10.1098/rsob.200253

The role of antioxidants in restoring MAPK 14 and a DNA damage marker level following autophagy suppression
Cited by: 3
Author(s): Abdalla Elbialy
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01290

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes
Cited by: 23
Author(s): Christina Böck, Michaela M. Salcher, Manfred Jensen, Ram Vinay Pandey, Jens Boenigk
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-020-74391-4

Analysis of gene expression from systemic lupus erythematosus synovium reveals myeloid cell-driven pathogenesis of lupus arthritis
Cited by: 9
Author(s): Erika L. Hubbard, Michelle D. Catalina, Sarah Heuer, Prathyusha Bachali, Robert Robl, Nicholas S. Geraci, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41398-020-01096-7

Gestational diabetes induces behavioral and brain gene transcription dysregulation in adult offspring
Cited by: 11
Author(s): Keren Aviel-Shekler, Yara Hamshawi, Worood Sirhan, Dmitriy Getselter, Kannan Srikanth, Assaf Malka, Ron Piran, Evan Elliott
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2020.558961

Identification of Prognostic Model and Biomarkers for Cancer Stem Cell Characteristics in Glioblastoma by Network Analysis of Multi-Omics Data and Stemness Indices
Cited by: 27
Author(s): Jianyang Du, Xiuwei Yan, Shan Mi, Yuan Li, Hang Ji, Kezuo Hou, Shuai Ma, Yixu Ba, Peng Zhou, Lei Chen, Rui Xie, Shaoshan Hu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-90250-2

Proteomic analysis-based discovery of a novel biomarker that differentiates intestinal Behçet’s disease from Crohn’s disease
Cited by: 4
Author(s): Jihye Park, Da-Eun Jeong, Youn Wook Chung, Seunghan Han, Da Hye Kim, Jongwook Yu, Jae Hee Cheon, Ji Hwan Ryu
Software Mentions: 4
Published: about 5 years ago

10.3390/vaccines5040037

Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward
Cited by: 8
Author(s): David J. Lemler, Hayden Brochu, Fang Yang, Erin Harrell, Xinxia Peng
Software Mentions: 4
Published: almost 9 years ago

10.3390/cells10071821

Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma
Cited by: 8
Author(s): Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Florian Weiß, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar M. Chromik, M. Bahra, Fritz Klein, Christian Pilarsky, Robert Grützmann, Markus M. Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0226057

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Cited by: 16
Author(s): Surendra Chaurasiya, Scott Widmann, Cindy Botero, Chin-Yo Lin, Jan‐Åke Gustafsson, Anders Ström
Software Mentions: 4
Published: over 6 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: over 7 years ago

10.3390/life11050367

Activation of Blood Vessel Development in Endometrial Stromal Cells In Vitro Cocultured with Human Peri-Implantation Embryos Revealed by Single-Cell RNA-Seq
Cited by: 4
Author(s): Bo Lv, Xiaoyu Xu, Xunyi Zhang, Lingbin Qi, He We, Lu Wang, Xian Chen, Luying Peng, Jinfeng Xue, Yao Ji, Zhigang Xue
Software Mentions: 4
Published: over 5 years ago

10.1186/s13326-015-0026-0

Ambiguity and variability of database and software names in bioinformatics
Cited by: 8
Author(s): Geraint Duck, Aleksandar Kovačević, David L. Robertson, Robert Stevens, Goran Nenadić
Software Mentions: 4
Published: about 11 years ago

10.1016/j.celrep.2017.08.010

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
Cited by: 92
Author(s): Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalvès, Clara Alsinet, Martín Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michaël Schubert, Stacey Price, James C. Wright, Lu Yu, Meizhu Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrão, Alvis Brāzma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Sáez-Rodríguez, Ultan McDermott, Jyoti S. Choudhary
Software Mentions: 4
Published: about 9 years ago

10.1016/j.celrep.2019.07.091

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes
Cited by: 204
Author(s): Myles Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John, David S. Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michèle Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 4
Published: about 7 years ago

10.1111/cpr.12861

RNA processing genes characterize RNA splicing and further stratify colorectal cancer
Cited by: 4
Author(s): Xiaofan Lu, Yu Jie Zhou, Jialin Meng, Liyun Jiang, Jun Gao, Changhong Yu, Hangyu Yan, Yang Wang, Bing Zhang, Xiaobo Li, Fangrong Yan
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: over 7 years ago

