Roman R. Stocsits

发表

The impact of rRN A secondary structur e consideration in alignment and tr ee r econstruction: simulated data and a case study on the ph ylogeny of hexapods.

Roman R. Stocsits, 2010 .

The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods.

H. Letsch, Roman R. Stocsits, P. Kück, 2010, Molecular biology and evolution.

Simultaneous alignment and folding of 28S rRNA sequences uncovers phylogenetic signal in structure variation.

H. Letsch, Roman R. Stocsits, P. Kück, 2009, Molecular phylogenetics and evolution.

A Toy Model of Chemical Reaction Networks

Michael T. Wolfinger, Ingrid G. Abfalter, P. Schuster, 2002 .

Absolute quantification of cohesin, CTCF and their regulators in human cells

J. Ellenberg, B. Novák, J. Peters, 2019, bioRxiv.

MCM complexes are barriers that restrict cohesin-mediated loop extrusion

Leonid A. Mirny, Wen Tang, Ilya M. Flyamer, 2020, Nature.

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

P. Stadler, Jana Hertel, H. Letsch, 2009, Nucleic acids research.

Nucleic Acid Sequence Alignments of Partly Coding Regions

Roman R. Stocsits, 2003 .

Recombination and the Structure of Globular Proteins

Michael T. Wolfinger, Ingrid G. Abfalter, P. Schuster, 2001 .

Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing

F. Pauler, D. Barlow, Katarzyna E. Warczok, 2012, Science.

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

J. Ellenberg, J. Peters, J. Zuber, 2017, The EMBO journal.

A Variation on Algorithms for Pairwise Global Alignments

Ingrid G. Abfalter, P. Schuster, P. Stadler, 2001 .

CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin

J. Ellenberg, J. Peters, J. Zuber, 2017, bioRxiv.

Conserved secondary structures in hepatitis B virus DNA

Peter F. Stadler, Ivo L. Hofacker, Roman R. Stocsits, 1999, German Conference on Bioinformatics.

HiCognition: a visual exploration and hypothesis testing tool for 3D genomics

D. Gerlich, Roman R. Stocsits, Christoph C. H. Langer, 2022, bioRxiv.

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

J. Peters, K. Mechtler, Erez Lieberman-Aiden, 2020, eLife.

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

J. Peters, J. Zuber, P. Fraser, 2020, Cell reports.

Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers

J. Peters, J. Zuber, P. Fraser, 2020, bioRxiv.

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

Erez Lieberman Aiden, J. Peters, K. Mechtler, 2019, bioRxiv.

Dynamics of sister chromatid resolution during cell cycle progression

J. Peters, D. Gerlich, Roman R. Stocsits, 2018, bioRxiv.

SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre‐mRNAs

J. Ellenberg, J. Peters, J. Schmitz, 2014, The EMBO journal.

Nucleome programming is required for the foundation of totipotency in mammalian germline development

L. Mirny, Y. Hiraoka, J. Majewski, 2022, The EMBO journal.

Accurate and efficient reconstruction of deep phylogenies from structured RNAs - Supplemental Material -

P. Stadler, Jana Hertel, H. Letsch, 2009 .

SNW 1 enables sister chromatid cohesion by mediating the splicing of sororin and APC 2 pre-mRNAs

J. Ellenberg, J. Peters, J. Schmitz, 2014 .

Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms

J. Peters, D. Gerlich, Roman R. Stocsits, 2022, bioRxiv.

Conserved RNA secondary structures in viral genomes: A survey

Peter F. Stadler, Ivo L. Hofacker, Roman R. Stocsits, 2004, German Conference on Bioinformatics.

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

Niels Galjart, Jan-Michael Peters, Elin Axelsson, 2017, Nature.

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

J. Wägele, H. Letsch, Roman R. Stocsits, 2009, BMC Evolutionary Biology.

Transcription shapes 3D chromatin organization by interacting with loop extrusion

L. Mirny, J. Peters, Roman R. Stocsits, 2022, bioRxiv.

Multiple sequence alignments of partially coding nucleic acid sequences

Peter F. Stadler, Ivo L. Hofacker, Claudia Fried, 2005, BMC Bioinformatics.

H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress

K. Mechtler, Roman R. Stocsits, Dominik Hartl, 2014, Genome research.

Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes

Sean T. Powell, J. Peters, A. Tedeschi, 2020, The Journal of cell biology.

Author response: Absolute quantification of cohesin, CTCF and their regulators in human cells

J. Ellenberg, B. Novák, J. Peters, 2019 .

Absolute quantification of cohesin, CTCF and their regulators in human cells.

J. Ellenberg, B. Novák, J. Peters, 2019, eLife.

Cohesin supercoils DNA during loop extrusion

Roman R. Stocsits, Kota Nagasaka, I. Davidson, 2024, bioRxiv.

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

J. Wägele, H. Letsch, Roman R. Stocsits, 2009, BMC Evolutionary Biology.

Absolute quantification of cohesin , CTCF and their regulators in human cells 1 2

B. Novák, J. Peters, K. Mechtler, 2019 .