UCSF

center for systems

& synthetic biology

an NIGMS national systems biology center

banner_graduateed.jpg
 
 
 

publications

***Acknowledgement of NIH Funding on the UCSF Center for Systems and Synthetic Biology Publications***

All peer-reviewed publications resulting from the utilization of Center resources are required to: credit the NIGMS Systems Biology Center grant P50 GM081879 in the acknowledgements, as well as submit to PubMed Central and be assigned a PMCID number [PubMed]

 

  

2015


 

Remote control of therapeutic T cells through a small molecule-gated chimeric receptor

Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA.

Science. 2015 Oct 16;350(6258):aab4077.  [PubMed] 

 

Synthetic biology approaches to engineer T cells

Wu CY, Rupp LJ, Roybal KT, Lim WA.

Curr Opin Immunol. 2015 Aug;35:123-30.  [PubMed] 

 

Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals "aging factors" and mechanism of lifespan asymmetry

Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11977-82.  [PubMed] 

 

Programmed synthesis of three-dimensional tissues

Todhunter ME, Jee NY, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ.

Nat Methods. 2015 Oct;12(10):975-81.  [PubMed] 

 

A Phase-Variable Surface Layer from the Gut Symbiont Bacteroides thetaiotaomicron

Taketani M, Donia MS, Jacobson AN, Lambris JD, Fischbach MA.

MBio. 2015 Sep 29;6(5). pii: e01339-15. [PubMed] 

 

Comparative mapping of host-pathogen protein-protein interactions

Shah PS, Wojcechowskyj JA, Eckhardt M, Krogan NJ.

2015 Aug 10;27:62-68. [Epub ahead of print].  [PubMed] 

 

Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson, M.

Cell Syst. 2015 Aug 26;1(2):117-129.  [PubMed] 

 

Computational approaches to natural product discovery

Medema MH, Fischbach MA.

Nat Chem Biol. 2015 Aug 18;11(9):639-48.  [PubMed] 

 

HUMAN MICROBIOTA: Small molecules from the human microbiota.

Donia MS, Fischbach MA.

Science. 2015 Jul 24;349(6246):1254766.  [PubMed] 

 

Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

Ding L, Paszkowski-Rogacz M, Winzi M, Chakraborty D, Theis M, Singh S, Ciotta G, Poser I, Roguev A, Chu WK, Choudhary C, Mann M, Stewart AF, Krogan NJ, Buchholz, F.

(2015). Cell Systems, 1(2), 141-151.   

 

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

Devlin AS, Fischbach MA.

Nat Chem Biol. 2015 Sep;11(9):685-90.  [PubMed] 

 

Prb1 Protease Activity is Required for its Recognition by the F box Protein Saf1

Mark KG, Meza Gutierrez F, Johnson JR, Newton BW, Krogan NJ, Toczyski DP.

Biochemistry. 2015 Jul 17. [Epub ahead of print]  [PubMed] 

 

Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection

Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T, Jäger S, Gopalakrishnan AM, Sherry J1, Dunn JD, Olive A, Penn B, Shales M, Cox JS, Starnbach MN, Derre I, Valdivia R, Krogan NJ, Engel J.

2015 Jun 24. pii: S1931-3128(15)00252-8. [Epub ahead of print]  [PubMed] 

 

Leakless DNA strand displacement systems

Thachuk C, Winfree E, Soloveichik D.

Proceedings of DNA Computing and Molecular Programming 21 (DNA21), 2015 (to appear).   

 

Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi)

Hawkins JS, Wong S, Peters JM, Almeida R, Qi LS.

Methods Mol Biol. 2015;1311:349-62.  [PubMed] 

 

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity

Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ.

Cell Rep. 2015 May 12. [Epub ahead of print].  [PubMed] 

 

Probability 1 computation with chemical reaction networks

Cummings R, Doty D, Soloveichik D.