10.3390/cells8121566

Stromal Cell Signature Associated with Response to Neoadjuvant Chemotherapy in Locally Advanced Breast Cancer
Cited by: 20
Author(s): Maria Lúcia Hirata Katayama, René Aloísio da Costa Vieira, Victor Piana de Andrade, Rosimeire Aparecida Roela, Luciana Lima, Lígia Maria Kerr, Adriano Polpo de Campos, Carlos Alberto Pereira, Pedro Adolpho de Menezes Pacheco Serio, Giselly Encinas, Simone Maistro, Matheus de Almeida Leite Petroni, Maria Mitzi Brentani, Maria Aparecida Azevedo Koike Folgueira
Software Mentions: 4
Published: over 6 years ago

10.1186/1868-7083-4-20

Genome-scale case-control analysis of CD4+ T-cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease
Cited by: 41
Author(s): Justine A. Ellis, Jane Munro, Raul A Chavez, Lavinia Gordon, Jihoon E. Joo, Jonathan Akikusa, Roger C. Allen, Anne‐Louise Ponsonby, Jeffrey M Craig, Richard Saffery
Software Mentions: 4
Published: almost 14 years ago

10.1038/s41421-021-00271-4

Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response
Cited by: 90
Author(s): Yu Wang, Yongfeng Liang, Haiyan Xu, Xiao Zhang, Tiebo Mao, Jiujie Cui, Jiyong Yao, Yongchao Wang, Feng Jiao, Xiuying Xiao, Jiong Hu, Qing Xia, Xiaofei Zhang, Xujun Wang, Yongwei Sun, Deliang Fu, Lei Shen, Ximing Xu, Jing Xue, Liwei Wang
Software Mentions: 4
Published: about 5 years ago

10.1111/jcmm.16343

Prognostic values and immune suppression of the S100A family in pancreatic cancer
Cited by: 23
Author(s): Hongkai Zhuang, Xinming Chen, Fengying Dong, Zedan Zhang, Zixuan Zhou, Zuyi Ma, Shanzhou Huang, Bin Chen, Chuanzhao Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-019-1420-5

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore
Cited by: 6
Author(s): Rita Gomes Rocha, Vanessa Magalhães, José V. López‐Bao, W. van der Loo, Luís Llaneza, Francisco Álvares, Pedro J. Esteves, Raquel Godinho
Software Mentions: 4
Published: over 7 years ago

10.1002/cbf.3491

Identification and functional analysis of long non‐coding RNAs in the synovial membrane of osteoarthritis patients
Cited by: 7
Author(s): Xiaolong Shui, Qipeng Xie, Shaomin Chen, Chengwei Zhou, Jianzhong Kong, Yi Wang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-64623-y

Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome
Cited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: about 6 years ago

10.1007/s00018-017-2695-6

Downregulation of p53 drives autophagy during human trophoblast differentiation
Cited by: 23
Author(s): Martin Gauster, Sabine Maninger, Monika Siwetz, Alexander Deutsch, Amin El‐Heliebi, Dagmar Kolb-Lenz, Ursula Hiden, Gernot Desoyé, Florian Herse, Andreas Prokesch
Software Mentions: 4
Published: almost 9 years ago

10.1111/jcmm.15650

Combined analysis of RNA‐sequence and microarray data reveals effective metabolism‐based prognostic signature for neuroblastoma
Cited by: 4
Author(s): Xinyao Meng, Chenzhao Feng, Erhu Fang, Jiexiong Feng, Xiang Zhao
Software Mentions: 4
Published: about 6 years ago

10.1186/s12935-020-01632-x

Targeting Lymphotoxin Beta and Paired Box 5: a potential therapeutic strategy for soft tissue sarcoma metastasis
Cited by: 0
Author(s): Runzhi Huang, Zhiwei Zeng, Penghui Yan, Huabin Yin, Xiaolong Zhu, Peng Hu, Juanwei Zhuang, Jiaju Li, Siqi Li, Dianwen Song, Tong Meng, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago

10.1186/s40478-021-01232-4

Metabolic and transcriptomic profiles of glioblastoma invasion revealed by comparisons between patients and corresponding orthotopic xenografts in mice
Cited by: 5
Author(s): Cristina Cudalbu, Pierre Bady, Marta Lai, Lijing Xin, Olga Gusyatiner, Marie‐France Hamou, Mario Lepore, Jean‐Philippe Brouland, Roy Thomas Daniel, Andreas F. Hottinger, Monika E. Hegi
Software Mentions: 4
Published: about 5 years ago

