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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
.... More specialized tools for this approach include the Peak Browser at ChIP Atlas (Oki et al. 2018) or browsing ChIPBase (Huang et al. 2023), which is especially strong for ncRNAs but can also be used for mRNA genes. The Eukaryotic Promoter Database ExPASy has the useful Mass Genome Annotation Archive...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...on ambiguous splice-site predictions. Furthermore, protein-coding gene validation by additional peptide evidence through high-resolution mass spectrometry can strongly improve the annotation as shown in various previous studies investigating individual species (Jaffe et al. 2004; Castellana et al. 2008...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...and peptide identification by tandem mass spectrometry. Proteomics 9: 3233–3243. doi:10.1002/pmic.200800955 D'Lima NG, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. 2017. Comparative proteomics enables identification of nonannotated cold shock proteins in E. coli. J Proteome...
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Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...@ucsd.eduAbstractThe V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin (IG) loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) are critical for studies of the adaptive...
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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
...in the similar biological process with their neighbors than those that are far apart, and the gold-standard gene pairs of the HumanNet v3 sharing pathway annotation (Kim et al. 2022a) are found to be more proximal than random gene pairs (Fig. 4E). Shorter CTG distances between gene pairs are associated...
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Method: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
...but in a different frame of translation. This revised frame of translation suggested the presence of chaperonin subunit 10 domain in the gene (Supplemental Fig. S3D). As most mature proteins are known to be acetylated in their N termini, N-terminally acetylated peptides discovered by mass spectrometry can assist...
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Methods: Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
- Nitin Gupta,
- Stephen Tanner,
- Navdeep Jaitly,
- Joshua N. Adkins,
- Mary Lipton,
- Robert Edwards,
- Margaret Romine,
- Andrei Osterman,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. September 2007 17: 1362-1377; Published in Advance August 9, 2007, doi:10.1101/gr.6427907
...sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first...
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Method: BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs
- Dmitry Meleshko,
- Hosein Mohimani,
- Vittorio Tracanna,
- Iman Hajirasouliha,
- Marnix H. Medema,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. August 2019 29: 1352-1362; Published in Advance June 3, 2019, doi:10.1101/gr.243477.118
...that have well-annotated BGCs. In the case when multiple feasible paths exist in the assembly graph, we recommend to experimentally verify biosyntheticSPAdes predictions, e.g., using targeted PCR amplification or matching against mass spectrometry data. Also, peptidogenomics tools (Mohimani et al. 2014a...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
...in XX samples. (B) Amino-acid sequence of EIF1AX/Y: X- and Y-specific amino acids are superscripted and subscripted, respectively. X-specific (gold), Y-specific (blue), and X–Y shared (purple) peptides detected by mass spectrometry are shown, along with the number of 11-plex experiments in which each...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...-type endopeptidase (Fig. 3B; Supplemental Table S8); we found an overlapping set of duckweed-specific significant GO terms (Fig. 3D). We took a look at the genes that made up these Wolffia unique OGs using our annotation and found that they are associated with cell wall architecture (Fasciclin-like arabinogalactan...
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