A Versatile and Upgraded Version of the LundTax Classification Algorithm Applied to Independent Cohorts

Authors: Cotillas, Elena Aramendía, Bernardo, Carina, Veerla, Srinivas, Liedberg, Fredrik, Sjödahl, Gottfrid, Eriksson, Pontus

Source: In The Journal of Molecular Diagnostics December 2024 26(12):1081-1101

Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer.

Authors: Hohmann, Lennart, Sigurjonsdottir, Kristin, Campos, Ana Bosch, Nacer, Deborah F., Veerla, Srinivas, Rosengren, Frida, Reddy, Poojaswini Thimmaraya, Häkkinen, Jari, Nordborg, Nicklas, Vallon-Christersson, Johan, Memari, Yasin, Black, Daniella, Bowden, Ramsay, Davies, Helen R., Borg, Åke, Nik-Zainal, Serena, Staaf, Johan

Source: Nature Communications; 3/5/2025, Vol. 16 Issue 1, p1-17, 17p

Subject Terms: SECONDARY primary cancer, MEDICAL sciences, BREAST cancer, BREAST tumors, IMMUNE response, BREAST

Tertiary lymphoid structures in high-grade serous tubo-ovarian carcinoma: anatomical site matters.

Authors: Westbom-Fremer, Sofia, Tran, Lena, Ebbesson, Anna, Martin de la Fuente, Laura, Jönsson, Jenny-Maria, Kannisto, Päivi, Veerla, Srinivas, Hedenfalk, Ingrid

Source: Cancer Immunology, Immunotherapy; Feb2025, Vol. 74 Issue 2, p1-12, 12p

Subject Terms: REGULATORY T cells, CYTOTOXIC T cells, MEDICAL sciences, B cells, T cells

SRIQ clustering: A fusion of Random Forest, QT clustering, and KNN concepts

Authors: Karlström, Jacob, Aine, Mattias, Staaf, Johan, Veerla, Srinivas

Source: Computational and Structural Biotechnology Journal. 20:1567-1579

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191323168.0x000001&indx=1&recIds=ETOCvdc_100191323168.0x000001

Tumor purity estimated from bulk DNA methylation can be used for adjusting beta values of individual samples to better reflect tumor biology.

Authors: Sasiain, Iñaki, Nacer, Deborah F, Aine, Mattias, Veerla, Srinivas, Staaf, Johan

Source: NAR Genomics & Bioinformatics; Dec2024, Vol. 6 Issue 4, p1-12, 12p

How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? A Study of Paired Core-Needle Biopsies and Surgical Specimens in Early Breast Cancer.

Authors: Saghir, Hani¹ (AUTHOR), Veerla, Srinivas¹ (AUTHOR), Malmberg, Martin^1,2 (AUTHOR), Rydén, Lisa^1,3 (AUTHOR), Ehinger, Anna^1,4 (AUTHOR), Saal, Lao H.¹ (AUTHOR), Vallon-Christersson, Johan¹ (AUTHOR), Borg, Åke¹ (AUTHOR), Hegardt, Cecilia¹ (AUTHOR), Larsson, Christer⁵ (AUTHOR), Haidar, Alaa⁶ (AUTHOR), Hedenfalk, Ingrid¹ (AUTHOR), Loman, Niklas^1,2 (AUTHOR), Kimbung, Siker¹ (AUTHOR) siker.kimbung@med.lu.se

Source: Cancers. Aug2022, Vol. 14 Issue 16, p4000. 16p.

Subject Terms: *BREAST cancer prognosis, *BIOMARKERS, *STATISTICS, *SEQUENCE analysis, *IMMUNOHISTOCHEMISTRY, *MICRORNA, *ESTROGEN receptors, *GENE expression profiling, *GENOMICS, *COLLECTION & preservation of biological specimens, *DATA analysis, *NEEDLE biopsy, *PROGESTERONE receptors, *LONGITUDINAL method, RESEARCH evaluation

A human antithrombin isoform dampens inflammatory responses and protects from organ damage during bacterial infection

Authors: Papareddy, Praveen, Rossnagel, Madlen, Doreen Hollwedel, Femke, Kilic, Gülcan, Veerla, Srinivas, Naudin, Clément, Smeds, Emanuel, Westman, Johannes, Martinez-Martinez, Irene, Egesten, Arne, de la Morena-Barrio, Maria Eugenia, Corral, Javier, Linder, Adam, Artoni, Andrea, Abbattista, Maria, Novembrino, Cristina, Herbert Brakebusch, Cord, Martinelli, Ida, Kasetty, Gopinath, Herwald, Heiko

Source: Nature microbiology. 4(12):2442-2455

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130017590.0x000001&indx=1&recIds=ETOCvdc_100130017590.0x000001

Cell-Type-Specific Gene Programs of the Normal Human Nephron Define Kidney Cancer Subtypes

Authors: Lindgren, David, Eriksson, Pontus, Krawczyk, Krzysztof, Nilsson, Helén, Hansson, Jennifer, Veerla, Srinivas, Sjölund, Jonas, Höglund, Mattias, Johansson, Martin E., Axelson, Håkan

Source: In Cell Reports 8 August 2017 20(6):1476-1489

Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification

Authors: Karlsson, Anna, Brunnström, Hans, Micke, Patrick, Veerla, Srinivas, Mattsson, Johanna, La Fleur, Linnea, Botling, Johan, Jönsson, Mats, Reuterswärd, Christel, Planck, Maria, Staaf, Johan

Source: In Journal of Thoracic Oncology August 2017 12(8):1257-1267

Promoter-associated proteins of EPAS1 identified by enChIP-MS – A putative role of HDX as a negative regulator

Authors: Hamidian, Arash, Vaapil, Marica, von Stedingk, Kristoffer, Fujita, Toshitsugu, Persson, Camilla U., Eriksson, Pontus, Veerla, Srinivas, De Preter, Katleen, Speleman, Frank, Fujii, Hodaka, Påhlman, Sven, Mohlin, Sofie

Source: Biochemical and biophysical research communications. 499(2):291-298

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100085322482.0x000001&indx=1&recIds=ETOCvdc_100085322482.0x000001

Kataegis in clinical and molecular subgroups of primary breast cancer.