10.1111/jcmm.16573

Development and validation of glycolysis‐related prognostic score for prediction of prognosis and chemosensitivity of pancreatic ductal adenocarcinoma
Cited by: 7
Author(s): Xiuping Zhang, Qinjunjie Chen, Qu Liu, Yang Wang, Fei Wang, Zhiming Zhao, Guodong Zhao, Wan Yee Lau, Yinghong Gao, Rong Liu
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.13997

ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies
Cited by: 9
Author(s): Chenchen Feng, Chao Song, Ziyu Ning, Bo Ai, Qiuyu Wang, Yong Xu, Meng Li, Xuefeng Bai, Jian Zhao, Yuejuan Liu, Xuecang Li, Jian Zhang, Chunquan Li
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12935-020-01587-z

Identified IGSF9 association with prognosis and hypoxia in nasopharyngeal carcinoma by bioinformatics analysis
Cited by: 6
Author(s): Danxia Huang, Qianqian Liu, Weijun Zhang, Chunyue Huang, Ronghui Zheng, Gaoqiang Xie, Hongmei Wang, Baochang Jia, Jianjun Shi, Yawei Yuan, Min Deng
Software Mentions: 3
Published: almost 6 years ago

10.7150/jca.51591

Increased Expression of <i>KNSTRN</i> in Lung Adenocarcinoma Predicts Poor Prognosis: A Bioinformatics Analysis Based on TCGA Data
Cited by: 11
Author(s): Pengbo Deng, Rongrong Zhou, Jinghui Zhang, Liming Cao
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.52170

Five-gene signature associating with Gleason score serve as novel biomarkers for identifying early recurring events and contributing to early diagnosis for Prostate Adenocarcinoma
Cited by: 10
Author(s): Lingyu Zhang, Li Yu, Xuchu Wang, Ying Ping, Danhua Wang, Ying Cao, Yibei Dai, Weiwei Liu, Zhihua Tao
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers12061642

The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B
Cited by: 13
Author(s): Jaideep Chakladar, Lauren Wong, Selena Z. Kuo, Wei Tse Li, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 3
Published: about 6 years ago

10.7150/jca.45553

The <i>miR-370</i>/UQCRC2 axis facilitates tumorigenesis by regulating epithelial-mesenchymal transition in Gastric Cancer
Cited by: 11
Author(s): Danwen Wang, Fei Su, Tao Zhang, Tiecheng Yang, Huaqiao Wang, Lei Yang, Fenfang Zhou, Feng Mao
Software Mentions: 3
Published: over 6 years ago

10.3390/cancers11121967

Pannexin1 Is Associated with Enhanced Epithelial-To-Mesenchymal Transition in Human Patient Breast Cancer Tissues and in Breast Cancer Cell Lines
Cited by: 25
Author(s): Nour Jalaleddine, Layal El-Hajjar, Hassan Dakik, Abdullah Shaito, Jessica Saliba, Rémi Safi, Kazem Zibara, Marwan El-Sabban
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jbc.2021.100285

Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice
Cited by: 4
Author(s): Katarína Lopušná, Paweł Nowialis, Jana Opavska, Ajay Abraham, Alberto Riva, Staci L. Haney, René Opavský
Software Mentions: 3
Published: over 5 years ago

10.1186/gm130

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes
Cited by: 228
Author(s): Iain J. Gallagher, Camilla Schéele, Pernille Keller, Annemette Nielsen, Judit Reményi, Christian P. Fischer, Karim Roder, John Babraj, Claes Wahlestedt, György Hutvágner, Bente Klarlund Pedersen, James A. Timmons
Software Mentions: 3
Published: over 16 years ago

10.1172/jci.insight.97011

Peripheral tissues reprogram CD8+ T cells for pathogenicity during graft-versus-host disease
Cited by: 19
Author(s): Pedro M. Sousa, Séverine Cire, Thomas Conlan, Laura Jardine, Claire Tkacz, Ivana R. Ferrer, C Lomas, Sophie Ward, Heather C. West, Simone Dertschnig, Sven Blobner, Terry K. Means, Stephen Henderson, Daniel H. Kaplan, Matthew Collin, Vincent Plagnol, Clare Bennett, Ronjon Chakraverty
Software Mentions: 3
Published: over 8 years ago

