Emmanouil Sifakis

Publikationer
Forskningsbidrag
Populärvetenskap och samverkan

Artiklar

Journal article: NAR GENOMICS AND BIOINFORMATICS. 2025;7(4):lqaf131
BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research
Yang Q; Hartman J; Sifakis EG
Article: NPJ PRECISION ONCOLOGY. 2025;9(1):310
Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data
Li T; Yang Q; Acs B; Sifakis EG; Toosi H; Engblom C; Thrane K; Lin Q; Mold JE; Sun W; Boyaci C; Steen S; Frisen J; Lagergren J; Lundeberg J; Chen X; Hartman J
Journal article: CLINICAL CANCER RESEARCH. 2025;31(12_Supplement):p4-01-30-p4-01-30
Abstract P4-01-30: Proteogenomic profiles of HER2-positive breast cancer and response to neoadjuvant anti-HER2 treatment
Wang K; Gaessler LF; Zerdes I; Zhu Y; Sifakis E; Salgkamis D; Harbers L; Crosetto N; Bergh J; Hatschek T; Johansson HJ; Matikas A; Lehtiö J; Foukakis T
Journal article: CLINICAL CANCER RESEARCH. 2025;31(12):p2-01-30-p2-01-30-P20130
Gene Expression patterns in early ER+/HER2-breast cancer treated with neoadjuvant chemotherapy versus CDK4/6 inhibitor therapy: results from the Swedish PREDIX Luminal B trial
Tzoras E; Sarafidis M; Sifakis EG; Salgkamis D; Acs B; Sun W; Zerdes I; Wang K; Bergh J; Hatschek T; Matikas A; Foukakis T
Journal article: ESMO OPEN. 2025;10:104584
30P Novel integrated tumor micro-/macro-environment (TMME) subtypes for prediction of treatment response to neoadjuvant anti-HER2 therapy
Zerdes I; Wang K; Manikis G; Salgkamis D; Zhu Y; Tzoras E; Mezheyeuski A; Acs B; Sifakis EG; Hartman J; Papakonstantinou A; Matikas A; Bergh J; Hatschek T; Foukakis T
Journal article: ESMO OPEN. 2025;10:104574
20P Evolution of early-stage ERBB2-mutant, HER2+ breast cancer under neoadjuvant therapy
Wang K; Zerdes I; Sifakis EG; Salgkamis D; Bergh J; Hatschek T; Matikas A; Foukakis T
Journal article: ESMO OPEN. 2025;10:104609
55P Single-nucleotide polymorphisms associated with haematological toxicities during adjuvant chemotherapy in high-risk early breast cancer patients: Results from the PANTHER phase III trial
Salgkamis D; Liu X; Rivera N; Papakonstantinou A; Hellström M; Agartz S; Sifakis EG; Zerdes I; Bergh J; Matikas A; Foukakis T
Journal article: ESMO OPEN. 2025;10:104559
4MO Development and validation of CDKPredX, a novel predictor of response to neoadjuvant endocrine therapy and CDK4/6 inhibitors versus chemotherapy in ER+/HER2- breast cancer: Correlative analysis of the randomized phase II PREDIX luminal B trial
Foukakis T; Tzoras E; Sarafidis M; Sifakis EG; Salgkamis D; Zerdes I; Wang K; Pascual T; Gavilá-Gregori J; Villacampa G; Prat A; Perou CM; Bergh J; Hatschek T; Matikas A
Journal article: ESMO OPEN. 2025;10:104631
77P The landscape of somatic mutations in high-risk early ER+/HER2- breast cancer patients: Analysis of the randomized phase II PREDIX luminal B trial
Sarafidis M; Tzoras E; Sifakis EG; Wang K; Salgkamis D; Zerdes I; Bergh J; Hatschek T; Matikas A; Foukakis T
Article: INTERNATIONAL JOURNAL OF CANCER. 2025;156(8):1621-1633
Prognostic and predictive implications of sterile alpha motif and HD domain-containing protein 1 (SAMHD1) expression in breast cancer
Kouvaraki M; Zerdes I; Sifakis EG; Sarafidis M; Matikas A; Tzoras E; Kjallquist U; Stathopoulou K; Lovrot J; Alkodsi A; Hartman J; Sotiriou C; Richard F; Hatschek T; Herold N; Bergh J; Rassidakis GZ; Foukakis T
Article: IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS. 2024;28(9):5312-5322
Unveiling the Power of Model-Agnostic Multiscale Analysis for Enhancing Artificial Intelligence Models in Breast Cancer Histopathology Images
Tsiknakis N; Manikis G; Tzoras E; Salgkamis D; Vidal JM; Wang K; Zaridis D; Sifakis E; Zerdes I; Bergh J; Hartman J; Acs B; Marias K; Foukakis T
Article: SCIENTIFIC REPORTS. 2024;14(1):18275
Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue
Salgkamis D; Sifakis EG; Agartz S; Wirta V; Hartman J; Bergh J; Foukakis T; Matikas A; Zerdes I
Article: ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE. 2024;2024:1-5
Ensuring Model Fairness via Stratified Training: TP53 Mutation Prediction with Estrogen Receptor Stratification in Breast Histopathology.