Authors: Veerla, Srinivas, Staaf, Johan

Source: NPJ Breast Cancer; 4/24/2024, Vol. 10 Issue 1, p1-13, 13p

The role of extracellular vesicle fusion with target cells in triggering systemic inflammation.

Authors: Papareddy, Praveen, Tapken, Ines, Kroh, Keshia, Varma Bhongir, Ravi Kiran, Rahman, Milladur, Baumgarten, Maria, Cim, Eda Irem, Györffy, Lilla, Smeds, Emanuel, Neumann, Ariane, Veerla, Srinivas, Olinder, Jon, Thorlacus, Henrik, Ryden, Cecilia, Bartakova, Eva, Holub, Michal, Herwald, Heiko

Source: Nature Communications; 2/7/2024, Vol. 15 Issue 1, p1-17, 17p

Prognostic Significance in Breast Cancer of a Gene Signature Capturing Stromal PDGF Signaling

Authors: Frings, Oliver, Augsten, Martin, Tobin, Nicholas P., Carlson, Joseph, Paulsson, Janna, Pena, Cristina, Olsson, Eleonor, Veerla, Srinivas, Bergh, Jonas, Östman, Arne, Sonnhammer, Erik L.L.

Source: In The American Journal of Pathology June 2013 182(6):2037-2047

Perturbation and stability of PAM50 subtyping in population-based primary invasive breast cancer.

Authors: Veerla, Srinivas, Hohmann, Lennart, Nacer, Deborah F., Vallon-Christersson, Johan, Staaf, Johan

Source: NPJ Breast Cancer; 10/19/2023, Vol. 9 Issue 1, p1-15, 15p

Retained Heterodisomy Is Associated with High Gene Expression in Hyperhaploid Inflammatory Leiomyosarcoma

Authors: Nord, Karolin H., Paulsson, Kajsa, Veerla, Srinivas, Wejde, Johan, Brosjö, Otte, Mandahl, Nils, Mertens, Fredrik

Source: In Neoplasia September 2012 14(9):807

DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status

Authors: Lauss, Martin, Aine, Mattias, Sjödahl, Gottfrid, Veerla, Srinivas, Patschan, Oliver, Gudjonsson, Sigurdur, Chebil, Gunilla, Lövgren, Kristina, Fernö, Mårten, Månsson, Wiking, Liedberg, Fredrik, Ringnér, Markus, Lindgren, David, Höglund, Mattias

Source: Epigenetics. 7(8):858-867

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100050753542.0x000001&indx=1&recIds=ETOCvdc_100050753542.0x000001

CD169 + Macrophages in Primary Breast Tumors Associate with Tertiary Lymphoid Structures, T regs and a Worse Prognosis for Patients with Advanced Breast Cancer.

Authors: Briem, Oscar, Källberg, Eva, Kimbung, Siker, Veerla, Srinivas, Stenström, Jenny, Hatschek, Thomas, Hagerling, Catharina, Hedenfalk, Ingrid, Leandersson, Karin

Source: Cancers; Feb2023, Vol. 15 Issue 4, p1262, 18p

Subject Terms: BREAST cancer prognosis, MACROPHAGES, LYMPHOID tissue

Interferon Alpha-Inducible Protein 27 Expression Is Linked to Disease Severity in Chronic Infection of Both HIV-1 and HIV-2.

Authors: Palm, Angelica A.¹, angelica.palm@med.lu.se, Veerla, Srinivas², Lindman, Jacob², Isberg, Per-Erik³, Johansson, Emil⁴, Biague, Antonio⁵, Månsson, Fredrik⁴, Norrgren, Hans², Esbjörnsson, Joakim⁴, Medstrand, Patrik⁴, Jansson, Marianne¹

Source: Frontiers in Virology; 6/13/2022, p1-8, 8p

CYP1A2--a novel genetic marker for early aromatase inhibitor response in the treatment of breast cancer patients.

Authors: Simonsson, Maria¹, Veerla, Srinivas¹, Markkula, Andrea¹, Rose, Carsten², Ingvar, Christian³, Jernström, Helena¹ helena.jernstrom@med.lu.se

Source: BMC Cancer. 3/31/2016, Vol. 16, p1-12. 12p. 1 Diagram, 2 Charts, 2 Graphs.

Subject Terms: *BREAST cancer patients, *BREAST cancer treatment, *AROMATASE inhibitors, *GENETIC markers, *CYTOCHROME P-450, *SINGLE nucleotide polymorphisms, *BIOMARKERS, *BREAST tumors, *COMPARATIVE studies, *GENETIC polymorphisms, *GENETIC techniques, *RESEARCH methodology, *MEDICAL cooperation, *OXIDOREDUCTASES, *PROGNOSIS, *RESEARCH, *AROMATASE, *EVALUATION research, *GENOTYPES

Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs

Authors: Ringnér Markus, Veerla Srinivas, Höglund Mattias

Source: BMC Genomics, Vol 11, Iss 1, p 145 (2010)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2164/11/145; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/694544dc3c954125b8c37d8c5dfad225