Searching journal content for articles similar to Mrowka et al. 11 (12): 1971.

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  1. Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
    • Siwei Chen,
    • Yuan Liu,
    • Yingying Zhang,
    • Shayne D. Wierbowski,
    • Steven M. Lipkin,
    • Xiaomu Wei,
    • and Haiyuan Yu
    Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
    ...confirm the validity of our findings in this study but also underscore the effectiveness of our full-proteome framework in characterizing mutational hotspots. Moreover, we recognize that the current human interactome may be subject to sampling bias from small-scale studies (Das and Yu 2012; Rolland et al...
  2. Research: Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly
    • Yuan Lu,
    • David Bierbach,
    • Jenny Ormanns,
    • Wesley C. Warren,
    • Ronald B. Walter,
    • and Manfred Schartl
    Genome Res. March 2021 31: 372-379; Published in Advance February 5, 2021, doi:10.1101/gr.268870.120
    ..._f1. bias_reversed,” “clonal.biased_f1.inconsistent,” “clonal.inconsistent_f1.no.bias,” and “clonal.inconsistent_f1.bias”). Among these genes, 2%–6% displayed allelic usage differences between the clonal P. formosa and the interspecies F1 hybrids among the three organs assessed: 0.4%–1.9% of genes...
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  3. 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
    ...). In a third stage, evidence is presented that virtually no biases remain when comparing protein parameters of all identified proteins to those called actively expressed, justifying the claim tohave identified a complete proteome expressed in a specific condition. Analysis of such a data set is expected...
  4. Resource: The Proteome Folding Project: Proteome-scale prediction of structure and function
    • Kevin Drew,
    • Patrick Winters,
    • Glenn L. Butterfoss,
    • Viktors Berstis,
    • Keith Uplinger,
    • Jonathan Armstrong,
    • Michael Riffle,
    • Erik Schweighofer,
    • Bill Bovermann,
    • David R. Goodlett,
    • Trisha N. Davis,
    • Dennis Shasha,
    • Lars Malmström,
    • and Richard Bonneau
    Genome Res. November 2011 21: 1981-1994; Published in Advance August 8, 2011, doi:10.1101/gr.121475.111
    ...The Proteome Folding Project: Proteome-scale prediction of structure and function Kevin Drew 1 , Patrick Winters 1 , Glenn L. Butterfoss 1 , Viktors Berstis 2 , Keith Uplinger 2 , Jonathan Armstrong 2 , Michael Riffle 3...
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  5. 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
    ...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 1 Center for Systems and Synthetic Biology, Institute for Cellular...
  6. Resource: Building better genome annotations across the tree of life
    • Adam H. Freedman and
    • Timothy B. Sackton
    Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
    ...-detection method.Our second level of analysis is for the “transcriptome,” consisting of the entirety of features that tools predict, agnostic to whether sequences are coding and their reading frames. For tools that only produce protein-coding predictions (BRAKER, CGP, TOGA, and MAKER), the proteome...
  7. 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
    .... Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome. Mol Cell 74: 481–493.e6. doi:10.1016/j.molcel.2019.02.017 ↵Mira A, Ochman H, Moran NA. 2001. Deletional bias and the evolution of bacterial s. Trends Genet 17: 589–596. doi:10.1016/S0168-9525(01)02447-7 Miranda-CasoLuengo AA...
  8. RESOURCE: ProtoBee: Hierarchical classification and annotation of the honey bee proteome
    • Noam Kaplan and
    • Michal Linial
    Genome Res. November 2006 16: 1431-1438; Published in Advance October 25, 2006, doi:10.1101/gr.4916306
    ...ProtoBee: Hierarchical classification and annotation of the honey bee proteome Noam Kaplan and Michal Linial 1 Department of Biological Chemistry, Life Science Institute, The Hebrew University, Jerusalem 91904, Israel Abstract The recently...
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  9. ARTICLE: Structural Characterization of the Human Proteome
    • Arne Müller,
    • Robert M. MacCallum,
    • and Michael J.E. Sternberg
    Genome Res. November 1, 2002 12: 1625-1641; doi:10.1101/gr.221202
    .... Nevertheless, the trend of increasing domain duplication, as the size of the proteome increases, is the same for SCOP and PFAM based analysis, suggesting that any bias from using just SCOP is not marked. The second assumption is that all the proteins have been identified in the , and one has to estimate...
  10. ARTICLE: The Complete Genome and Proteome of Mycoplasma mobile
    • Jacob D. Jaffe,
    • Nicole Stange-Thomann,
    • Cherylyn Smith,
    • David DeCaprio,
    • Sheila Fisher,
    • Jonathan Butler,
    • Sarah Calvo,
    • Tim Elkins,
    • Michael G. FitzGerald,
    • Nabil Hafez,
    • Chinnappa D. Kodira,
    • John Major,
    • Shunguang Wang,
    • Jane Wilkinson,
    • Robert Nicol,
    • Chad Nusbaum,
    • Bruce Birren,
    • Howard C. Berg,
    • and George M. Church
    Genome Res. August 2004 14: 1447-1461; doi:10.1101/gr.2674004
    ...not computationally predicted were detected by proteomics (identification methods for each gene call can be seen in the Supplemental Table of Computational and Proteomic Predictions). There was no detectable size or functional category bias to these proteins, but eight of the 26 were <100 amino acids. Thirty...
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