Magda Bienko

Publications
Grants
Public outreach and news

Selected publications

Article: NATURE COMMUNICATIONS. 2024;15(1):1768

scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.

Chen JP; Diekmann C; Wu H; Chen C; Della Chiara G; Berrino E; Georgiadis KL; Bouwman BAM; Virdi M; Harbers L; Bellomo SE; Marchiò C; Bienko M; Crosetto N

Articles

Article: BIOLOGY OPEN. 2023;12(10):bio060113

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.

Mastropasqua F; Oksanen M; Soldini C; Alatar S; Arora A; Ballarino R; Molinari M; Agostini F; Poulet A; Watts M; Rabkina I; Becker M; Li D; Anderlid B-M; Isaksson J; Lundin Remnelius K; Moslem M; Jacob Y; Falk A; Crosetto N; Bienko M; Santini E; Borgkvist A; Bölte S; Tammimies K
Article: DEVELOPMENT. 2023;150(15):dev201548

Separation of transcriptional repressor and activator functions in Drosophila HDAC3.

Tang M; Regadas I; Belikov S; Shilkova O; Xu L; Wernersson E; Liu X; Wu H; Bienko M; Mannervik M
Article: CURRENT OPINION IN GENETICS & DEVELOPMENT. 2023;78:102020

A GC-centered view of 3D genome organization.

Bouwman BA; Crosetto N; Bienko M
Article: JTO CLINICAL AND RESEARCH REPORTS. 2022;3(12):100435

Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases.

Nicoś M; Harbers L; Patrucco E; Kramer-Drauberg M; Zhang X; Voena C; Kowalczyk A; Bożyk A; Pęksa R; Jarosz B; Szumiło J; Simonetti M; Żuk M; Wasąg B; Reszka K; Duchnowska R; Milanowski J; Chiarle R; Bienko M; Krawczyk P; Jassem J; Ambrogio C; Crosetto N
Article: NATURE COMMUNICATIONS. 2022;13(1):6680

FRET-FISH probes chromatin compaction at individual genomic loci in single cells.

Mota A; Berezicki S; Wernersson E; Harbers L; Li-Wang X; Gradin K; Peuckert C; Crosetto N; Bienko M
Article: SCIENTIFIC DATA. 2022;9(1):400

An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.

Ballarino R; Bouwman BAM; Agostini F; Harbers L; Diekmann C; Wernersson E; Bienko M; Crosetto N
Article: SCIENTIFIC DATA. 2022;9(1):47

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.

Mota A; Schweitzer M; Wernersson E; Crosetto N; Bienko M
Article: CURRENT OPINION IN CELL BIOLOGY. 2022;74:7-12

RNA gradients: Shapers of 3D genome architecture.

Bouwman BAM; Crosetto N; Bienko M
Article: DEVELOPMENTAL CELL. 2022;57(2):180-196.e7

piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development.

Cornes E; Bourdon L; Singh M; Mueller F; Quarato P; Wernersson E; Bienko M; Li B; Cecere G
Article: NATURE COMMUNICATIONS. 2021;12(1):3903

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.

Simonetti M; Zhang N; Harbers L; Milia MG; Brossa S; Huong Nguyen TT; Cerutti F; Berrino E; Sapino A; Bienko M; Sottile A; Ghisetti V; Crosetto N
Article: FRONTIERS IN ONCOLOGY. 2021;11:700568

Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas.

Harbers L; Agostini F; Nicos M; Poddighe D; Bienko M; Crosetto N
Article: NATURE PROTOCOLS. 2020;15(12):3894-3941

Genome-wide detection of DNA double-strand breaks by in-suspension BLISS.

Bouwman BAM; Agostini F; Garnerone S; Petrosino G; Gothe HJ; Sayols S; Moor AE; Itzkovitz S; Bienko M; Roukos V; Crosetto N
Article: NATURE COMMUNICATIONS. 2020;11(1):5445

Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.

Tarbier M; Mackowiak SD; Frade J; Catuara-Solarz S; Biryukova I; Gelali E; Menéndez DB; Zapata L; Ossowski S; Bienko M; Gallant CJ; Friedländer MR
Article: NATURE BIOTECHNOLOGY. 2020;38(10):1184-1193

GPSeq reveals the radial organization of chromatin in the cell nucleus.