Proceedings of the 20th International Meeting on DNA Computing and Molecular Programming, (Kyoto, Japan, Sept 22-26, 2014), in press.

 

Differential genetic interactions of yeast stress response MAPK pathways

Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ.

Mol Syst Biol. 2015 Apr 17;11(4):800.  [PubMed] 

 

Synthetic microbes as drug delivery systems

Claesen J, Fischbach MA.

ACS Synth Biol. 2015 Apr 17;4(4):358-64.  [PubMed] 

 

NF-κB-Activating Complex Engaged in Response to EGFR Oncogene Inhibition Drives Tumor Cell Survival and Residual Disease in Lung Cancer

Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJ, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS, Newton W, Bobb KL, Fouts TR, Meshulam J, Gubens MA, Jablons DM4, Johnson JR, Bandyopadhyay S, Krogan NJ, Bivona TG.

Cell Rep. 2015 Apr 7;11(1):98-110.  [PubMed] 

 

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C.

PLoS Genet. 2015 Mar 31;11(3):e1005074.  [PubMed]  

 

A systematic comparison of mathematical models for inherent measurement of ciliary length: how a cell can measure length and volume

Ludington WB, Ishikawa H, Serebrenik YV, Ritter A, Hernandez-Lopez RA, Gunzenhauser J, Kannegaard E, Marshall WF.

Biophys J. 2015 Mar 24;108(6):1361-79.  [PubMed] 

 

Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks

Lipinski-Kruszka J, Stewart-Ornstein J, Chevalier MW, El-Samad H.

2015 Mar 20;4(3):258-64. [PubMed] 

 

Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.

Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ.

Curr Protoc Bioinformatics. 2015 Mar 9;49:8.19.1-8.19.16.  [PubMed] 

 

An Evolutionary Role for HIV Latency in Enhancing Viral Transmission

Rouzine IM, Weinberger AD, Weinberger LS.

Cell. 2015 Feb 26;160(5):1002-12.  [PubMed] 

 

 

A Hardwired HIV Latency Program

Razooky BS, Pai A, Aull K, Rouzine IM, Weinberger LS.

Cell. 2015 Feb 26;160(5):990-1001.  [PubMed] 

 

 

Early telomerase inactivation accelerates aging independently of telomere length

Xie Z, Jay KA, Smith DL, Zhang Y, Liu Z, Zheng J, Tian R, Li H, Blackburn EH.

Cell. 2015 Feb 26;160(5):928-39. [PubMed] 

 

 

Population diversification in a yeast metabolic program promotes anticipation of environmental shifts

Venturelli OS, Zuleta I, Murray RM, El-Samad H.

PLoS Biol. 2015 Jan 27;13(1):e1002042. doi: 10.1371/journal.pbio.1002042. eCollection 2015.  [PubMed] 

 

 

A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity

Cerchiari AE, Garbe JC, Jee NY, Todhunter ME, Broaders KE, Peehl DM, Desai TA, LaBarge MA, Thomson M, Gartner ZJ.

Proc Natl Acad Sci U S A. 2015 Jan 29. pii: 201410776. [Epub ahead of print]. [PubMed] 

  

  

Global Mapping of Herpesvirus-Host Protein Complexes Reveals a Transcription Strategy for Late Genes

Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, Maher MC, Johnson T, Newton W, Jäger S, Shales M, Horner J, Hernandez RD, Krogan NJ, Glaunsinger BA.

Mol Cell. 2015 Jan 22;57(2):349-60. [PubMed] 

 

 

A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay

Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M.

Mol Cell. 2015 Jan 22;57(2):329-40. [PubMed] 

 

 

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA.

Cell. 2015 Jan 15;160(1-2):339-50. [PubMed] 

  

 

Reliable cell cycle commitment in budding yeast is ensured by signal integration

Liu X, Wang X, Yang X, Liu S, Jiang L, Qu Y, Hu L, Ouyang Q, Tang C.

