bioconductor: genefu | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0158259

Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers
Cited by: 15
Author(s): Inna Tishchenko, Heloisa Helena Milioli, Carlos Riveros, Pablo Moscato
Software Mentions: 9
Published: over 8 years ago

10.1186/s13058-019-1123-2

Separation of breast cancer and organ microenvironment transcriptomes in metastases
Cited by: 33
Author(s): Mohammad A. Alzubi, Tia H. Turner, Amy L. Olex, Sahib S. Sohal, Nicholas P. Tobin, Susana Garcia Recio, Jonas Bergh, Thomas Hatschek, Joel S. Parker, Carol A. Sartorius, Charles M. Perou, Mikhail G. Dozmorov, J. Chuck Harrell
Software Mentions: 8
Published: almost 6 years ago

10.7554/eLife.58810

Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in mouse models of breast cancer
Cited by: 38
Author(s): Syn Kok Yeo, Xiaoting Zhu, Takaaki Okamoto, Mingang Hao, Cailian Wang, Peixin Lu, Long Lu, Jun‐Lin Guan
Software Mentions: 8
Published: over 4 years ago

10.1186/s13058-016-0758-5

Patient survival and tumor characteristics associated with CHEK2:p.I157T – findings from the Breast Cancer Association Consortium
Cited by: 37
Author(s): Taru Muranen, Carl Blomqvist, Thilo Dörk, Anna Jakubowska, Päivi Heikkilä, Rainer Fagerholm, Dario Greco, Kristiina Aittomäki, Stig E. Bojesen, Mitul Shah, Alison M. Dunning, Valerie Rhenius, Per Hall, Kamila Czene, Judith S. Brand, Hatef Darabi, Jenny Chang–Claude, Anja Rudolph, Børge G. Nordestgaard, Fergus J. Couch, Steven N. Hart, Jonine D. Figueroa, Montserrat García‐Closas, Peter A. Fasching, Matthias W. Beckmann, Jingmei Li, Jing Liu, Irene L. Andrulis, Robert Winqvist, Katri Pylkäs, Arto Mannermaa, Vesa Kataja, Annika Lindblom, Sara Margolin, Jan Lubiński, Natalia Dubrowinskaja, Manjeet K. Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, Douglas F. Easton, Paul D.P. Pharoah, Marjanka K. Schmidt, Heli Nevanlinna
Software Mentions: 8
Published: about 8 years ago

10.3389/fphar.2020.593247

Identification of FPR3 as a Unique Biomarker for Targeted Therapy in the Immune Microenvironment of Breast Cancer
Cited by: 7
Author(s): Jian Qi, Yu Liu, Jiliang Hu, Li Lu, Zhen Dou, Haiming Dai, Hongzhi Wang, Wulin Yang
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmolb.2021.619110

Screening and Identification of Key Common and Specific Genes and Their Prognostic Roles in Different Molecular Subtypes of Breast Cancer
Cited by: 7
Author(s): Na Sun, Peng Gao, Yanling Li, Zexuan Yan, Zaihui Peng, Yi Zhang, Fei Han, Xiaowei Qi
Software Mentions: 6
Published: almost 4 years ago

10.7150/jca.37637

Tumour-Infiltrating Immune Cell-Based Subtyping and Signature Gene Analysis in Breast Cancer Based on Gene Expression Profiles
Cited by: 15
Author(s): Jingxin Jiang, Weiwei Pan, Yazhang Xu, Chao Ni, Dan Xue, Zhigang Chen, Wuzhen Chen, Jian Huang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12859-021-04215-3

Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis
Cited by: 5
Author(s): Xiaomei Li, Buu Truong, Taosheng Xu, Lin Liu, Jiuyong Li, Thuc Duy Le
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-014-0431-1

Genome-driven integrated classification of breast cancer validated in over 7,500 samples
Cited by: 173
Author(s): H. Raza Ali, Oscar M. Rueda, Suet-Feung Chin, Christina Curtis, Mark J. Dunning, Samuel Aparicio, Carlos Caldas
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0129610

Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach
Cited by: 4
Author(s): Nilotpal Chowdhury, Shantanu Sapru
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0021681

An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction
Cited by: 8
Author(s): Herman M. J. Sontrop, Wim Verhaegh, Marcel J. T. Reinders, Perry D. Moerland
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-017-02761-6

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype
Cited by: 27
Author(s): Willian A. da Silveira, Patrícia Vianna Bonini Palma, Renata Danielle Sicchieri, Rolando A R Villacis, Larissa Raquel Mouro Mandarano, Tatiane Oliveira, Heriton Mr Antonio, Jurandyr Moreira de Andrade, Valdair Francisco Muglia, Sílvia Regina Rogatto, Charles Theillet, Stanislas du Manoir, Daniel Guimarães Tiezzi
Software Mentions: 4
Published: over 7 years ago

10.1186/s12920-016-0185-6

Breast cancer subtype predictors revisited: from consensus to concordance?
Cited by: 5
Author(s): Herman M. J. Sontrop, Marcel J. T. Reinders, Perry D. Moerland
Software Mentions: 3
Published: over 8 years ago

10.3390/cancers10110397

DNA Methylation Predicts the Response of Triple-Negative Breast Cancers to All-Trans Retinoic Acid
Cited by: 19
Author(s): Krysta M. Coyle, Cheryl A. Dean, Margaret Lois Thomas, Dejan Vidovic, Carman A. Giacomantonio, Lucy Helyer, Paola Marcato
Software Mentions: 3
Published: about 6 years ago

10.3389/fphar.2019.00574

LncRNA Profile Study Reveals a Three-LncRNA Signature Associated With the Pathological Complete Response Following Neoadjuvant Chemotherapy in Breast Cancer
Cited by: 20
Author(s): Ying Zeng, Wei Guo, Chengfang Zhou, Hai Bo Zhang, Hong Sun, Wei Zhang, Hong‐Hao Zhou, Rong Liu, Yuan‐Shan Zhu
Software Mentions: 3
Published: over 5 years ago

10.15252/emmm.201607084

<scp>CDK</scp>4 phosphorylation status and a linked gene expression profile predict sensitivity to palbociclib
Cited by: 62
Author(s): Eric Raspé, Katia Coulonval, Jaime Miguel Gomes Pita, Sabine Paternot, Françoise Rothé, Laure Twyffels, Sylvain Brohée, Ligia Craciun, Denis Larsimont, Véronique Kruys, Flavienne Sandras, Isabelle Salmon, Steven Van Laere, Martine Piccart, Michail Ignatiadis, Christos Sotiriou, Pierre P. Roger
Software Mentions: 3
Published: over 7 years ago

10.1186/s12885-019-6363-0

The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Cited by: 26
Author(s): Michał Marczyk, Chunxiao Fu, Rosanna Lau, Lili Du, Alexander J. Trevarton, Bruno Valentin Sinn, Rebekah E. Gould, Lajos Pusztai, Christos Hatzis, W. Fraser Symmans
Software Mentions: 3
Published: about 5 years ago

10.1186/s12916-015-0416-2

Constitutive phosphorylated STAT3-associated gene signature is predictive for trastuzumab resistance in primary HER2-positive breast cancer
Cited by: 44
Author(s): Amir Sonnenblick, Sylvain Brohée, Debora Fumagalli, Delphine Vincent, David Venet, Michail Ignatiadis, Roberto Salgado, Gert Van den Eynden, Françoise Rothé, Christine Desmedt, Patrick Neven, Sibylle Loibl, Carsten Denkert, Heikki Joensuu, Sherene Loi, Nicolas Sirtaine, Pirkko–Liisa Kellokumpu-Lehtinen, Martine Piccart, Christos Sotiriou
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0129711

The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set
Cited by: 28
Author(s): Heloisa Helena Milioli, Renato Vimieiro, Carlos Riveros, Inna Tishchenko, Regina Berretta, Pablo Moscato
Software Mentions: 3
Published: over 9 years ago