Girelli G; Custodio J; Kallas T; Agostini F; Wernersson E; Spanjaard B; Mota A; Kolbeinsdottir S; Gelali E; Crosetto N; Bienko M
Article: CELL. 2019;179(7):1647-1660.e19

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Asp M; Giacomello S; Larsson L; Wu C; Fürth D; Qian X; Wärdell E; Custodio J; Reimegård J; Salmén F; Österholm C; Ståhl PL; Sundström E; Åkesson E; Bergmann O; Bienko M; Månsson-Broberg A; Nilsson M; Sylvén C; Lundeberg J
Article: NATURE COMMUNICATIONS. 2019;10(1):4732

CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples.

Zhang X; Garnerone S; Simonetti M; Harbers L; Nicoś M; Mirzazadeh R; Venesio T; Sapino A; Hartman J; Marchiò C; Bienko M; Crosetto N
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019;116(19):9443-9452

Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration.

Li D; Kular L; Vij M; Herter EK; Li X; Wang A; Chu T; Toma M-A; Zhang L; Liapi E; Mota A; Blomqvist L; Gallais Sérézal I; Rollman O; Wikstrom JD; Bienko M; Berglund D; Ståhle M; Sommar P; Jagodic M; Landén NX
Article: NATURE COMMUNICATIONS. 2019;10(1):1636

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture.

Gelali E; Girelli G; Matsumoto M; Wernersson E; Custodio J; Mota A; Schweitzer M; Ferenc K; Li X; Mirzazadeh R; Agostini F; Schell JP; Lanner F; Crosetto N; Bienko M
Journal article: PROTOCOL EXCHANGE. 2019

iFISH:a publically available resource enabling versatile DNA FISH to study genome architecture

Crosetto N; Bienko M; Gelali E; Girelli G; Matsumoto M; Wernersson E; Custodio J; Mota A; Schweitzer M; Ferenc K; Li X; Mirzazadeh R; Agostini F; Schell JP; Lanner F
Article: METHODS IN MOLECULAR BIOLOGY. 2018;1672:167-194

Genome-Wide Profiling of DNA Double-Strand Breaks by the BLESS and BLISS Methods.

Mirzazadeh R; Kallas T; Bienko M; Crosetto N
Article: COMMUNICATIONS BIOLOGY. 2018;1:209

RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.

Wu C; Simonetti M; Rossell C; Mignardi M; Mirzazadeh R; Annaratone L; Marchiò C; Sapino A; Bienko M; Crosetto N; Nilsson M
Article: METHODS IN MOLECULAR BIOLOGY. 2018;1766:303-333

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

Gelali E; Custodio J; Girelli G; Wernersson E; Crosetto N; Bienko M
Journal article: PROTOCOL EXCHANGE. 2017

Breaks Labeling in situ and sequencing (BLISS)

Mirzazadeh R; Yan WX; Mirzazadeh R; Garnerone S; Scott D; Schneider MW; Kallas T; Custodio J; Wernersson E; Li Y; Gao L; Federova Y; Zetsche B; Zhang F; Bienko M; Crosetto N
Article: NATURE COMMUNICATIONS. 2017;8:15058

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.

Yan WX; Mirzazadeh R; Garnerone S; Scott D; Schneider MW; Kallas T; Custodio J; Wernersson E; Li Y; Gao L; Federova Y; Zetsche B; Zhang F; Bienko M; Crosetto N
Article: ONCOTARGET. 2017;8(12):18680-18698

Quantification of HER2 and estrogen receptor heterogeneity in breast cancer by single-molecule RNA fluorescence in situ hybridization.

Annaratone L; Simonetti M; Wernersson E; Marchiò C; Garnerone S; Scalzo MS; Bienko M; Chiarle R; Sapino A; Crosetto N
Article: NATURE COMMUNICATIONS. 2016;7:13182

Massive and parallel expression profiling using microarrayed single-cell sequencing.

Vickovic S; Ståhl PL; Salmén F; Giatrellis S; Westholm JO; Mollbrink A; Navarro JF; Custodio J; Bienko M; Sutton L-A; Rosenquist R; Frisén J; Lundeberg J
Article: CELL. 2015;163(1):134-147

Genome-wide maps of nuclear lamina interactions in single human cells.