Elife. 2015 Jan 14;4. doi: 10.7554/eLife.03977. [PubMed] 

 

   

Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts

Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM.

Mol Cell Biol. 2015 Jan;35(2):468-78. doi: 10.1128/MCB.01157-14. Epub 2014 Nov 10.  [PubMed] 

 

 

Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, Gcn5 and Esa1

Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP.

Mol Cell Proteomics. 2015 Jan;14(1):162-76. [PubMed] 

 

 

2014


 

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

Chevalier MW, El-Samad H.

J Chem Phys. 2014 Dec 7;141(21):214108. [PubMed] 

 

 

Regulation of Sufu activity by p66β and Mycbp provides new insight into vertebrate Hedgehog signaling

Lin C, Yao E, Wang K, Nozawa Y, Shimizu H, Johnson JR, Chen JN, Krogan NJ, Chuang PT.

Genes Dev. 2014 Nov 15;28(22):2547-63.  [PubMed]  

 

 

Environmental statistics and optimal regulation.

Sivak DA, and Thomson M.

PLoS Comput Biol. 2014 Sep 25;10(9):e1003826.  [PubMed] 

 

 

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA.

PLoS Comput Biol. 2014 Dec 4;10(12):e1004016.  [PubMed] 

 

 

Quantitative analysis of triple mutant genetic interactions

Braberg H, Alexander R, Shales M, Xu J, Franks-Skiba KE, Wu Q, Haber JE and Krogan NJ.

Nature Protocols. 2014 Aug;9(8):1867-81.  [PubMed] 

 

 

Book Review of Synthetic Biology: A Lab Manual

Hsueh JC and Helmke KJ.

ACS Synth Biol. 2014 Dec 19;3(12):939-40. [PubMed] 

 

 

Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

Ji W, Lee D, Wong E, Dadlani P, Dinh D, Huang V, Kearns K, Teng S, Chen S, Haliburton J, Heimberg G, Heineike B, Ramasubramanian A, Stevens T, Helmke KJ, Zepeda V, Qi LS, Lim WA.

ACS Synth Biol. 2014 Dec 19;3(12):929-31. [PubMed] 

 

 

Production and Targeting of Monovalent Quantum Dots

Seo D, Farlow J, Southard K, Jun YW, Gartner ZJ.

J. Vis. Exp. 2014 Oct 23;(92):e52198. [PubMed] 

 

 

Formation of spatially and geometrically controlled 3D tissues in soft gels by Sacrificial Micromolding

Cerchiari A, Garbe J, Todhunter M, Jee N, Pinney J, LaBarge M, Desai T, Gartner Z.

Tissue Eng Part C Methods. 2014 Oct 29. 2015 Jun;21(6):541-7.  [PubMed] 

 

Efficient targeting of fatty-acid modified oligonucleotides to live cell membranes through step-wise assembly

Weber RJ, Liang SI, Selden NS, Desai TA, Gartner ZJ.

Biomacromolecules. 2014 Dec 8;15(12):4621-6. [PubMed] 

 

 

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD.

Cell. 2014 Oct 23;159(3):635-46. [PubMed] 

 

 

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS.

Cell. 2014 Oct 23;159(3):635-46. [PubMed] 

 

 

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine

Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA.

Cell Host Microbe. 2014 Oct 8;16(4):495-503. [PubMed] 

 

 

A modular approach for assembling aldehyde-tagged proteins on DNA scaffolds

Liang SI, McFarland JM, Rabuka D, Gartner ZJ.

J Am Chem Soc. 2014 Aug 6;136(31):10850-3. [PubMed] 

 

 

A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics

Donia MS, Cimermancic P, Schulze CJ, Wieland Brown LC, Martin J, Mitreva M, Clardy J, Linington RG, Fischbach MA.

Cell. 2014 Sep 11;158(6):1402-14. [PubMed] 

 

 

Sending mixed messages for cell population control

Youk H, Lim WA.