Tsiknakis N; Wang K; Salgkamis D; Tzoras E; Manikis GC; Sifakis E; Bergh J; Zerdes I; Marias K; Matikas A; Foukakis T
Article: SCIENTIFIC REPORTS. 2024;14(1):12542
PIK3CA mutations in endocrine-resistant breast cancer
Schagerholm C; Robertson S; Toosi H; Sifakis EG; Hartman J
Article: NATURE COMMUNICATIONS. 2024;15(1):3837
Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer
Wang K; Zerdes I; Johansson HJ; Sarhan D; Sun Y; Kanellis DC; Sifakis EG; Mezheyeuski A; Liu X; Loman N; Hedenfalk I; Bergh J; Bartek J; Hatschek T; Lehtio J; Matikas A; Foukakis T
Journal article: CANCER RESEARCH. 2024;84(9):po5-13-02-po5-13-02
BRCA mutational profiles of endocrineresistant breast cancer
Karlsson E; Schagerholm C; Robertson S; Toosi H; Sifakis E; Hartman J
Journal article: CANCER RESEARCH. 2024;84(9):po3-16-04-po3-16-04
Distribution of intrinsic subtypes in endocrineresistant and endocrine-sensitive breast cancer
Schagerholm C; Robertson S; Karlsson E; Sifakis E; Hartman J
Journal article: ESMO OPEN. 2024;9:103074
68P Application of a machine learning model for identifying an ultra-low risk group of early breast cancer patients
Sarafidis M; Sifakis EG; Bergh J; Foukakis T; Matikas A
Article: BREAST CANCER RESEARCH. 2024;26(1):24
Prognostic impact of HER2 biomarker levels in trastuzumab-treated early HER2-positive breast cancer
Ronnlund C; Sifakis EG; Schagerholm C; Yang Q; Karlsson E; Chen X; Foukakis T; Weidler J; Bates M; Fredriksson I; Robertson S; Hartman J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2023;120(1):e2209856120
Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction
Chen X; Sifakis EG; Robertson S; Neo SY; Jun S-H; Tong L; Min ATH; Lovrot J; Hellgren R; Margolin S; Bergh J; Foukakis T; Lagergren J; Lundqvist A; Ma R; Hartman J
Journal article: ANNALS OF ONCOLOGY. 2022;33:s640
223P Gene expression profiles in endocrine-resistant breast cancer
Schagerholm C; Robertson S; Sifakis EG; Hases L; Williams C; Hartman J
Article: NUCLEIC ACIDS RESEARCH. 2020;48(19):10867-10876
MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells
Sumida N; Sifakis EG; Kiani NA; Ronnegren AL; Scholz BA; Vestlund J; Gomez-Cabrero D; Tegner J; Gondor A; Ohlsson R
Article: ESMO OPEN. 2020;5(6):e001032
PD-1 protein and gene expression as prognostic factors in early breast cancer
Matikas A; Zerdes I; Lovrot J; Sifakis E; Richard F; Sotiriou C; Rassidakis G; Bergh J; Valachis A; Foukakis T
Article: MOLECULAR ONCOLOGY. 2020;14(5):951-963
Programmed death-ligand 1 gene expression is a prognostic marker in early breast cancer and provides additional prognostic value to 21-gene and 70-gene signatures in estrogen receptor-positive disease
Zerdes I; Sifakis EG; Matikas A; Chretien S; Tobin NP; Hartman J; Rassidakis GZ; Bergh J; Foukakis T
Article: NATURE GENETICS. 2019;51(12):1723-1731
WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating
Scholz BA; Sumida N; de Lima CDM; Chachoua I; Martino M; Tzelepis I; Nikoshkov A; Zhao H; Mehmood R; Sifakis EG; Bhartiya D; Gondor A; Ohlsson R
Article: CANCERS. 2019;11(10):E1479-1479
STAT3 Activity Promotes Programmed-Death Ligand 1 Expression and Suppresses Immune Responses in Breast Cancer
Zerdes I; Wallerius M; Sifakis EG; Wallmann T; Betts S; Bartish M; Tsesmetzis N; Tobin NP; Coucoravas C; Bergh J; Rassidakis GZ; Rolny C; Foukakis T
Article: BREAST CANCER RESEARCH. 2019;21(1):34
The long-term prognostic and predictive capacity of cyclin D1 gene amplification in 2305 breast tumours