Kind J; Pagie L; de Vries SS; Nahidiazar L; Dey SS; Bienko M; Zhan Y; Lajoie B; de Graaf CA; Amendola M; Fudenberg G; Imakaev M; Mirny LA; Jalink K; Dekker J; van Oudenaarden A; van Steensel B
Article: NATURE BIOTECHNOLOGY. 2015;33(3):285-289

Integrated genome and transcriptome sequencing of the same cell.

Dey SS; Kester L; Spanjaard B; Bienko M; van Oudenaarden A
Article: CELL REPORTS. 2014;6(1):18-23

FuseFISH: robust detection of transcribed gene fusions in single cells.

Semrau S; Crosetto N; Bienko M; Boni M; Bernasconi P; Chiarle R; van Oudenaarden A
Article: NATURE METHODS. 2013;10(4):361-365

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.

Crosetto N; Mitra A; Silva MJ; Bienko M; Dojer N; Wang Q; Karaca E; Chiarle R; Skrzypczak M; Ginalski K; Pasero P; Rowicka M; Dikic I
Article: NATURE METHODS. 2013;10(2):122-124

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Bienko M; Crosetto N; Teytelman L; Klemm S; Itzkovitz S; van Oudenaarden A
Article: METHODS IN MOLECULAR BIOLOGY. 2012;832:163-171

Role of UbL family modifiers and their binding proteins in cell signaling.

van Wijk SJL; Bienko M; Dikic I
Article: MOLECULAR CELL. 2010;37(3):408-417

Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1.

Bomar MG; D'Souza S; Bienko M; Dikic I; Walker GC; Zhou P
Article: MOLECULAR CELL. 2010;37(3):396-407

Regulation of translesion synthesis DNA polymerase eta by monoubiquitination.

Bienko M; Green CM; Sabbioneda S; Crosetto N; Matic I; Hibbert RG; Begovic T; Niimi A; Mann M; Lehmann AR; Dikic I
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2008;283(50):35173-35185

Human Wrnip1 is localized in replication factories in a ubiquitin-binding zinc finger-dependent manner.

Crosetto N; Bienko M; Hibbert RG; Perica T; Ambrogio C; Kensche T; Hofmann K; Sixma TK; Dikic I
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2008;283(8):4658-4664

Requirements for the interaction of mouse Polkappa with ubiquitin and its biological significance.

Guo C; Tang T-S; Bienko M; Dikic I; Friedberg EC
Article: MOLECULAR AND CELLULAR BIOLOGY. 2006;26(23):8892-8900

Ubiquitin-binding motifs in REV1 protein are required for its role in the tolerance of DNA damage.

Guo C; Tang T-S; Bienko M; Parker JL; Bielen AB; Sonoda E; Takeda S; Ulrich HD; Dikic I; Friedberg EC
Article: SCIENCE. 2005;310(5755):1821-1824

Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis.

Bienko M; Green CM; Crosetto N; Rudolf F; Zapart G; Coull B; Kannouche P; Wider G; Peter M; Lehmann AR; Hofmann K; Dikic I
Journal article: GBM ANNUAL FALL MEETING BERLIN/POTSDAM 2005. 2005;2005(Fall)

Regulation of cell signalling by ubiquitylation

Dikic I; Bienko M; Hoeller D; Crosetto N; Zapart G; Hofmann K
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All other publications

Editorial comment: MOLECULAR CELL. 2024;84(1):12-13

Compartmentalizing damaged DNA: A double-edged sword.

Georgiades E; Crosetto N; Bienko M
Preprint: BIORXIV. 2023

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue

Zhang N; Harbers L; Simonetti M; Diekmann C; Verron Q; Berrino E; Bellomo SE; Longo GMC; Ratz M; Schultz N; Tarish F; Su P; Han B; Wang W; Onorato S; Giordano S; Yang Q; Sapino A; Frisén J; Alkass K; Druid H; Roukos V; Helleday T; Marchiò C; Bienko M; Crosetto N
Editorial comment: NATURE REVIEWS GENETICS. 2023;24(7):418

How Hi-C ignited the era of 3D genome biology.