Cell. 2014 Aug 28;158(5):973-5. [PubMed] 

 

 

E pluribus unum, no more: from one crystal, many conformations

Woldeyes RA, Sivak DA, Fraser JS.

Curr Opin Struct Biol. 2014 Aug 8;28C:56-62. [PubMed] 

 

 

Probability 1 computation with chemical reaction networks

Cummings R, Doty D, Soloveichik D.

DNA 2014: Proceedings of the 20th International Meeting on DNA Computing and Molecular Programming, (Kyoto, Japan, Sept 22-26, 2014).[PubMed in process] 

 

 

Speed faults in computation by chemical reaction networks

Chen HL, Cummings R, Doty D, Soloveichik D.

DISC 2014: Proceedings of the 28th International Symposium on DIStributed Computing, (Austin, Texas, USA, Oct 12-15, 2014).[PubMed in process] 

 

 

Synthetic microbes as drug delivery systems

Claesen J, Fischbach MA.

ACS Synth Biol. 2014 Jul 31. [Epub ahead of print].[PubMed] 

 

 

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters

Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA.

Cell. 2014 Jul 17;158(2):412-21. [PubMed] 

 

 

Screening for noise in gene expression identifies drug synergies

Dar RD, Hosmane NN, Arkin MR, Siliciano RF, Weinberger LS.

2014 Jun 20;344(6190):1392-6. doi: 10.1126/science.1250220. Epub 2014 Jun 5.[PubMed] 

 

 

Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR

Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS.

2014 May 28. pii: S0969-2126(14)00140-3. doi: 10.1016/j.str.2014.04.016. [Epub ahead of print].[PubMed] 

 

 

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: Exploring the applications of high-resolution genetic interaction mapping of point mutations

Braberg H, Moehle EA, Shales M, Guthrie C, Krogan NJ.

Bioessays. 2014 Jul;36(7):706-13. [PubMed] 

 

 

A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation

Kabeche R, Roguev A, Krogan NJ, Moseley JB.

J Cell Sci. 2014 Mar 15;127(Pt 6):1318-26. doi: 10.1242/jcs.143545. Epub 2014 Jan 16.[PubMed] 

 

 

The prevalence of species and strains in the human microbiome: a resource for experimental efforts

Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M.

PLoS One. 2014 May 14;9(5):e97279. doi: 10.1371/journal.pone.0097279. eCollection 2014.[PubMed]

 

 

Conditional Genetic Interactions of RTT107, SLX4, and HRQ1 Reveal Dynamic Networks Upon DNA Damage in Saccharomyces cerevisiae

Leung GP, Aristizabal MJ, Krogan NJ, Kobor MS.

G3 (Bethesda). 2014 Apr 2. pii: g3.114.011205v1. doi: 10.1534/g3.114.011205. [Epub ahead of print] [PubMed]

 

 

Adventures in time and space: intron retention and RNA polymerase II elongation rate

Moehle, E. A., H. Braberg, N. J. Krogan and C. Guthrie.

RNA Biology. 2014 Apr; 11(4):313-9. [PubMed]

 

 

Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal

Park JS, Rhau B, Hermann A, McNally KA, Zhou C, Gong D, Weiner OD, Conklin BR, Onuffer J, Lim WA.

PNAS. 2014 Apr 22; 111(16):5896-901. [PubMed]

 

 

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

Sivak DA, Chodera JD, Crooks GE.

J Phys Chem B. 2014 Mar 17. [Epub ahead of print] [PubMed]

 

 

Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry

Zuleta IA, Aranda-Díaz A, Li H, El-Samad H.

Nat Methods. 2014 Mar 9. doi: 10.1038/nmeth.2879. [Epub ahead of print] [PubMed]

 

 

Population diversification in a yeast metabolic program promots anticipation of environmental shifts

Venturelli OS, Zuleta I, Murray RM, El-Samad H.

