Systems analysis

Systems analysis is the study of a complex system’s interacting parts, while keeping a eye on their function in the integrated whole. Systems analysis is often called upon to evaluate the safety of complex systems that have grown haphazardly, as when computers and the internet faced the Y2K problem.

Latest Research and Reviews

  • Research | | open

    The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

    • Jason Lloyd-Price
    • , Cesar Arze
    • , Ashwin N. Ananthakrishnan
    • , Melanie Schirmer
    • , Julian Avila-Pacheco
    • , Tiffany W. Poon
    • , Elizabeth Andrews
    • , Nadim J. Ajami
    • , Kevin S. Bonham
    • , Colin J. Brislawn
    • , David Casero
    • , Holly Courtney
    • , Antonio Gonzalez
    • , Thomas G. Graeber
    • , A. Brantley Hall
    • , Kathleen Lake
    • , Carol J. Landers
    • , Himel Mallick
    • , Damian R. Plichta
    • , Mahadev Prasad
    • , Gholamali Rahnavard
    • , Jenny Sauk
    • , Dmitry Shungin
    • , Yoshiki Vázquez-Baeza
    • , Richard A. White III
    • , Jason Bishai
    • , Kevin Bullock
    • , Amy Deik
    • , Courtney Dennis
    • , Jess L. Kaplan
    • , Hamed Khalili
    • , Lauren J. McIver
    • , Christopher J. Moran
    • , Long Nguyen
    • , Kerry A. Pierce
    • , Randall Schwager
    • , Alexandra Sirota-Madi
    • , Betsy W. Stevens
    • , William Tan
    • , Johanna J. ten Hoeve
    • , George Weingart
    • , Robin G. Wilson
    • , Vijay Yajnik
    • , Jonathan Braun
    • , Lee A. Denson
    • , Janet K. Jansson
    • , Rob Knight
    • , Subra Kugathasan
    • , Dermot P. B. McGovern
    • , Joseph F. Petrosino
    • , Thaddeus S. Stappenbeck
    • , Harland S. Winter
    • , Clary B. Clish
    • , Eric A. Franzosa
    • , Hera Vlamakis
    • , Ramnik J. Xavier
    •  & Curtis Huttenhower
    Nature 569, 655-662
  • Research |

    CRISPR screens identify JNK–JUN family genes as repressors of definitive endoderm differentiation in human pluripotent stem cells. JUN co-occupies stem cell enhancers with OCT4, NANOG, SMAD2 and SMAD3 and inhibits the exit from pluripotency.

    • Qing V. Li
    • , Gary Dixon
    • , Nipun Verma
    • , Bess P. Rosen
    • , Miriam Gordillo
    • , Renhe Luo
    • , Chunlong Xu
    • , Qiong Wang
    • , Chew-Li Soh
    • , Dapeng Yang
    • , Miguel Crespo
    • , Abhijit Shukla
    • , Qing Xiang
    • , Friederike Dündar
    • , Paul Zumbo
    • , Matthew Witkin
    • , Richard Koche
    • , Doron Betel
    • , Shuibing Chen
    • , Joan Massagué
    • , Ralph Garippa
    • , Todd Evans
    • , Michael A. Beer
    •  & Danwei Huangfu
    Nature Genetics 51, 999-1010
  • Research | | open

    Alborz Mazloomian et al. use small molecule inhibitors to disrupt EIF4A3’s ATPase and helicase function which affects alternative splicing and nonsense mediated decay of transcripts. They define a genome-wide pattern of motifs of RNA-binding proteins associated with EIF4A3 and find that stress granules are downregulated upon EIF4A3 inhibition.

    • Alborz Mazloomian
    • , Shinsuke Araki
    • , Momoko Ohori
    • , Amal M. El-Naggar
    • , Damian Yap
    • , Ali Bashashati
    • , Shoichi Nakao
    • , Poul H. Sorensen
    • , Atsushi Nakanishi
    • , Sohrab Shah
    •  & Samuel Aparicio

News and Comment

  • Editorial |

    Systems models of the ways transcription factor networks operate and evolve are essential for understanding cell identity, developmental commitment and regulatory variation. Terminologies from different techniques and disciplines may need to be adapted or put aside to make and test these models effectively.

  • News and Views |

    Characterization of the mutational landscape of tumors is important to understanding disease etiology but does not provide mechanistic insight into the functional role of specific mutations. A new study introduces a statistical mechanical framework that draws on biophysical data from SH2 domain–phosphoprotein interactions to predict the functional effects of mutations in cancer.

    • Andrea Califano
    Nature Genetics 46, 1252-1253