10.1186/s13073-015-0168-9

Widespread intron retention diversifies most cancer transcriptomes
Cited by: 254
Author(s): Heidi Dvinge, Robert K. Bradley
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.24447

Molecular and clinical features of the <i>TP53</i> signature gene expression profile in early-stage breast cancer
Cited by: 11
Author(s): Shigeo Yamaguchi, Shin Takahashi, Kaoru Mogushi, Yuki Izumi, Yumi Nozaki, Tadashi Nomizu, Yoichiro Kakugawa, Toru Ishida, Noriaki Ohuchi, Chikashi Ishioka, Shunsuke Kato
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12920-020-0688-z

Highly robust model of transcription regulator activity predicts breast cancer overall survival
Cited by: 3
Author(s): Chuanpeng Dong, Jiannan Liu, Steven Chen, Tianhan Dong, Guanglong Jiang, Yue Wang, Huanmei Wu, Jill L. Reiter, Yunlong Liu
Software Mentions: 2
Published: over 4 years ago

10.1155/2020/1363827

Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers
Cited by: 2
Author(s): Michael Kenn, Dan Cacsire Castillo‐Tong, Christian F. Singer, Michael Cibena, H. Kölbl, Wolfgang Schreiner
Software Mentions: 2
Published: over 4 years ago

10.1038/s41416-021-01455-1

Cancer Grade Model: a multi-gene machine learning-based risk classification for improving prognosis in breast cancer
Cited by: 12
Author(s): Elmira Amiri Souri, Alicia Chenoweth, Anthony Cheung, Sophia N. Karagiannis, Sophia Tsoka
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1002875

Significance Analysis of Prognostic Signatures
Cited by: 30
Author(s): Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schroeder, Thomas S. Risch, John Quackenbush, Benjamin Haibe‐Kains
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0087415

Development and Validation of a Gene Expression Score That Predicts Response to Fulvestrant in Breast Cancer Patients
Cited by: 25
Author(s): Steen Knudsen, Thomas E. Jensen, Anker Hansen, Wiktor Mazin, Justin P.O. Lindemann, Irene Kuter, Naomi Laing, Elizabeth J. Anderson
Software Mentions: 2
Published: almost 11 years ago

10.3390/cancers12123506

An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier
Cited by: 8
Author(s): Mi Kyoung Seo, Soonmyung Paik, Sangwoo Kim
Software Mentions: 2
Published: about 4 years ago

10.3390/cancers12092638

How Different Are the Molecular Mechanisms of Nodal and Distant Metastasis in Luminal A Breast Cancer?
Cited by: 2
Author(s): Petr Lapčík, Anna Pospíšilová, Lucia Janáčová, Peter Grell, Pavel Fabián, Pavel Bouchal
Software Mentions: 2
Published: over 4 years ago

10.1038/cddis.2015.65

Regulation of anti-apoptotic signaling by Kruppel-like factors 4 and 5 mediates lapatinib resistance in breast cancer
Cited by: 31
Author(s): Farrugia Mk, Sharma Sb, Lin Cc, Sarah L. McLaughlin, Vanderbilt Db, Ammer Ag, Mohamad A. Salkeni, Peter Stoilov, YM Agazie, CJ Creighton, Ruppert Jm
Software Mentions: 2
Published: almost 10 years ago

10.1002/jcp.27049

<b>Intratumor lactate levels reflect HER2 addiction status in HER2‐positive breast cancer</b>
Cited by: 29
Author(s): Lorenzo Castagnoli, Egidio Iorio, Matteo Dugo, Ada Koschorke, Simona Faraci, Rossella Canese, Patrizia Casalini, Patrizia Nanni, Claudio Vernieri, Massimo Di Nicola, Daniele Morelli, Elda Tagliabue, Serenella M. Pupa
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms19030693