BioRxiv. 2014 Feb 21. Doi:10.1101/002907.[Epub ahead of print]

 

 

Secreting and sensing the same molecule allows cells to achieve versatile social behaviors

Youk H, Lim WA.

Science. 2014 Feb 7. doi: 343(6171):1242782. doi: 10.1126/science.1242782.[Epub ahead of print] [PubMed]

 

 

Genetic properties of random gene regulatory networks

Li Z, Bianco S, Zhang Z, Tang C.

Higher Education Press. 2014 Jan 27. doi: 10.1007/s40484-014-0026-6.[Epub ahead of print]

 

 

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons

Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ.

Epigenetics. 2014 Jan 17. [Epub ahead of print][PubMed]

 

 

A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation

Kabeche R, Roguev A, Krogan NJ, Moseley JB.

J Cell Sci. 2014 Jan 16. [Epub ahead of print][PubMed]

 

 

AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation

Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E15-24. doi: 10.1073/pnas.1318503111. Epub 2013 Dec 23. [PubMed]

 

 

2013


 

Optimal control of transitions between nonequilibrium steady states,
Zulkowski PR, Sivak DA, DeWeese MR.
PLoS One. 2013 Dec 26;8(12):e82754. doi: 10.1371/journal.pone.0082754. eCollection 2013.[PubMed]

 

High-resolution network biology: connecting sequence with function

Ryan CJ, Cimermančič P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ.

Nat Rev Genet. 2013 Dec;14(12):865-79. doi: 10.1038/nrg3574.[PubMed]

 

 

Evolution and functional cross-talk of protein post-translational modifications

Beltrao P, Bork P, Krogan NJ, van Noort V.

Mol Syst Biol. 2013 Dec 22;9(1):714. doi: 10.1002/msb.201304521.[PubMed]

 

 

Chemical Genetics of Rapamycin-Insensitive TORC2 in S. cerevisiae

Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM.

Cell Rep. 2013 Dec 26;5(6):1725-36. doi: 10.1016/j.celrep.2013.11.040.[PubMed]

 

 

IFI16 DNA Sensor Is Required for Death of Lymphoid CD4 T Cells Abortively Infected with HIV

Monroe KM, Yang Z, Johnson JR, Geng X, Doitsh G, Krogan NJ, Greene WC.

Science. 2014 Jan 24;343(6169):428-32. doi: 10.1126/science.1243640.[PubMed]

 

 

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B.

Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001.[PubMed]

 

 

Using optogenetics to interrogate the dynamic control of signal transmission by the ras/erk module

Toettcher JE, Weiner OD, Lim WA.

Cell. 2013 Dec 5;155(6):1422-34. doi: 10.1016/j.cell.2013.11.004.[PubMed]

 

 

Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells

Huang V, Zheng J, Qi Z, Wang J, Place RF, Yu J, Li H, Li LC.

PLoS Genet. 2013 Sep;9(9):e1003821. doi: 10.1371/journal.pgen.1003821. Epub 2013 Sep 26.[PubMed]



Genetic sensor for strong methylating compounds

Moser F, Horwitz A, Chen J, Lim WA, Voigt CA.

ACS Synth Biol. 2013 Oct 9. [Epub ahead of print][PubMed]



Msn2 coordinates a stoichiometric gene expression program

Stewart-Ornstein J, Nelson C, Derisi J, Weissman JS, El-Samad H.

Curr Biol. 2013 Nov 6. doi:pii: S0960-9822(13)01190-1. 10.1016/j.cub.2013.09.043. [Epub ahead of print][PubMed]



Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory

Puchner EM, Walter JM, Kasper R, Huang B, Lim WA.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16015-20. doi: 10.1073/pnas.1309676110. Epub 2013 Sep 16.[PubMed]



CRISPR interference (CRISPRi) for sequence-specific control of gene expression

Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS.

