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Showing 1–19 of 19 results
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  • Jonathan Park’s scientific interests changed after caring for a person with cancer. He ended up bidding an amicable farewell to Mark Gerstein, a supportive supervisor who had taught him a lot.

    • Jonathan Park
    • Mark Gerstein
    Comments & Opinion
    Nature

  • With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

    • Matthew H. Bailey
    • William U. Meyerson
    • Christian von Mering
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-27

  • Pseudogenes constitute many of the non-coding DNA sequences that make up large parts of genomes. Once considered merely protein fossils, it now emerges that some of them have active regulatory roles.

    • Rajkumar Sasidharan
    • Mark Gerstein
    News & Views
    Nature
    Volume: 453, P: 729-731

  • Most of the human genome consists of non-protein-coding DNA. This article describes the progress made in annotating this non-coding portion of the genome by combining data from comparative and functional genomics analyses.

    • Roger P. Alexander
    • Gang Fang
    • Mark B. Gerstein
    Reviews
    Nature Reviews Genetics
    Volume: 11, P: 559-571

  • A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties.

    • Mark B. Gerstein
    • Anshul Kundaje
    • Michael Snyder
    ResearchOpen Access
    Nature
    Volume: 489, P: 91-100

  • By combining data from gene expression and DNA-binding experiments, a computational algorithm identifies the genetic regulatory network in yeast.

    • Zhaolei Zhang
    • Mark Gerstein
    News & Views
    Nature Biotechnology
    Volume: 21, P: 1295-1297

  • The development of high-throughput DNA sequencing methods provides a new method for mapping and quantifying transcriptomes — RNA sequencing (RNA-Seq). This article explains how RNA-Seq works, the challenges it faces and how it is changing our view of eukaryotic transcriptomes.

    • Zhong Wang
    • Mark Gerstein
    • Michael Snyder
    Reviews
    Nature Reviews Genetics
    Volume: 10, P: 57-63

  • Repetitive sequences and chromatin accessibility can confound scoring of chromatin immunoprecipitation data generated by high–throughput sequencing. Using data sets they produce for human RNA polymerase II and the transcription factor STAT1, Rozowsky et al. compensate for these biases by correcting for 'mappability' and normalizing the data against an input–DNA control.

    • Joel Rozowsky
    • Ghia Euskirchen
    • Mark B Gerstein
    Research
    Nature Biotechnology
    Volume: 27, P: 66-75

  • Genomic analyses of cancer genomes have largely focused on mutations in protein-coding regions, but the functional importance of alterations to non-coding regions is becoming increasingly appreciated through whole-genome sequencing. This Review discusses our current understanding of non-coding sequence variants in cancer — both somatic mutations and germline variants, and their interplay — including their identification, computational and experimental evidence for functional impact, and their diverse mechanisms of action for dysregulating coding genes and non-coding RNAs.

    • Ekta Khurana
    • Yao Fu
    • Mark Gerstein
    Reviews
    Nature Reviews Genetics
    Volume: 17, P: 93-108

  • A whole-genome and transcriptome analysis of 20 human induced pluripotent stem-cell lines shows that reprogramming does not necessarily add de novo copy number variants to what is already present in the somatic cells from which they originated.

    • Alexej Abyzov
    • Jessica Mariani
    • Flora M. Vaccarino
    Research
    Nature
    Volume: 492, P: 438-442

  • Sequencing a person's genome may reveal large DNA insertions and other structural rearrangements, but assessing their effects requires pinpointing them to nucleotide resolution. Lam et al. use a library of previously discovered rearrangements to map and analyze genetic variation.

    • Hugo Y K Lam
    • Xinmeng Jasmine Mu
    • Mark B Gerstein
    Research
    Nature Biotechnology
    Volume: 28, P: 47-55

  • Transcription factors (TFs) are essential for gene expression, but very little is known about the majority of human TFs. This Analysis article provides a manually curated repertoire of sequence-specific human TFs as a foundation for future research, and examines patterns of TF expression and conservation.

    • Juan M. Vaquerizas
    • Sarah K. Kummerfeld
    • Nicholas M. Luscombe
    Research
    Nature Reviews Genetics
    Volume: 10, P: 252-263

  • Protein–RNA interactions are central to the regulation of gene expression. Emerging technologies for pinpointing these interactions, both in large complexes and between individual proteins and RNA, are discussed. Methods for analysing these data are also considered.

    • Julian König
    • Kathi Zarnack
    • Jernej Ule
    Reviews
    Nature Reviews Genetics
    Volume: 13, P: 77-83