Bienko M
Preprint: RESEARCH SQUARE. 2023

scCUTseq is a versatile framework for spatially resolved single-cell genomic analyses of intratumor heterogeneity

Zhang N; Simonetti M; Harbers L; Helleday T; Roukos V; Marchio C; Bienko M; Crosetto N
Preprint: RESEARCH SQUARE. 2023

scCircle-seq unveils the diversity and complexity of circular DNAs in single cells

Chen JP; Bouwman B; Wu H; Chen C; Bienko M; Crosetto N
Review: FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY. 2023;11:1303862

Enhancers dysfunction in the 3D genome of cancer cells.

Della Chiara G; Jiménez C; Virdi M; Crosetto N; Bienko M
Review: TRENDS IN GENETICS. 2022;38(10):1062-1075

The era of 3D and spatial genomics.

Bouwman BAM; Crosetto N; Bienko M
Preprint: BIORXIV. 2022

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

Mastropasqua F; Oksanen M; Soldini C; Alatar S; Arora A; Ballarino R; Molinari M; Agostini F; Poulet A; Watts M; Rabkina I; Becker M; Li D; Anderlid B-M; Isaksson J; Remnelius KL; Moslem M; Jacob Y; Falk A; Crosetto N; Bienko M; Santini E; Borgkvist A; Bölte S; Tammimies K
Preprint: BIORXIV. 2022

Separation of transcriptional repressor and activator functions in HDAC3

Tang M; Regadas I; Belikov S; Shilkova O; Xu L; Wernersson E; Liu X; Wu H; Bienko M; Mannervik M
Editorial comment: MOLECULAR CELL. 2022;82(10):1783-1785

Dangerous RNA links pave the way to glioblastoma.

Bienko M
Preprint: RESEARCH SQUARE. 2022

Comparative genomic profiling identifies targetable brain metastasis drivers in non-small cell lung cancer

Nicos M; Harbers L; Patrucco E; Kramer-Drauberg M; Zhang X; Voena C; Kowalczyk A; Bozyk A; Peksa R; Jarosz B; Szumilo J; Simonetti M; Zuk M; Wasag B; Reszka K; Duchnowska R; Milanowski J; Chiarle R; Bienko M; Krawczyk P; Jassem J; Ambrogio C; Crosetto N
Preprint: RESEARCH SQUARE. 2022

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

Wernersson E; Gelali E; Girelli G; Wang S; Castillo D; Langseth CM; Nguyen H; Chattoraj S; Casals AM; Lundberg E; Nilsson M; Marti-Renom M; Wu C-T; Crosetto N; Bienko M
Conference publication: EUROPEAN JOURNAL OF HUMAN GENETICS. 2022;30(SUPPL 1):16

Sequencing Genome Organization

Girelli G; Custodio J; Kallas T; Agostini F; Wernersson E; Spanjaard B; Mota A; Kolbeinsdottir S; Gelali E; Crosetto N; Bienko M
Preprint: RESEARCH SQUARE. 2021

FRET-FISH probes chromatin compaction at individual genomic loci in single cells

Mota A; Wernersson E; Li-Wang X; Gradin K; Crosetto N; Bienko M
Preprint: RESEARCH SQUARE. 2021

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue

Crosetto N; Zhang N; Harbers L; Simonetti M; Longo G; Berrino E; Schultz N; Tarish F; Su P; Han B; Wang W; Onorato S; Yang Q; Helleday T; Roukos V; Marchiò C; Bienko M
Preprint: RESEARCH SQUARE. 2021

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

Simonetti M; Zhang N; Harbers L; Milia MG; Brossa S; Nguyen TTH; Cerruti F; Berrino E; Sapino A; Bienko M; Sottile A; Ghisetti V; Crosetto N
Preprint: RESEARCH SQUARE. 2021

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

Simonetti M; Zhang N; Harbers L; Milia MG; Brossa S; Nguyen TTH; Cerruti F; Berrino E; Sapino A; Bienko M; Sottile A; Ghisetti V; Crosetto N
Preprint: RESEARCH SQUARE. 2021

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

Simonetti M; Zhang N; Harbers L; Milia MG; Nguyen TTH; Brossa S; Bienko M; Sapino A; Sottile A; Ghisetti V; Crosetto N
Preprint: RESEARCH SQUARE. 2021

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

Simonetti M; Zhang N; Harbers L; Milia MG; Nguyen T; Brossa S; Bienko M; Sapino A; Sottile A; Ghisetti V; Crosetto N
Preprint: RESEARCH SQUARE. 2020

GPSeq reveals the radial organization of chromatin in the cell nucleus

Custodio J; Kallas T; Girelli G; Agostini F; Wernersson E; Spanjaard B; Mota A; Kolbeinsdottir S; Gelali E; Crosetto N; Bienko M
Review: FRONTIERS IN GENETICS. 2020;11:33

Radial Organization in the Mammalian Nucleus.

