo, David M. Mosser, Najib M. El-Sayed
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmicb.2017.02366

Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes
Cited by: 3
Author(s): J. Saraiva, Cristina Zubiría-Barrera, Tilman E. Klassert, Maximilian Julius Lautenbach, Markus Blaess, Ralf A. Claus, Hortense Slevogt, Rainer König
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13073-015-0180-0

The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells
Cited by: 14
Author(s): Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi, Sebastian Dango
Software Mentions: 3
Published: about 11 years ago

10.1186/s12859-017-1467-5

Identifying miRNA sponge modules using biclustering and regulatory scores
Cited by: 21
Author(s): Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
Software Mentions: 3
Published: over 9 years ago

10.1186/s12885-015-1994-2

Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells
Cited by: 28
Author(s): Ruud Weijer, Mans Broekgaarden, Rowan F. van Golen, Esther Bulle, E. E. S. Nieuwenhuis, Aldo Jongejan, Perry D. Moerland, Antoine H. C. van Kampen, Thomas M. van Gulik, Michal Heger
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-017-3621-x

Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo
Cited by: 22
Author(s): Jesper L.V. Mååg, Dominik C. Kaczorowski, Debabrata Panja, Timothy J. Peters, Clive R. Bramham, Karin Wibrand, Marcel E. Dinger
Software Mentions: 3
Published: over 9 years ago

10.1155/2021/5033416

A Novel Expression Signature from the Perspective of Mesenchymal-Epithelial Transition for Hepatocellular Carcinoma with Regard to Prognosis, Clinicopathological Features, Immune Cell Infiltration, Chemotherapeutic Efficacy, and Immunosuppressive Molecules
Cited by: 3
Author(s): Li Xu, Qing Zheng
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-56994-8

Characterization of potential biomarkers of reactogenicity of licensed antiviral vaccines: randomized controlled clinical trials conducted by the BIOVACSAFE consortium
Cited by: 19
Author(s): January Weiner, David Lewis, Jeroen Maertzdorf, Hans-Joachim Mollenkopf, Caroline L. Bodinham, Kat Pizzoferro, Catherine Linley, Aldona Greenwood, Alberto Mantovani, Barbara Bottazzi, Philippe Denoël, Geert Leroux‐Roels, Kent E. Kester, Ingileif Jónsdóttir, Robert A. van den Berg, Stefan H. E. Kaufmann, Giuseppe Del Giudice
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20201482

Survival prediction in patients with colon adenocarcinoma via multiomics data integration using a deep learning algorithm
Cited by: 21
Author(s): Jiudi Lv, Junjie Wang, Shang XiuJuan, Fangfang Liu, Shanshan Guo
Software Mentions: 3
Published: almost 6 years ago