Lundberg A; Lindstroem LS; Li J; Harrell JC; Darai-Ramqvist E; Sifakis EG; Foukakis T; Perou CM; Czene K; Bergh J; Tobin NP
Article: IN VIVO. 2018;32(4):945-954
Correlation Between Contrast-enhanced Ultrasound Characteristics (Qualitative and Quantitative) and Pathological Prognostic Factors in Breast Cancer
Vraka I; Panourgias E; Sifakis E; Koureas A; Galanis P; Dellaportas D; Gouliamos A; Antoniou A
Article: MOLECULAR CELL. 2015;59(6):984-997
PARP1-and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription
Zhao H; Sifakis EG; Sumida N; Millan-Arino L; Scholz BA; Svensson JP; Chen X; Ronnegren AL; de Lima CDM; Varnoosfaderani FS; Shi C; Loseva O; Yammine S; Israelsson M; Rathje L-S; Nemeti B; Fredlund E; Helleday T; Imreh MP; Gondor A
Article: IEEE TRANSACTIONS ON IMAGE PROCESSING. 2014;23(9):3762-3772
Robust Carotid Artery Recognition in Longitudinal B-Mode Ultrasound Images
Sifakis EG; Golemati S
Article: IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS. 2014;18(3):817-823
A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip
Valavanis I; Sifakis EG; Georgiadis P; Kyrtopoulos S; Chatziioannou AA
Article: COMPUTERS IN BIOLOGY AND MEDICINE. 2012;42(1):19-29
Evaluating the effect of various background correction methods regarding noise reduction, in two-channel microarray data
Sifakis EG; Prentza A; Koutsouris D; Chatziioannou AA
Article: JOURNAL OF CLINICAL BIOINFORMATICS. 2011;1:36
Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach.
Sifakis EG; Lambrou GI; Prentza A; Vlahopoulos S; Koutsouris D; Tzortzatou-Stathopoulou F; Chatziioannou AA
Article: ULTRASOUND IN MEDICINE AND BIOLOGY. 2007;33(12):1918-1932
Using the hough transform to segment ultrasound images of longitudinal and transverse sections of the carotid artery
Golemati S; Stoitsis J; Sifakis EG; Balkizas T; Nikita KS
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Alla övriga publikationer

Conference publication: CLINICAL CANCER RESEARCH. 2025;31(12):p5-06-12-p5-06-12-P50612
BreastSubtypeR: Streamlining Intrinsic Molecular Subtyping in Breast Cancer Research with a User-Friendly R Package
Yang Q; Chen X; Hartman J; Sifakis EG
Conference publication: ESMO OPEN. 2024;9:103031
23P Longitudinal evaluation of PAM50 molecular subtypes in patients receiving neoadjuvant HER2-targeted therapy in the PREDIX HER2 trial
Zhu Y; Sifakis EG; Wang K; Zerdes I; Bergh J; Hatschek T; Matikas A; Foukakis T
Conference publication: ESMO OPEN. 2024;9:103075
69P Deep learning prognostication through prediction of TP53 gene mutation status on breast cancer hematoxylin and eosin slides
Tsiknakis N; Salgkamis D; Tzoras E; Wang K; Liu X; Manikis G; Sifakis EG; Bergh J; Marias K; Zerdes I; Matikas A; Foukakis T
Conference publication: ESMO OPEN. 2024;9:103063
56P Longitudinal circulating plasma protein immune profiling reveals biomarkers of treatment response to neoadjuvant trastuzumab-emtansine (T-DM1) in early HER2-positive breast cancer: A secondary analysis of the phase II PREDIX HER2 trial
Zerdes I; Wang K; Salgkamis D; Zhu Y; Sifakis EG; Acs B; Hartman J; Hatschek T; Bergh J; Matikas A; Foukakis T
Conference publication: CANCER RESEARCH. 2024;84(9):po4-01-05-po4-01-05
The prognostic importance of biological pathway enrichment patterns in trastuzumab-treated early HER2-positive breast cancer
Ronnlund C; Yang Q; Schagerholm C; Foukakis T; Fredriksson I; Chen X; Robertson S; Sifakis E; Hartman J
Meeting abstract: CANCER RESEARCH. 2024;84(9):po2-07-06-po2-07-06
