Genome Research (GENOME RES)

Publisher: Cold Spring Harbor Laboratory Press

Journal description

The journal focuses on genome studies in all species, and presents research that provides or aids in genome-based analyses of biological processes. The journal represents a nexus point where genomic information, applications, and technology come together with biological information to create a more global understanding of all biological systems.

Current impact factor: 14.63

Impact Factor Rankings

2016 Impact Factor Available summer 2017
2014 / 2015 Impact Factor 14.63
2013 Impact Factor 13.852
2012 Impact Factor 14.397
2011 Impact Factor 13.608
2010 Impact Factor 13.588
2009 Impact Factor 11.342
2008 Impact Factor 10.176
2007 Impact Factor 11.224
2006 Impact Factor 10.256
2005 Impact Factor 10.139
2004 Impact Factor 10.382
2003 Impact Factor 9.635
2002 Impact Factor 9.863
2001 Impact Factor 8.559
2000 Impact Factor 7.615
1999 Impact Factor 7.062

Impact factor over time

Impact factor
Year

Additional details

5-year impact 15.57
Cited half-life 6.10
Immediacy index 3.20
Eigenfactor 0.14
Article influence 8.37
Website Genome Research website
Other titles Genome research (Online), Genome research
ISSN 1088-9051
OCLC 37589079
Material type Online system or service, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Cold Spring Harbor Laboratory Press

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Author's pre-print on preprint server
    • Author's pre-print must be updated with citation, DOI and link to article upon publication
    • Publisher's version/PDF may be used after 6 months
    • Publisher's version/PDF and Author's post-print on author's personal website, institutional repository, funder's designated repository
    • Authors retain copyright
    • Content automatically sent to PubMed Central after 6 months
    • Publisher copyright and source must be acknowledged
    • Publisher last contacted on 15/07/2013
  • Classification
    green