The Complex Subtype-Dependent Role of Connexin 43 (GJA1) in Breast Cancer
Cited by: 27
Author(s): Mélanie Busby, Michael Hallett, Isabelle Plante
Software Mentions: 2
Published: almost 7 years ago

10.3390/cancers13040906

The Claudin-Low Subtype of High-Grade Serous Ovarian Carcinoma Exhibits Stem Cell Features
Cited by: 5
Author(s): Chiara Romani, Davide Capoferri, Elisabetta Grillo, M. Silvestri, Michela Corsini, Laura Zanotti, Paola Todeschini, Antonella Ravaggi, Eliana Bignotti, Franco Odicino, Enrico Sartori, Stefano Calza, Stefania Mitola
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12916-015-0504-3

Genomic aberrations in young and elderly breast cancer patients
Cited by: 75
Author(s): Hatem Hamdy Abdel Azim, Bastien Nguyen, Sylvain Brohée, Gabriele Zoppoli, Christos Sotiriou
Software Mentions: 1
Published: about 9 years ago

10.1186/s13058-014-0425-7

Attenuated transforming growth factor beta signaling promotes metastasis in a model of HER2 mammary carcinogenesis
Cited by: 21
Author(s): Sergey V. Novitskiy, Elizabeth Forrester, Michael W. Pickup, Agnieszka E. Gorska, Anna Chytil, Mary Aakre, Dina Polosukhina, Philip Owens, Dilyara R Yusupova, Zhiguo Zhao, Fei Ye, Yu Shyr, Harold L. Moses
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-019-48570-x

Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series
Cited by: 36
Author(s): Johan Vallon‐Christersson, Jari Häkkinen, Cecilia Hegardt, Lao H. Saal, Christer Larsson, Anna Ehinger, Henrik Lindman, Helena Olofsson, Tobias Sjöblom, Fredrik Wärnberg, Lisa Rydén, Niklas Loman, Martin Malmberg, Åke Borg, Johan Staaf
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-82418-7

Decision theory for precision therapy of breast cancer
Cited by: 3
Author(s): Michael Kenn, Dan Cacsire Castillo‐Tong, Christian F. Singer, Rudolf Karch, Michael Cibena, Heinz Koelbl, Wolfgang Schreiner
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13046-014-0084-7

A four-long non-coding RNA signature in predicting breast cancer survival
Cited by: 134
Author(s): Meng Ji, Ping Li, Qing Zhang, Zhangru Yang, Shihua Fu
Software Mentions: 1
Published: about 10 years ago

10.1186/2051-1426-3-S1-O3

Clinico-pathological and transcriptomic determinants of SLFN11 expression in invasive breast carcinoma
Cited by: 2
Author(s): Gabriele Zoppoli, Sylvain Brohée, Christine Desmedt, Christos Sotiriou, Alberto Ballestrero
Software Mentions: 1
Published: over 9 years ago

10.1186/s13058-016-0748-7

WNT4 mediates estrogen receptor signaling and endocrine resistance in invasive lobular carcinoma cell lines
Cited by: 52
Author(s): Matthew J. Sikora, Britta M. Jacobsen, Kevin M. Levine, Jian Chen, Nancy E. Davidson, Adrian V. Lee, Caroline M. Alexander, Steffi Oesterreich
Software Mentions: 1
Published: over 8 years ago

10.1186/gb-2010-11-2-r18

A fuzzy gene expression-based computational approach improves breast cancer prognostication
Cited by: 48
Author(s): Benjamin Haibe‐Kains, Christine Desmedt, Françoise Rothé, Martine Piccart, Christos Sotiriou, Gianluca Bontempi
Software Mentions: 1
Published: almost 15 years ago

10.3389/fonc.2020.00783

DGM-CM6: A New Model to Predict Distant Recurrence Risk in Operable Endocrine-Responsive Breast Cancer
Cited by: 3
Author(s): Lei Lei, Xiao-Jia Wang, Yin‐Yuan Mo, Skye Hung-Chun Cheng, Yunyun Zhou
Software Mentions: 1
Published: over 4 years ago

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