10.1111/cns.13254

High expression of <i>COPB2</i> predicts adverse outcomes: A potential therapeutic target for glioma
Cited by: 13
Author(s): Yan Zhou, Xuan Wang, Xing Huang, Xu‐Dong Li, Kai Chen, Hao Yu, Yujie Zhou, Ping Lv, Xiao Jiang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12885-021-08687-7

A novel survival model based on a Ferroptosis-related gene signature for predicting overall survival in bladder cancer
Cited by: 22
Author(s): Yingchun Liang, Fangdie Ye, Chenyang Xu, Lina Zou, Yun Hu, Jimeng Hu, Haowen Jiang
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41438-020-0249-9

Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model
Cited by: 10
Author(s): Wenfang Zeng, Liang Niu, Zhaohui Wang, Xiaobei Wang, Yan Wang, Lei Pan, Zhenhua Lü, Guochao Cui, Weining Weng, Mingqiao Wang, Xianghong Meng, Zhiqiang Wang
Software Mentions: 3
Published: over 6 years ago

10.1038/s41438-020-0287-3

Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera
Cited by: 39
Author(s): Zhaodong Hao, Siqin Liu, Lingfeng Hu, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 6 years ago

10.1186/s41065-019-0096-6

Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico
Cited by: 45
Author(s): Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang, Yongjie Zhang, Yichao Zhu
Software Mentions: 3
Published: about 7 years ago

10.1186/s41065-021-00183-z

RTP4 is a novel prognosis-related hub gene in cutaneous melanoma
Cited by: 7
Author(s): Yiqi Li, Jue Qi, Jiankang Yang
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0177819

Network architecture associated with the highly specialized hindlimb of frogs
Cited by: 17
Author(s): Daniel Andrés Dos Santos, Jéssica Fratani, María Laura Ponssa, Virginia Abdala
Software Mentions: 3
Published: over 9 years ago

10.1136/gutjnl-2019-320430

Western-type diet influences mortality from necrotising pancreatitis and demonstrates a central role for butyrate
Cited by: 57
Author(s): Fons F van den Berg, Demi van Dalen, Sanjiv Hyoju, Hjalmar C. van Santvoort, Marc G. Besselink, W. Joost Wiersinga, Olga Zaborina, Marja A. Boermeester, John C. Alverdy
Software Mentions: 3
Published: almost 6 years ago

10.3390/ht8010004

A Selective Review of Multi-Level Omics Data Integration Using Variable Selection
Cited by: 127
Author(s): Cen Wu, Fei Zhou, Jie Ren, Xiaoxi Li, Yu Jiang, Shuangge Ma
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giz138

Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
Cited by: 64
Author(s): Gareth Linsmith, Stéphane Rombauts, Sara Montanari, Cecilia Deng, Jean‐Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles‐Eric Durel, Riccardo Velasco, David B. Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco
Software Mentions: 3
Published: over 6 years ago

10.1111/cns.13380

Molecular and clinical characterization of PARP9 in gliomas: A potential immunotherapeutic target
Cited by: 13
Author(s): Hao Xu, Songshan Chai, Yihao Wang, Jiajing Wang, Dongdong Xiao, Junjun Li, Nanxiang Xiong
Software Mentions: 3
Published: over 6 years ago

10.1590/1414-431X20198333

Screening potential prognostic biomarkers of long non-coding RNAs for predicting the risk of chronic kidney disease
Cited by: 11
Author(s): Na Li, Yan Cui, Min Yin, Feng Liu
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0203275

Genetic diversity and biogeography of T. officinale inferred from multi locus sequence typing approach
Cited by: 3
Author(s): Mahdi Jafari, Waheed Akram, Yanju Pang, Aqeel Ahmad, Shakeel Ahmed, Nasim Ahmad Yasin, Tehmina Anjum, Basharat Ali, Xiangdong Hu, Xiaohua Li, Shuang-Lin Dong, Qian Cai, Matteo Ciprian, Monika Bielec, Sheng Hu, Fatemeh Sefidkon, Xuebo Hu
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-017-3237-1

Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue
Cited by: 26
Author(s): Bojana Jovanović, Quanhu Sheng, Robert S. Seitz, Kasey Lawrence, Stephan W. Morris, Lance R. Thomas, David R. Hout, Brock L. Schweitzer, Yan Guo, Jennifer A. Pietenpol, Brian D. Lehmann
Software Mentions: 3
Published: over 9 years ago

10.1111/jcmm.15193

To construct a ceRNA regulatory network as prognostic biomarkers for bladder cancer
Cited by: 45
Author(s): Jiazhi Jiang, Yaqiong Bi, Xiaoping Li, Donghu Yu, Xin Yan, Jie Yao, Tongzu Liu, Li Sheng
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0224477

Are we ready for scaling up restoration actions? An insight from Mediterranean macroalgal canopies
Cited by: 21
Author(s): Laura Tamburello, Loredana Papa, Giuseppe Guarnieri, Laura Basconi, Serena Zampardi, Maria Beatrice Scipione, Antonio Terlizzi, Valerio Zupo, Simonetta Fraschetti
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0037108

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation
Cited by: 10
Author(s): Jamie Bates, Julia Salzman, Damon May, Patty B. Garcia, Gregory J. Hogan, Martin W. McIntosh, Mark S. Schlissel, Pat Brown
Software Mentions: 3
Published: about 14 years ago

10.1186/s13059-017-1301-4

Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis
Cited by: 60
Author(s): Jacki Heraud-Farlow, Alistair M. Chalk, Sandra Linder, Qin Li, Scott Taylor, Joshua M. White, Lokman Pang, Brian Liddicoat, Ankita Gupte, Carl R. Walkley
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12915-020-00943-9

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia
Cited by: 45
Author(s): Hao Song, Ximing Guo, Lina Sun, Qianghui Wang, Fengming Han, Haiyan Wang, Gregory A. Wray, Phillip L. Davidson, Qing Wang, Zhi Hu, Cong Zhou, Zhi Yu, Mei‐Jie Yang, Jie Feng, Shi Pu, Yi Zhou, Libin Zhang, Tao Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-017-1194-2

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort
Cited by: 222
Author(s): Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J. Kangas, Pasi Soininen, Zeneng Wang, Mika Ala‐Korpela, Stanley L. Hazen, Markku Laakso, Aldons J. Lusis
Software Mentions: 3
Published: over 9 years ago

10.1172/jci.insight.145928

Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells
Cited by: 29
Author(s): Wouter A van der Heijden, Lisa Van de Wijer, Farid Keramati, Wim Trypsteen, Sofie Rutsaert, Rob ter Horst, Martin Jaeger, Hans J. P. M. Koenen, Hendrik G. Stunnenberg, Irma Joosten, Paul E. Verweij, Jan van Lunzen, Charles A. Dinarello, Linos Vandekerckhove, Mihai G. Netea, A.J.A.M. van der Ven, Quirijn de Mast
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13102452

Efficacy and Safety of Durvalumab Combined with Daratumumab in Daratumumab-Refractory Multiple Myeloma Patients
Cited by: 9
Author(s): Kristine A. Frerichs, Christie P.M. Verkleij, Meletios Α. Dimopoulos, Jhon A. Marin Soto, Sonja Zweegman, Mary Young, Kathryn J. Newhall, Tuna Mutis, Niels W.C.J. van de Donk
Software Mentions: 3
Published: about 5 years ago

10.3390/genes12050753

Weighted Gene Co-Expression Network Analysis Reveals Hub Genes Contributing to Fuzz Development in Gossypium arboreum
Cited by: 6
Author(s): Feng Xu, Liyan Shang, Hongyan Cheng, Dongyun Zuo, Youping Zhang, Qiaolian Wang, Limin Lv, Guoli Song
Software Mentions: 3
Published: over 5 years ago

10.3390/genes11070760

Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response
Cited by: 90
Author(s): Radhakrishnan Vishnubalaji, Hibah Shaath, Nehad M. Alajez
Software Mentions: 3
Published: about 6 years ago

10.3390/genes10070536

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut
Cited by: 16
Author(s): Xiaobo Zhao, Li‐Ming Gan, Yan Cheng, Chunjuan Li, Quanxi Sun, Juan Wang, Cuiling Yuan, Hao Zhang, Shiguang Shan, Jian Ning Liu
Software Mentions: 3
Published: about 7 years ago

