March 14, 2014

Dr. Noa Pinter Wollman (UCSD BioCircuits Institute) – Network Motifs: Simple Building Blocks of Complex Networks (Science. 2002. Milo. R. et al) Science-2002-Milo-824-7

Prof. Bing Ren (UCSD School of Medicine) – Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing (Nature Biotechnology. 2013. Selvaraj S. et al) HaploSeq_NBT_2013

March 21, 2014

Dr. Amina Bouslimani (UCSD – Chemistry and Biochemistry; Pieter Dorrestein Lab) Topographical molecular analysis of the skin from a man and a woman (in press)

Matan Hofree  (UCSD – School of Medicine; Trey Ideker Lab) Network-based Stratification of Tumor Mutations (Nature. 2013. Hofree M et al) nmeth.2651

SDCSB Greatest Hits of Systems Biology Recommended List:

1. Recent research work funded by SDCSB

Cell. 2012.08.011
A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways
Paul Michael Loriaux and Alexander Hoffmann
pcbi.1002932

Cell.2012.08.011
CAND1 controls in vivo dynamics of the Cullin 1-RING ubiquitin ligase repertoire
Shuangding Wu et al
nihms448129

PLos Biology. 2008
A Gene Wiki for Community Annotation of Gene Function
Huss JW et al
pbio.0060175

Cell Host Microbe. 2012 March 15; 11(3): 306–318
Co-factors Required for TLR7- and TLR9- dependent Innate Immune Responses
Chih-yuan Chiang et al
nihms361160

Nature Biotechnology. 2013.
Selvaraj S, Dixon JR, Bansal V, Ren B
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
HaploSeq_NBT_2013

2. Other Labs’ recent research work in past 3 years

Nature . 2010
Network organization of the human autophagy system
Christian Behrends et al.
nihms-208952

Molecular Systems Biology 7:553 (2011)
Bree B Aldridge et al.
Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis
msb201185

Nature 10098.doi:10.1038
Bjoern Schwanhaeusser et al.
Global quantification of mammalian gene expression control
nature10098

Molecular Systems Biology 7:553 (2011)
Bree B Aldridge et al.
Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis
msb201185

Cell 2013.03.030
Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease
Bin Zhang et al
Cell2013.Zhang

Cell.2011.10.022
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
Nicolas Chevrier et al.
1-s2.0-S0092867411012700-main
Cell 2012
Circuitry and dynamics of human transcription factor regulatory networks
Shane Neph et al.
nihms405401

Cell . 2012 August 31; 150(5): 1068–1081.
A Census of Human Soluble Protein Complexes
Pierre C. Havugimana et al
nihms402232

Nature . 2011 May 5; 473(7345): 43–49.
The accessible chromatin landscape of the human genome
Robert E. Thurman et al.
nihms377833

Functional Discovery via a Compendium of Expression Profiles (Cell. 2010)  Timothy R. Hughes et al. Cell 2000 Hughes & The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (Nature. 2012) Jordi Barretina et al. Nature2012.Barretina

Nature 467:174 (2010).
Fundamental limits on the suppression of molecular fluctuations
I. Lestas, G. Vinnicombe, J. Paulsson
nihms220662

Mol. Syst. Biol. 2012 Jun 26;8:589.
Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death.
Graham NA et al.
msb201220

Cell. 2012 Apr 13;149(2):307-21.
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.
Duncan JS et al.
cell2012.02.053

PNAS. 2012.
Ottesen E. et al.
Pattern and synchrony of gene expression among sympatric marine microbial populations
pnasE488

Cell 2012.
Duncan JS et al.
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer
cell2012.02.053

3. SDCSB Labs’ best Systems Biology papers of all time

Science  292, 929 (2001);
Trey Ideker et al.
Integrated Genomic and Proteomic Analyses of a Systematically perturbed Metabolic
Science-2001-Ideker-929-34
Nature 467:174 (2010)
I. Lestas, G. Vinnicombe, J. Paulsson).
Fundamental limits on the suppression of molecular fluctuations
nihms220662