Crosetto N; Bienko M
Preprint: RESEARCH SQUARE. 2019

CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples

Zhang X; Garnerone S; Simonetti M; Harbers L; Nicoś M; Mirzazadeh R; Venesio T; Sapino A; Hartman J; Marchiò C; Bienko M; Crosetto N
Preprint: RESEARCH SQUARE. 2019

Breaks Labeling in situ and sequencing (BLISS)

Yan WX; Mirzazadeh R; Garnerone S; Scott D; Schneider MW; Kallas T; Custodio J; Li Y; Gao L; Federova Y; Wernersson E; Zetsche B; Zhang F; Bienko M; Crosetto N
Preprint: RESEARCH SQUARE. 2019

CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples

Zhang X; Garnerone S; Simonetti M; Harbers L; Nicoś M; Mirzazadeh R; Venesio T; Sapino A; Hartman J; Marchiò C; Bienko M; Crosetto N
Preprint: BIORXIV. 2019

Nuclear gene proximity and protein interactions shape transcript covariances in mammalian single cells

Tarbier M; Mackowiak SD; Frade J; Catuara-Solarz S; Biryukova I; Gelali E; Menéndez DB; Zapata L; Ossowski S; Bienko M; Gallant CJ; Friedländer MR
Conference publication: JOURNAL OF INVESTIGATIVE DERMATOLOGY. 2019;139(9):S323

Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration

Li D; Kular L; Vij M; Li X; Wang A; Toma M; Zhang L; Blomqvist L; Serezal I; Bienko M; Berglund D; Stahle M; Sommar P; Jagodic M; Landen NX
Preprint: RESEARCH SQUARE. 2019

CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples

Zhang X; Garnerone S; Simonetti M; Nicoś M; Harbers L; Marchiò C; Mirzazadeh R; Venesio T; Sapino A; Hartman J; Bienko M; Crosetto N
Corrigendum: METHODS IN MOLECULAR BIOLOGY. 2018;1766:E1

Correction to: An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

Gelali E; Custodio J; Girelli G; Wernersson E; Crosetto N; Bienko M
Preprint: SSRN ELECTRONIC JOURNAL. 2018

An Organ-Wide Gene Expression Atlas of the Developing Human Heart

Asp M; Giacomello S; Fürth D; Reimegård J; Wärdell E; Custodio J; Salmén F; Sundström E; Åkesson E; Bienko M; Månsson‐Broberg A; Ståhl PL; Sylvén C; Lundeberg J
Preprint: BIORXIV. 2016

BLISS: quantitative and versatile genome-wide profiling of DNA breaks in situ

Yan WX; Mirzazadeh R; Garnerone S; Scott D; Schneider MW; Kallas T; Custodio J; Wernersson E; Gao L; Li Y; Federova Y; Zetsche B; Zhang F; Bienko M; Crosetto N
Review: NATURE REVIEWS GENETICS. 2015;16(1):57-66

Spatially resolved transcriptomics and beyond.

Crosetto N; Bienko M; van Oudenaarden A
Letter: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2009;106(8):E20

Ubiquitin-binding motif of human DNA polymerase eta is required for correct localization.

Sabbioneda S; Green CM; Bienko M; Kannouche P; Dikic I; Lehmann AR
Review: MOLECULAR CANCER RESEARCH. 2006;4(12):899-904

Ubiquitin hubs in oncogenic networks.

Crosetto N; Bienko M; Dikic I
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Grants

Enabling Targeted Spatial Omics for Research and Diagnostics

Swedish Research Council

1 January 2021 - 31 December 2024
Illuminating Genome Architecture in Health and Disease

Swedish Research Council

1 January 2021 - 31 December 2025

Selected publications

Articles

All other publications

Grants

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