10.3390/nu11020418

Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids
Cited by: 40
Author(s): Nijiati Abulizi, Candice Quin, Kirsty Brown, Yee Kwan Chan, S K Gill, Deanna L. Gibson
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0208400

Using a coupled dynamic factor – random forest analysis (DFRFA) to reveal drivers of spatiotemporal heterogeneity in the semi-arid regions of southern Africa
Cited by: 4
Author(s): Jane Southworth, Erin Bunting, Likai Zhu, Sadie J. Ryan, Hannah Victoria Herrero, Peter R. Waylen, Rafael Muñoz‐Carpena, Miguel Ángel Campo‐Bescós, D. A. Kaplan
Software Mentions: 3
Published: over 7 years ago

10.3390/genes10020074

Macrophages from Susceptible and Resistant Chicken Lines have Different Transcriptomes following Marek’s Disease Virus Infection
Cited by: 17
Author(s): Pankaj Chakraborty, Richard Kuo, Lonneke Vervelde, Bernadette M. Dutia, Pete Kaiser, Jacqueline Smith
Software Mentions: 3
Published: over 7 years ago

10.1016/j.ccell.2018.08.015

The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation
Cited by: 75
Author(s): N Martinez-Soria, Lynsey McKenzie, Julia Draper, Anetta Ptasińska, Hasan Issa, Sandeep Potluri, Helen J. Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Dan Coleman, Sirintra Nakjang, Salam A. Assi, Victoria J. Forster, Mojgan Reza, Edward Law, Philip Berry, Dorothée Mueller, Cameron S. Osborne, Alex Elder, Simon Bomken, Deepali Pal, James M. Allan, Gareth J. Veal, Peter N. Cockerill, Christian Wichmann, Josef Vormoor, Georges Lacaud, Constanze Bonifer, Olaf Heidenreich
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12967-021-02845-y

Identification of an immune classification for cervical cancer and integrative analysis of multiomics data
Cited by: 7
Author(s): Xintong Lyu, Guang Li, Qiao Qiao
Software Mentions: 3
Published: over 5 years ago

10.1155/2019/8265958

Competing Endogenous RNA and Coexpression Network Analysis for Identification of Potential Biomarkers and Therapeutics in association with Metastasis Risk and Progression of Prostate Cancer
Cited by: 9
Author(s): Xu Pang, Ying Zhao, Jinhua Wang, Wan Li, Qian Xiang, Zhuo Zhang, Shi-Liang Wu, Ailin Liu, Guanhua Du, Yimin Chen
Software Mentions: 3
Published: about 7 years ago

10.1186/s13068-021-02032-7

Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed
Cited by: 17
Author(s): Keqi Li, Jie Wang, Lieqiong Kuang, Ze Tian, Xinfa Wang, Xiaoling Dun, Jinxing Tu, Hanzhong Wang
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-15-162

A multivariate approach to the integration of multi-omics datasets
Cited by: 214
Author(s): Chen Meng, Bernhard Küster, Aedín C. Culhane, Amin Moghaddas Gholami
Software Mentions: 3
Published: about 12 years ago

10.1186/s12967-020-02691-4

Model based on five tumour immune microenvironment-related genes for predicting hepatocellular carcinoma immunotherapy outcomes
Cited by: 24
Author(s): Xinyu Gu, Jun Guan, Jia Xu, Qiuxian Zheng, Chao Chen, Qin Yang, ChunHong Huang, Wang Gang, Haibo Zhou, Zhi Chen, Haihong Zhu
Software Mentions: 3
Published: over 5 years ago

10.1186/s13018-021-02329-1

Machine learning analysis of gene expression profile reveals a novel diagnostic signature for osteoporosis
Cited by: 5
Author(s): Xinlei Chen, Guangping Liu, Shuxiang Wang, Haiyang Zhang, Peng Xue
Software Mentions: 3
Published: over 5 years ago

10.3390/genes8100269

The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome
Cited by: 27
Author(s): Ludivine Renaud, Willian A. da Silveira, E. Starr Hazard, Jonathan Simpson, Silvia Falcinelli, Dongjun Chung, Oliana Carnevali, Gary Hardiman
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12967-020-02611-6

Putative positive role of inflammatory genes in fat deposition supported by altered gene expression in purified human adipocytes and preadipocytes from lean and obese adipose tissues
Cited by: 5
Author(s): Sang-Hyeop Lee, Nak-Hyeon Choi, In-Uk Koh, Bong-Jo Kim, Song Lee, Song Cheol Kim, Sun Shim Choi
Software Mentions: 3
Published: almost 6 years ago

