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Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

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10.1016/j.bbagrm.2022.194811
Rodriguez-Martinez, Alejandra; Vuorinen, Elisa M.; Shcherban, Anastasia; Uusi-Mäkelä, Joonas; Rajala...
Biochimica et biophysica acta: gene regulatory mechanisms2022

Differential ATAC-seq and ChIP-seq peak detection using ROTS

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10.1093/nargab/lqab059
Faux Thomas, Rytkönen Kalle T., Mahmoudian Mehrad, Paulin Niklas, Junttila Sini, Laiho Asta, Elo Lau...
NAR Genomics and Bioinformatics: Nucleic Acids Research Genomics and Bioinformatics2021

Pool-seq driven proteogenomic database for Group G Streptococcus

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10.1016/j.jprot.2019.04.015
Weldatsadik, R. G.; Datta, N.; Kolmeder, C.; Vuopio, J.; Kere, J.; Wilkman, S. V.; Flatt, J. W.; Vue...
Journal of proteomics2019

Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.

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10.1186/s12864-016-3428-1
Ampuja, M;Rantapero, T;Rodríguez, Martínez A;Palmroth, M;Alarmo, EL;Nykter, M;Kallioniemi, A;Kallion...
bmc genomics2017

RNA-seq Data Analysis:A Practical Approach

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Korpelainen, Eija; Tuimala, Jarno; Somervuo, Panu Juhani; Huss, Mikael; Wong, Garry
CRC Press, Taylor & Francis Group2014

DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq

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10.1007/s11103-020-01108-6
Kaeppel, Sandra; Eggeling, Ralf; Ruempler, Florian; Groth, Marco; Melzer, Rainer; Theissen, Guenter
Plant Molecular Biology2021

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data

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10.7717/peerj.3742
Dzida, Tomasz; Iqbal, Mudassar; Charapitsa, Iryna; Reid, George; Stunnenberg, Henk; Matarese, Filome...
PeerJ2017

Robustness of differential gene expression analysis of RNA-seq

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10.1016/j.csbj.2021.05.040
Stupnikov, A.; McInerney, C. E.; Savage, K. I.; McIntosh, S. A.; Emmert-Streib, F.; Kennedy, R.; Sal...
Computational and structural biotechnology journal2021

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women

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10.3390/genes9120574
Rekker, Kadri; Altmae, Signe; Suhorutshenko, Marina; Peters, Maire; Martinez-Blanch, Juan F.; Codone...
Genes2018

Dirichlet process mixture models for single-cell RNA-seq clustering

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10.1242/bio.059001
Adossa Nigatu A., Rytkönen Kalle T, Elo Laura
Biology Open2022

Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

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Öppen tillgång
DOI
10.1016/j.bbagrm.2022.194811
2022

Differential ATAC-seq and ChIP-seq peak detection using ROTS

Referentgranskad
Öppen tillgång
DOI
10.1093/nargab/lqab059
2021

Pool-seq driven proteogenomic database for Group G Streptococcus

Referentgranskad
Öppen tillgång
DOI
10.1016/j.jprot.2019.04.015
2019

Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.

Referentgranskad
Öppen tillgång
DOI
10.1186/s12864-016-3428-1
2017

RNA-seq Data Analysis:A Practical Approach

Referentgranskad
2014

DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq

Referentgranskad
Öppen tillgång
DOI
10.1007/s11103-020-01108-6
2021

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data

Referentgranskad
Öppen tillgång
DOI
10.7717/peerj.3742
2017

Robustness of differential gene expression analysis of RNA-seq

Referentgranskad
Öppen tillgång
DOI
10.1016/j.csbj.2021.05.040
2021

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women

Referentgranskad
Öppen tillgång
DOI
10.3390/genes9120574
2018

Dirichlet process mixture models for single-cell RNA-seq clustering

Referentgranskad
Öppen tillgång
DOI
10.1242/bio.059001
2022