Multimodal learning predictor of HER2-positive breast cancer therapy response in the randomized PREDIX HER2 trial
Wang K; Zhu Y; Zerdes I; Sifakis E; Manikis G; Salgkamis D; Tsiknakis N; Harbers L; Crosetto N; Bergh J; Matikas A; Hatschek T; Foukakis T
Meeting abstract: EUROPEAN JOURNAL OF CANCER. 2024;200:113830
Multiomic profiling reveals predictive molecular characteristics of response to neoadjuvant antibody-drug conjugate versus chemotherapy and dual HER2 blockade in HER2 positive breast cancer
Foukakis T; Wang K; Zerdes I; Zhu Y; Sifakis E; Tsiknakis N; Manikis G; Salgkamis D; Harbers L; Bergh J; Johansson H; Crosetto N; Lehtio J; Matikas A; Hatschek T
Meeting abstract: CANCER RESEARCH. 2023;83(5):p5-02-20-p5-02-20
Correlative and longitudinal transcriptomic profiling predicts patient outcomes and the efficacy of neoadjuvant HER2-targeted treatments in the randomized PREDIX HER2 trial
Wang K; Zhu Y; Zerdes I; Matikas A; Sifakis E; Salgkamis D; Bjohle J; Elinder E; Margolin S; Campos AB; Pekar G; Lindman H; Schiza A; Einbeigi Z; Adra J; Andersson A; Carlsson L; Dreifaldt AC; Isaksson-Friman E; Agartz S; Johansson H; Hellstrom M; Azavedo E; Hartman J; Bergh J; Hatschek T; Foukakis T
Meeting abstract: CANCER RESEARCH. 2023;83(5):p2-21-02-p2-21-02
Longitudinal tumor-immune microenvironment changes in patients with clinical luminal A early breast cancer treated with neoadjuvant palbociclib and endocrine therapy: results from the Swedish randomized PREDIX Luminal A trial
Zerdes I; Salgkamis D; Matikas A; Selander L; Wang K; Tzoras E; Sifakis E; Agartz S; Chen X; Hellstrom M; Hartman J; Bergh J; Foukakis T; Hatschek T
Conference publication: VIRCHOWS ARCHIV. 2022;481(SUPPL 1):S42-S43
PIK3CA mutations in endocrine-resistant breast cancer
Schagerholm C; Robertson S; Holm B; Awier H; Toosi H; Sifakis E; Hartman J
Meeting abstract: ANNALS OF ONCOLOGY. 2022;33(7):S640
Gene expression profiles in endocrine-resistant breast cancer
Schagerholm C; Robertson S; Sifakis EG; Hases L; Williams C; Hartman J
Meeting abstract: ANNALS OF ONCOLOGY. 2022;33(7):S614
The prognostic importance of high HER2 copy numbers and high HER2/CEP17 ratio in trastuzumab-treated early breast cancer
Ronnlund C; Robertson S; Sifakis EG; Fredriksson I; Foukakis T; Hartman J
Meeting abstract: ANNALS OF ONCOLOGY. 2022;33(7):S1306
Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction
Chen X; Sifakis EG; Robertson S; Neo SY; Jun S-H; Tong L; Lovrot J; Tay A; Hellgren R; Margolin S; Bergh J; Foukakis T; Lagergren J; Lundqvist A; Ma R; Hartman J
Meeting abstract: ANNALS OF ONCOLOGY. 2022;33:S125
Longitudinal proteogenomic profiling reveals therapeutic vulnerabilities of immunometabolism in breast cancer
Wang K; Zerdes I; Sifakis EG; Johansson HJ; Mezheyeuski A; Lehtio J; Bergh J; Hatschek T; Matikas A; Foukakis T
Meeting abstract: CANCER RESEARCH. 2022;82(4):p1-07-07-p1-07-07
Endoresist: Prognostic and predictive gene profiles in endocrine-resistant breast cancers
Schagerholm C; Robertson S; Holm B; Lindberg K; Sifakis E; Hases L; Williams C; Hartman J
Corrigendum: NATURE GENETICS. 2020;52(11):1265
WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating (vol 51, pg 1723, 2019)
Scholz BA; Sumida N; de Lima CDM; Chachoua I; Martino M; Tzelepis I; Nikoshkov A; Zhao H; Mehmood R; Sifakis EG; Bhartiya D; Gondor A; Ohlsson R
Conference publication: JOURNAL OF CLINICAL ONCOLOGY. 2020;38(15)
PD-1 protein and gene expression in early breast cancer: Prognostic implications.