Publications in this journal

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Megabase-scale copy number variants (CNVs) can have profound phenotypic consequences. Germline CNVs of this magnitude are associated with disease and experience negative selection. However, it is unknown whether organismal function requires that every cell maintain a balanced genome. It is possible that large somatic CNVs are tolerated or even positively selected. Single cell sequencing is a useful tool for assessing somatic genomic heterogeneity but its performance in CNV detection has not been rigorously tested. Here we develop an approach that allows for reliable detection of megabase-scale CNVs in single somatic cells. We discover large CNVs in 8-9% of cells across tissues and identify two recurrent CNVs. We conclude that large CNVs can be tolerated in subpopulations of cells and that particular CNVs are relatively prevalent within and across individuals.
    Preview · Article · Jan 2016 · Genome Research
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The S. cerevisiae Forkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. As stimulators of early origin activation, we hypothesized that Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, were not well suited to quantitative, genome-wide measurements of origin firing between strains and conditions. To overcome this limitation, we developed qBrdU-seq, a quantitative method for BrdU incorporation analysis of replication dynamics, and applied it to show that overexpression of Fkh1 and Fkh2 advance the initiation timing of many origins throughout the genome resulting in a higher total level of origin initiations in early S phase. The higher initiation rate is accompanied by slower replication fork progression, thereby maintaining a normal length of S phase without causing detectable Rad53 checkpoint kinase activation. The advancement of origin firing time, including that of origins in heterochromatic domains, was established in late G1 phase, indicating that origin timing can be reset subsequently to origin licensing. These results provide novel insights into the mechanisms of origin timing regulation by identifying Fkh1 and Fkh2 as rate-limiting factors for origin firing that determine the ability of replication origins to accrue limiting factors and have the potential to reprogram replication timing late in G1 phase.
    Preview · Article · Jan 2016 · Genome Research
  • [Show abstract] [Hide abstract]
    ABSTRACT: RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear intron that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complimentary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of intron does not require U2AF65, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.
    No preview · Article · Nov 2015 · Genome Research
  • [Show abstract] [Hide abstract]
    ABSTRACT: While Next-generation sequencing (NGS) has become the primary technology for discovering gene fusions we are still faced with the challenge of ensuring that causative mutations are not missed while minimizing false positives. Currently, there are many computational tools that predict structural variations (SV) and gene fusions using whole genome (WGS) and transcriptome sequencing (RNA-seq) data separately. However, as both WGS and RNA-seq have their limitations when used independently we hypothesize that the orthogonal validation from integrating WGS and RNA-seq could generate a sensitive and specific approach for detecting high confidence gene fusion predictions. Fortunately, decreasing NGS costs have resulted in a growing quantity of patients with available genome and transcriptome sequencing data. Therefore, we developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read mapping. To evaluate INTEGRATE we compared it with eight additional gene fusion discovery tools using the well-characterized breast cell line HCC1395 and peripheral blood lymphocytes derived from the same patient (HCC1395BL). The predictions subsequently underwent a targeted validation leading to the discovery of 131 novel fusions in addition to the seven previously reported fusions. Overall, INTEGRATE only missed 6 out of the 138 validated gene fusions and had the highest accuracy of the nine tools evaluated. Additionally, we applied INTEGRATE to 62 breast cancer patients from the TCGA and found multiple recurrent gene fusions including a subset involving estrogen receptor. Taken together, INTEGRATE is a highly sensitive and accurate tool that is freely available for academic use.
    No preview · Article · Nov 2015 · Genome Research
  • [Show abstract] [Hide abstract]
    ABSTRACT: Forward genetic screens using Sleeping Beauty (SB) mobilized T2/Onc transposons have been used to identify Common Insertion Sites (CIS) associated with tumor formation. Recurrent sites of transposon insertion are commonly identified using Ligation Mediated PCR (LM-PCR). Here, we use RNA-sequencing (RNA-seq) data to directly identify transcriptional events mediated by T2/Onc. Surprisingly, the majority (~80%) of LM-PCR identified junction fragments do not lead to observable changes in RNA transcripts. However, in CIS regions, direct transcriptional effects of transposon insertions are observed. We developed an automated method to systematically identify T2/Onc-genome RNA fusion sequences in RNA-seq data. RNA fusion based CIS were identified corresponding to both DNA based CIS (Cdkn2a, Mycl1, Nf2, Pten, Sema6d and Rere) and additional regions strongly associated with cancer that were not observed by LM-PCR (Myc, Akt1, Pth, Csf1r, Fgfr2, Wisp1, Map3k5 and Map4k3). In addition to calculating recurrent CIS, we also present complementary methods to identify potential driver events via determination of strongly supported fusions and fusions with large transcript level changes in the absence of multi-tumor recurrence. These methods independently identify CIS regions, and also point to cancer-associated genes like Braf. We anticipate RNA-seq analyses of tumors from forward genetic screens will become an efficient tool to identify causal events.
    No preview · Article · Nov 2015 · Genome Research
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: It has been almost 15 years since the first microarray-based studies creating multigene biomarkers to subtype and predict survival of cancer patients. This Perspective looks at why only a handful of genomic biomarkers have reached clinical application and what advances are needed over the next 15 years to grow this number. I discuss challenges in creating biomarkers and reproducing them at the genomic and computational levels, including the problem of spatio-genomic heterogeneity in an individual cancer. I then outline the challenges in translating newly discovered genome-wide or regional events, like trinucleotide mutation signatures, kataegis, and chromothripsis, into biomarkers, as well as the importance of incorporating prior biological knowledge. Lastly, I outline the practical problems of pharmaco-economics and adoption: Are new biomarkers viewed as economically rational by potential funders? And if they are, how can their results be communicated effectively to patients and their clinicians? Genomic-based diagnostics have immense potential for transforming the management of cancer. The next 15 years will see a surge of research into the topics here that, when combined with a stream of new targeted therapies being developed, will personalize the cancer clinic.
    Preview · Article · Oct 2015 · Genome Research
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field.
    Preview · Article · Oct 2015 · Genome Research
  • [Show abstract] [Hide abstract]
    ABSTRACT: Arevolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast "landscape" of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.
    No preview · Article · Oct 2015 · Genome Research
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The past two decades have been marked by a surge in research to understand the microbial communities that live in association with the human body, in part stimulated by affordable, high-throughput DNA sequencing technology. In the context of the skin, this Perspective focuses on the current state of genomic- and metagenomic-based host–microbe research and future challenges and opportunities to move the field forward. These include elucidating nonbacterial components of the skin microbiome (i.e., viruses); systematic studies to address common perturbations to the skin microbiome (e.g., antimicrobial drugs, topical cosmetic/hygienic products); improved approaches for identifying potential microbial triggers for skin diseases, including species- and strain-level resolution; and improved, clinically relevant models for studying the functional and mechanistic roles of the skin microbiome. In the next 20 years, we can realistically expect that our knowledge of the skin microbiome will inform the clinical management and treatment of skin disorders through diagnostic tests to stratify patient subsets and predict best treatment modality and outcomes and through treatment strategies such as targeted manipulation or reconstitution of microbial communities.
    Preview · Article · Oct 2015 · Genome Research
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
    Preview · Article · Oct 2015 · Genome Research