10.1002/psp4.12091

Model-Based Network Meta-Analysis: A Framework for Evidence Synthesis of Clinical Trial Data
Cited by: 48
Author(s): David Mawdsley, Meg Bennetts, Sofia Dias, Martin Boucher, Nicky J Welton
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pmed.1003100

Metabolic risk factors and incident advanced liver disease in non-alcoholic fatty liver disease (NAFLD): A systematic review and meta-analysis of population-based observational studies
Cited by: 177
Author(s): Helen Jarvis, Dawn Craig, Robert Barker, Gemma Spiers, Daniel Stow, Quentin M. Anstee, Barbara Hanratty
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1006706

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease
Cited by: 174
Author(s): Lasse Folkersen, Eric B. Fauman, Maria Sabater‐Lleal, Rona J. Strawbridge, Mattias Frånberg, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E. Humphries, Rainer Rauramaa, Ulf dé Fairé, Andries J. Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Stefan Enroth, Åsa Johansson, Sofia Bosdotter Enroth, Stefan Gustafsson, Lars Lind, Cecilia M. Lindgren, Andrew P. Morris, Vilmantas Giedraitis, Angela Silveira, Anders Franco‐Cereceda, Elena Tremoli, Ulf Gyllensten, Erik Ingelsson, Søren Brunak, Per Eriksson, Daniel Ziemek, Anders Hamsten, Anders Mälarstig
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1003400

Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation
Cited by: 75
Author(s): Cécile Esnault, Guillaume Cornelis, Odile Heidmann, Thiérry Heidmann
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.1007822

De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders
Cited by: 74
Author(s): Hongjian Qi, Lan Yu, Xueya Zhou, Julia Wynn, Haoquan Zhao, Yicheng Guo, Na Zhu, Alexander Kitaygorodsky, Rebecca Hernan, Guðrún Aspelund, Foong‐Yen Lim, Timothy M. Crombleholme, Robert A. Cusick, Kenneth S. Azarow, Melissa E. Danko, Dai H. Chung, Brad W. Warner, George B. Mychaliska, Douglas A. Potoka, Amy J. Wagner, Mahmoud Elfiky, Jay M. Wilson, Debbie Nickerson, Michael J. Bamshad, Frances A. High, Mauro Longoni, Patricia K. Donahoe, Wendy K. Chung, Yufeng Shen
Software Mentions: 3
Published: over 7 years ago

10.1016/j.isci.2021.102686

PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα
Cited by: 14
Author(s): Evelyn Ramberger, Valeria Sapozhnikova, Elisabeth Kowenz‐Leutz, Karin Zimmermann, Nathalie Nicot, Petr V. Nazarov, Daniel Pérez-Hernández, Ulf Reimer, Philipp Mertins, Gunnar Dittmar, Achim Leutz
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1006294

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts
Cited by: 44
Author(s): Maléne E. Lindholm, Stefania Giacomello, Beata Werne Solnestam, Håkan Fischer, Mikael Huss, Sanela Kjellqvist, Carl Johan Sundberg
Software Mentions: 3
Published: almost 10 years ago

10.3389/fimmu.2020.02039

Crosstalk Between the MSI Status and Tumor Microenvironment in Colorectal Cancer
Cited by: 160
Author(s): Anqi Lin, Jian Zhang, Peng Luo
Software Mentions: 3
Published: about 6 years ago

10.1186/s12974-020-01898-y

Meta-analysis of mouse transcriptomic studies supports a context-dependent astrocyte reaction in acute CNS injury versus neurodegeneration
Cited by: 54
Author(s): Sudeshna Das, Zhaozhi Li, Ayush Noori, Bradley T. Hyman, Alberto Serrano-Pozo
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2105-14-212

Linear combination test for gene set analysis of a continuous phenotype
Cited by: 8
Author(s): Irina Dinu, Xiaoming Wang, Linda E. Kelemen, Shabnam Vatanpour, Saumyadipta Pyne
Software Mentions: 3
Published: about 13 years ago

