Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules.

Zelmina Lubovac Zelmina Lubovac-Pilav

Hendrik A. de Weerd Dimitri Guala Mika Gustafsson Jane Synnergren Jesper Tegnér Zelmina Lubovac-Pilav Rasmus Magnusson Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules. 101093 2024 5 Patterns 11 https://doi.org/10.1016/j.patter.2024.101093 db/journals/patterns/patterns5.html#WeerdGGSTLM24 streams/journals/patterns

Julia Åkesson Zelmina Lubovac-Pilav Rasmus Magnusson Mika Gustafsson ComHub: Community predictions of hubs in gene regulatory networks. 58 2021 22 BMC Bioinform. 1 https://doi.org/10.1186/s12859-021-03987-y db/journals/bmcbi/bmcbi22.html#AkessonLMG21

Rasmus Magnusson Zelmina Lubovac-Pilav TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes. 440 2021 22 BMC Bioinform. 1 https://doi.org/10.1186/s12859-021-04357-4 https://www.wikidata.org/entity/Q113242223 db/journals/bmcbi/bmcbi22.html#MagnussonL21

Hendrik A. de Weerd Tejaswi V. S. Badam David Martínez-Enguita Julia Åkesson Daniel Muthas Mika Gustafsson Zelmina Lubovac-Pilav MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks. 3918-3919 2020 36 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btaa235 https://www.wikidata.org/entity/Q91763285 db/journals/bioinformatics/bioinformatics36.html#WeerdBMAMGL20

Holger Weishaupt Patrik Johansson Anders Sundström Zelmina Lubovac-Pilav Björn Olsson Sven Nelander Fredrik J. Swartling Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes. 3357-3364 2019 35 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btz066 https://www.wikidata.org/entity/Q91329465 db/journals/bioinformatics/bioinformatics35.html#WeishauptJSLONS19

Emmy Borgmästars Hendrik A. de Weerd Zelmina Lubovac-Pilav Malin Sund miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer. 393:1-393:17 2019 20 BMC Bioinform. 1 https://doi.org/10.1186/s12859-019-2974-3 https://www.wikidata.org/entity/Q91932289 db/journals/bmcbi/bmcbi20.html#BorgmastarsWLS19

Jörg Linde Björn Olsson Zelmina Lubovac Network Properties for Ranking Predicted miRNA Targets in Breast Cancer. 2009 2009 Adv. Bioinformatics https://doi.org/10.1155/2009/182689 https://www.wikidata.org/entity/Q39441873 db/journals/abi/abi2009.html#LindeOL09 182689:1-182689:7

Thomas Zichner Zelmina Lubovac Björn Olsson Temporal Analysis of Oncogenesis Using MicroRNA Expression Data. 128-137 2008 German Conference on Bioinformatics conf/gcb/2008 db/conf/gcb/gcb2008.html#ZichnerLO08 https://dl.gi.de/handle/20.500.12116/21209 http://subs.emis.de/LNI/Proceedings/Proceedings136/article2248.html Zelmina Lubovac David Corne Jonas Gamalielsson Björn Olsson Weighted Cohesiveness for Identification of Functional Modules and Their Interconnectivity. 185-198 2007 conf/bird/2007 BIRD https://doi.org/10.1007/978-3-540-71233-6_15 db/conf/bird/bird2007.html#LubovacCGO07

Angelica Lindlöf Zelmina Lubovac Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks. 2005 5 Silico Biol. 3 http://content.iospress.com/articles/in-silico-biology/isb00183 http://www.bioinfo.de/isb/abstracts/05/0023.html db/journals/isb/isb5.html#LindlofL05 239-249

Per Jonsson Kim Laurio Zelmina Lubovac Björn Olsson Magnus L. Andersson Using functional annotation to improve clusterings of gene expression patterns. 183-194 2002 145 Inf. Sci. 3-4 https://doi.org/10.1016/S0020-0255(02)00230-X db/journals/isci/isci145.html#JonssonLLOA02

Per Jonsson Kim Laurio Zelmina Lubovac Björn Olsson Magnus L. Andersson Using Functional Annotation to Improve Clusterings of Gene Expression Patterns. 1257-1262 2002 conf/jcis/2002 JCIS db/conf/jcis/jcis2002.html#JonssonLLOA02 Julia Åkesson Magnus L. Andersson Tejaswi V. S. Badam Emmy Borgmästars David W. CorneDavid Corne Jonas Gamalielsson Dimitri Guala Mika Gustafsson Patrik Johansson Per Jonsson Kim Laurio Jörg Linde Angelica Lindlöf Rasmus Magnusson David Martínez-Enguita Daniel Muthas Sven Nelander Björn Olsson Malin Sund Anders Sundström Fredrik J. Swartling Jane Synnergren Jesper Tegnér Hendrik A. de Weerd Holger Weishaupt Thomas Zichner