Zerdes I; Matikas A; Lovrot J; Sifakis EG; Richard F; Sotiriou C; Rassidakis GZ; Bergh JCS; Valachis A; Foukakis T
Conference publication: JOURNAL OF CLINICAL ONCOLOGY. 2020;38(15_suppl):545
PD-1 protein and gene expression in early breast cancer: Prognostic implications.
Zerdes I; Matikas A; Lövrot J; Sifakis EG; Richard F; Sotiriou C; Rassidakis GZ; Bergh JCS; Valachis A; Foukakis T
Meeting abstract: CANCER RESEARCH. 2020;80(4):p3-08-07-p3-08-07
Expression of the novel tumor suppressor gene SAMHD1 correlates with favourable clinical outcome in basal-like (BL) early breast cancer
Kouvaraki M; Sifakis EG; Zerdes I; Herold N; Bergh J; Rassidakis GZ; Foukakis T
Meeting abstract: JOURNAL OF CLINICAL ONCOLOGY. 2019;37(15):550
Prognostic value of PD-L1 gene expression with Recurrence Score and 70-gene signature in patients with ER+/HER2-early breast cancer.
Zerdes I; Sifakis EG; Tobin N; Bergh JCS; Matikas A; Foukakis T
Meeting abstract: CANCER RESEARCH. 2019;79(4):p2-08-25-p2-08-25
PD-L1 expression at the protein and RNA levels as prognostic factor in early breast cancer
Zerdes I; Sifakis E; Matikas A; Tobin NP; Charlotte R; Rassidakis GZ; Bergh J; Foukakis T
Preprint: BIORXIV. 2018
The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulatingMYCin 3D: Implications for the fitness of cancer cells
Sumida N; Sifakis E; Scholz B; Fernandez-Woodbridge A; Kiani N; Gomez-Cabrero D; Svensson P; Tegner J; Göndör A; Ohlsson R
Book chapter: ENCYCLOPEDIA OF INFORMATION SCIENCE AND TECHNOLOGY, THIRD EDITION: ADVANCES IN INFORMATION QUALITY AND MANAGEMENT. 2014;p. 5593-5606
Microarrays
Khosrow-Pour M; Lambrou GI; Braoudaki M; Sifakis E; Zaravinos A
Conference publication: 2013;:1-5
Identifying Gender Independent Biomarkers Responsible for Human Muscle Aging Using Microarray Data
Sifakis EG; Valavanis I; Papadodima O; Chatziioannou AA
Book chapter: ENGINEERING APPLICATIONS OF NEURAL NETWORKS: COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE. 2013;p. 249-256
Derivation of Cancer Related Biomarkers from DNA Methylation Data from an Epidemiological Cohort
Valavanis I; Sifakis EG; Georgiadis P; Kyrtopoulos S; Chatziioannou AA
Conference publication: 2012;:632-637
Analysis of DNA Methylation Epidemiological Data through a Generic Composite Statistical Framework
Valavanis I; Sifakis E; Georgiadis P; Kyrtopoulos S; Chatziioannou AA
Conference publication: 2010;:122-129
SETTING A RATIONAL FRAMEWORK FOR EXPERIMENTAL DESIGN AND ANALYSIS OF HIGH-THROUGHPUT DNA MICROARRAY EXPERIMENTS AND DATA
LAMBROU GI; CHATZIIOANNOU A; SIFAKIS E; PRENTZA A; KOUTSOURIS D; KOULTOUKI E; TZORTZATOU-STATHOPOULOU F
Conference publication: 2009;:1-5
Comparative Computational Methods for Identification of Inherent or Acquired Mechanisms of Resistance to Prednisolone in Acute Lymphoblastic Leukemia Cells
Lambrou GI; Sifakis EG; Prentza A; Chatziioannou A; Koutsouris D; Koultouki E; Tzortzatou-Stathopoulou F
Conference publication: 2008;:1-6
cDNA microarray analysis of a glucocorticoid treated acute lymphoblastic leukemia cell line
Sifakis EG; Lambrou GI; Prentza A; Koutsouris D; Tzortzatou-Stathopoulou F
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Forskningsbidrag

Optimizing treatment in HER2 positive breast cancer through insights in tumor biology
Swedish Research Council
1 January 2019 - 31 December 2021

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