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Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- Ulrich Omasits,
- Maxime Quebatte,
- Daniel J. Stekhoven,
- Claudia Fortes,
- Bernd Roschitzki,
- Mark D. Robinson,
- Christoph Dehio,
- and Christian H. Ahrens
Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
..., orthology, and other information to enable further analyses. Genome Research 1917 www..org Covering complete expressed prokaryotic proteomes protein-coding genes actively transcribed in a given state (Ahrens et al. 2010). A recent proteogenomics study of 46 prokaryotes indicated that, on average, only 0...
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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
...for extension of the predicted genemodel aswell as the presence of additional unannotated exons. The novel transcripts along with the proteomic data were used for improving the assembly and annotation errors using a novel integrative proteogenomic analysis pipeline (Fig. 1). The relative utility...
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Research: Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
- Nadine Borchert,
- Christoph Dieterich,
- Karsten Krug,
- Wolfgang Schütz,
- Stephan Jung,
- Alfred Nordheim,
- Ralf J. Sommer,
- and Boris Macek
Genome Res. June 2010 20: 837-846; Published in Advance March 17, 2010, doi:10.1101/gr.103119.109
...Alfred Nordheim N Borchert Ralf Sommer Jung Stephan Schütz Wolfgang Krug, Karsten Jung, Stephan R.J. Sommer R Sommer genome;gr.103119.109 10.1101/gr.103119.109 1088-9051 Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models Research Proteogenomics of Pristionchus...
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Methods: Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
- Sébastien Gallien,
- Emmanuel Perrodou,
- Christine Carapito,
- Caroline Deshayes,
- Jean-Marc Reyrat,
- Alain Van Dorsselaer,
- Olivier Poch,
- Christine Schaeffer,
- and Odile Lecompte
Genome Res. January 2009 19: 128-135; Published in Advance October 27, 2008, doi:10.1101/gr.081901.108
...sequencing projects provides biologists with an invaluable framework to integrate experimental results and design new experiments at different scales. However, several recent studies have highlighted the prevalence of gene prediction errors, even in the “simple” prokaryotic s. Genome sequencing itself...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...310022, China; 9State Key Laboratory for Macromolecule Drugs and Large-scale Manufacturing, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325030, China ↵10 These authors contributed equally to this work. Corresponding authors: wuyf@immunol.org, reny@genomics.cn, jingang...
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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
...of bacterial innovation. Nature 405: 299–304. doi:10.1038/35012500 Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, et al. 2017. An integrative strategy to identify the entire protein coding potential of prokaryotic s by proteogenomics...
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Method: Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
- Alexandre Lomsadze,
- Karl Gemayel,
- Shiyuyun Tang,
- and Mark Borodovsky
Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117
...to the one introduced in GeneMarkS (Besemer et al. 2001).View larger version: In this window In a new window Figure 1. Principal state diagram of the generalized hidden Markov model (GHHM) of prokaryotic genomic sequence. States shown in the top panel were used to model a gene in the direct strand. Genes...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
..., proteogenomics, ribosome profiling, and massively parallel sequencing studies have revealed that prokaryotic and eukaryotic s contain a substantial number of as-yet-uncharacterized and unannotated open reading frames (ORFs) (Firth and Brierley 2012; Andrews and Rothnagel 2014; Prabakaran et al. 2014; Albuquerque...
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LETTER: Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias
- Rong Wang,
- John T. Prince,
- and Edward M. Marcotte
Genome Res. August 2005 15: 1118-1126; doi:10.1101/gr.3994105
...the false-negative protein identification rate in the mass spectrometry experiment. The extreme case of this strategy is to compare the MS/MS spectral data against raw, uninterpreted genomic sequence data ( Arthur and Wilkins 2003 ), even without predicting genes ( Jaffe et al. 2004 ). In this mode...
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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
...Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation Nitin Gupta 1 , 7 , 8 , Stephen Tanner 1 , 7 , Navdeep Jaitly 2 , Joshua N. Adkins 2 , Mary Lipton 2...

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