Science 309, 1857 (2005);
Shannon L. Werner et al.
Stimulus Specificity of Gene Expression Programs Determined by Temporal Control of IKK Activity
Science-2005-Werner-1857-61

Cell. 2008 October 3; 135(1): 49–60.
Renate König et al.
Global analysis of host-pathogen interactions that regulate early stage HIV-1 replication
nihms73737

Cell . 2012 September 28; 151(1): 138–152.
Nathanael J. Spann et al
Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses
nihms404764

Nature. 2011 February 10; 470(7333): 264–268.
9p21 DNA variants associated with Coronary Artery Disease impair IFNγ signaling response
Olivier Harismendy et al
nihms259054

Mol Cell. 2009 October 9; 36(1): 141–152.
Zhe Sha et al
The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries
nihms149903

Plant Cell. 2013 Aug 16. [Epub ahead of print]
Hauser F, Chen W, Deinlein U, Chang K, Ossowski S, Fitz J, Hannon GJ, Schroeder JI.
A Genomic-Scale Artificial MicroRNA Library as a Tool to Investigate the Functionally Redundant Gene Space in Arabidopsis.

Plos Biology. 2008
Huss JW, et al.
A Gene Wiki for Community Annotation of Gene Function
pbio.0060175

4. Non-SDCSB labs’ best Systems Biology papers of all time

Science 303, 808 (2004);
Amy Hin Yan Tong et al.
Global Mapping of the Yeast Genetic Interaction Network
Science-2004-Tong-808-13

Science 294, 2364 (2001);
Amy Hin Yan Tong et al.
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Science-2001-Tong-2364-8-1

Science 285, 901 (1999);
Elizabeth A. Winzeler et al.
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
Science-1999-Winzeler-901-6

Science 286, 2179 (1999);
Kevin P. White et al.
Microarray Analysis of Drosophila Development During Metamorphosis
Science-1999-White-2179-84

Nature. 2009 May 7; 459(7243)
Nathaniel D. Heintzman et al.
Histone Modifications at Human Enhancers Reflect Global Cell Type-Specific Gene Expression
nihms144932

Molecular Systems Biology (2006)
Kanae Oda and Hiroaki Kitano
A comprehensive map of the toll-like receptor signaling network
msb4100057

J. Physiol. (I952) I I7, 500-544
A. L. Hodgkin and A. F. Huxley
A Quantitative Description of Membrane Current and its Application to Conduction and Excitation in Nerve.
jphysiol01442-0106

Nature. 2011
Jason Ernst et al.
Systematic analysis of chromatin state dynamics in nine human cell types
nihms-270546

Cell . 2012 July 20; 150(2): 389–401
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Jonathan R. Karr1, et al.
nihms391296

Science 301, 102 (2003)
Timothy S. Gardner et al.
Action via Expression Profiling Inferring Genetic Networks and Identifying Compound Mode of
Science-2003-Gardner-102-5

Jacques Monod and Francois Jacob
Teleonomic mechanisms in cellular metabolism, growth, and differentiation
Monod_Jacob_1962

Nature 03842. (2005)
Dekel, E., & Alon, U.
Optimality and evolutionary tuning of the expression level of a protein
nature03842

Science. 2002.
Milo. R. et al
Network Motifs: Simple Building Blocks of Complex Networks
Science-2002-Milo-824-7

Science. 2005.
Sachs K et al
Causal protein-signaling networks derived from multiparameter single-cell data
nature03842

Nature 467:174. 2010.
I. Lestas, G. Vinnicombe, J. Paulsson
Fundamental limits on the suppression of molecular fluctuations”. 
nihms220662

PNAS, 2009.
Mahowald et al.
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
PNAS-2009

Nature, 2010.
Behrends et al.
Network organization of the human autophagy system
Nature 2010 Behrends

Nature. 2005
Dekel, E., & Alon, U. 
Optimality and evolutionary tuning of the expression level of a protein. 
nature03842

Science. 2002.
Milo. R. et al
Network Motifs: Simple Building Blocks of Complex Networks 
Science-2002-Milo-824-7