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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...of proteomes (Aebersold and Mann 2016). The field developed from assessing proteins, peptides, and associated co- and post-translational modifications (CTMs/PTMs) in a few specimens to large-scale studies in medicine and systems biology comprising hundreds of specimens to resolve regulatory mechanisms...
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Method: Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
- Van Hoan Do,
- Francisca Rojas Ringeling,
- and Stefan Canzar
Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
...that form nonconvex regions. On a variety of data types, this flexibility has allowed spectral clustering methods to produce more accurate clusterings than competing methods (Shi and Malik 2000). The high computational complexity, however, renders its application to large-scale problems infeasible. For n...
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Method: PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments
- Peng Liu,
- Alexandra A. Soukup,
- Emery H. Bresnick,
- Colin N. Dewey,
- and Sündüz Keleş
Genome Res. November 2020 30: 1655-1666; Published in Advance September 21, 2020, doi:10.1101/gr.252445.119
...sets, we developed a novel ‘1-Step’ approach named Pooling RNA-seq and Assembling Models (PRAM) that builds transcript models from pooled RNA-seq data sets. We demonstrate in a computational benchmark that 1-Step outperforms 2-Step approaches in predicting overall transcript structures and individual...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...fidelity by facilitating elongation, preventing cryptic initiation, and restoring chromatin compaction (Carrozza et al. 2005; Kim et al. 2016; Lee et al. 2021). These modifications form a complex and dynamic network controlling chromatin structure and gene expression (Martin and Zhang 2005). Histone...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...). Complementary approaches such as optical mapping of single >150-kb molecules via nanochannel arrays (Lam et al. 2012) or chromatin interaction mapping (Lieberman-Aiden et al. 2009) likewise facilitate assemblies of ever-increasing contiguity and completeness. Apart from intensely studied model organisms, e...
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Research: A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development
- Claus Schertel,
- Monica Albarca,
- Claudia Rockel-Bauer,
- Nicholas W. Kelley,
- Johannes Bischof,
- Korneel Hens,
- Erik van Nimwegen,
- Konrad Basler,
- and Bart Deplancke
Genome Res. April 2015 25: 514-523; Published in Advance January 7, 2015, doi:10.1101/gr.181305.114
...A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development Claus Schertel 1 , 4 , Monica Albarca 2 , 4 , Claudia Rockel-Bauer 1 , Nicholas W. Kelley 3...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...are heavily involved in the establishment of different cell states. We have developed a diffusion-based method, Hi-C to geometry (CTG), to obtain reliable geometric information on the chromatin from Hi-C data. CTG produces a consistent and reproducible framework for the 3D genomic structure and provides...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...for mouse Chromosome 1:113–136 Mbp and Drosophila Chromosome 2LAt large scales, the checkerboard-like patterns observed in Hi-C maps suggest that chromatin compartments are spatially segregated. Typical configuration snapshots from our simulations in Drosophila (Fig. 2H) and mouse (Fig. 2F) indeed...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
...protein-coding gene promoters and enhancers.Large-scale transcriptomic studies, enabled by improvements in total RNA enrichment and high-throughput RNA profiling technologies, unexpectedly revealed extensive transcription outside the boundaries of known protein-coding genes (Kapranov et al. 2002; Okazaki...
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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
...Nuclear hormone receptors are TFs specifically activated in response to hormone exposure. Once activated, they bind to specific hormone response elements (HREs) where they regulate gene expression, often in conjunction with the binding of cofactors and remodeling of the chromatin structure. Glucocorticoid (GC...

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