10.2196/jmir.5391

Toward a Mixed-Methods Research Approach to Content Analysis in The Digital Age: The Combined Content-Analysis Model and its Applications to Health Care Twitter Feeds
Cited by: 56
Author(s): Eradah O Hamad, Marie Y. Savundranayagam, Jeffrey D. Holmes, Elizabeth Anne Kinsella, Andrew M. Johnson
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms22158249

Transcriptome-Based WGCNA Analysis Reveals Regulated Metabolite Fluxes between Floral Color and Scent in Narcissus tazetta Flower
Cited by: 20
Author(s): Jingwen Yang, Yujun Ren, Deyu Zhang, Xuewei Chen, Jiazhi Huang, Yun Xu, Cristina Belén Aucapiña Criollo, Yu Zhang, Ying Miao
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22169081

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
Cited by: 10
Author(s): Aljaž Gaber, Miha Pavšič
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2021.666370

lncRNA-HEIM Facilitated Liver Fibrosis by Up-Regulating TGF-β Expression in Long-Term Outcome of Chronic Hepatitis B
Cited by: 9
Author(s): Jian Yao, Changpo Lin, Jingjing Jiang, Xujun Zhang, Fengxia Li, Tianxing Liu, Hongyan Diao
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms221810117

LncRNA-CR11538 Decoys Dif/Dorsal to Reduce Antimicrobial Peptide Products for Restoring Drosophila Toll Immunity Homeostasis
Cited by: 9
Author(s): Hongjian Zhou, Shengjie Li, Shanshan Wu, Jin Park, Fei Ma
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2019.00869

Immunomodulatory Effects and Induction of Apoptosis by Different Molecular Weight Chitosan Oligosaccharides in Head Kidney Macrophages From Blunt Snout Bream (Megalobrama amblycephala)
Cited by: 17
Author(s): Changcai Wu, Yishan Dai, Gailing Yuan, Jian Su, Xiaoling Liu
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2020.604785

JNK1 Signaling Downstream of the EGFR Pathway Contributes to Aldara®-Induced Skin Inflammation
Cited by: 3
Author(s): Aurore Le, Abdulkader Azouz, Séverine Thomas, Nicolas Istaces, Muriel Nguyen, Stanislas Goriely
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22031167

Glutamine Uptake via SNAT6 and Caveolin Regulates Glutamine–Glutamate Cycle
Cited by: 14
Author(s): Nikhil R. Gandasi, Vasiliki Arapi, Michel‐Edwar Mickael, Prajakta A. Belekar, Louise Granlund, Lakshmi Kothegala, Robert Fredriksson, Sonchita Bagchi
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1004584

Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models
Cited by: 369
Author(s): Annalisa Mazzoni, Henrik Lindén, Hermann Cuntz, Anders Lansner, Stefano Panzeri, Gaute T. Einevoll
Software Mentions: 3
Published: over 10 years ago

10.3389/fmed.2020.606461

Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
Cited by: 3
Author(s): Melissa A Nickles, Huang Kai, Yi-Shin Chang, Maria M. Tsoukas, Nadera J. Sweiss, David L. Perkins, Patricia W. Finn
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-016-1005-1

Ligation-free ribosome profiling of cell type-specific translation in the brain
Cited by: 47
Author(s): Nicholas Hornstein, Daniela Torres, Sohani Das Sharma, Guomei Tang, Peter Canoll, Peter A. Sims
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2021.616388

Transcriptome Characterization of Short Distance Transport Stress in Beef Cattle Blood
Cited by: 14
Author(s): Hailin Zhao, Xiaoqin Tang, Mingli Wu, Qi Li, Xiaohua Yi, Shirong Liu, Junyi Jiang, Shuhui Wang, Xiuzhu Sun
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.17011

Association between PSCA gene polymorphisms and the risk of cancer: an updated meta-analysis and trial sequential analysis
Cited by: 6
Author(s): Zhiqiang Qin, Jingyuan Tang, Xiao Li, Yu Yan, Chuanjie Zhang, Peng Han, Ran Li, Xin Jiang, Chengying Yang, Wei Wang, Min Tang, Wei Zhang
Software Mentions: 3
Published: over 9 years ago

10.3390/cancers10080273

Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer
Cited by: 26
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Sahib Zada, Jin Seok Hwang, Trang Minh Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pcbi.1000920

Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers
Cited by: 48
Author(s): Joseph E. Lucas, Hsiu‐Ni Kung, Jen‐Tsan Chi
Software Mentions: 3
Published: almost 16 years ago