Nat Protoc. 2013 Nov;8(11):2180-96. doi: 10.1038/nprot.2013.132. Epub 2013 Oct 17.[PubMed]



High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8

Caristizabal MJ, Negri GL, Benschop JJ, Holstege FC, Krogan NJ, Kobor MS.

PLoS Genet. 2013 Aug;9(8):e1003758. doi: 10.1371/journal.pgen.1003758. Epub 2013 Aug 29.[PubMed]



Programmable chemical controllers made from DNA

Chen YJ, Dalchau N, Srinivas N, Phillips A, Cardelli L, Soloveichik D, Seelig G.

Nat nantechnol. 2013 Oct;8;(10):755-762. doi: 10.1038/nnano.2013.189. Epub 2013 Sep 29.[PubMed]



Design Principles of the Yeast G1/S Switch

Yang X, Lau K, Sevim V, Chao T.

PLoS Biol 11(10): e1001673. doi:10.1371/journal.pbio.1001673. Epub 2013 Oct 1.[PubMed]



A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and bilayer stress

Surma M, Klose C, Peng D, Shales M, Mrejen C, Stefanko A, Braberg H, Gordon D, Ejsing C, Farese R, Simons K, Krogan NJ, Ernst R.

Mol. Cell 2013 doi: 10.1016/j.molcel.2013.06.014. Epub 2013 Jul 25. [PubMed]



A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast

Yang X, Jost APT, Weiner OD, Tang C.

Mol Biol Cell. 2013 Aug; 24(15):2419-30. [PubMed]

 

 

Deterministic Function Computation with Chemical Reaction Networks

Chen HL, Doty D, Soloveichik D.

Natural Computing. 10.1007/s11047-013-9393-6 (2013). [PDF]

 

 

From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II

Braberg H, Jin H, Moehle E, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Fraser JS, Hu F, Tang LK, Holstege FPC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ.

Cell. 2013 Aug 15;154(4):775-788. [PubMed]



Formation of targeted monovalent quantum dots by steric exclusion

Farlow J, Seo D, Broaders KE, Taylor M, Gartner ZJ, Jun YW.

Nat Methods. 2013 Dec;10(12):1203-5. doi: 10.1038/nmeth.2682. Epub 2013 Oct 13.[PubMed]

 

 

The prefoldin complex regulates chromatin dynamics during transcription elongation

Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-JiménezL, Morillo-Huesca M, Krogan N, Chávez S.

PLoS Genet. 2013;9(9):e1003776. doi: 10.1371/journal.pgen.1003776. [PubMed]

 

 

Exploitation of latent allostery enables the evolution of new modes of MAP kinase regulation

Coyle SM, Flores J, Lim, WA.

Cell. 2013 Aug 15: 154(4): 875-887. [PubMed]



Building Robust Functionality in Synthetic Circuits Using Engineered Feedback Regulation

Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H.

Curr Opin Biotechnol. 2013 Aug; 24(4):790-6. [PubMed]



CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes

Gilbert LA,Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA,Weissman JS, Qi LS.

Cell. 2013 Jul 18;154(2):442-51. [PubMed]



Improved Blue, Green, and Red Fluorescent Protein Tagging Vectors for S. cerevisiae

Lee S, Lim WA, Thorn KS. 

PLoS ONE 2013 Jul 2; 8(7): e67902. [PubMed]



All or nothing: protein complexes flip essentiality between distantly related eukaryotes

Ryan CJ, Krogan NJ, Cunningham P, Cagney G.

Genome Biol Evol. 2013; 5(6):1049-59. [PubMed]

 

 

N- and O-glycosylation in the murine synaptosome

Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF.

Mol Cell Proteomics 2013 Jul 1. 10.1074/mcp.M113.030007 [Epub ahead of print]. [PubMed]

 

 

Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2 binding motif in chimp and human, which enables the detection of evolutionarily novel regulatory targets

Nelson C, Fuller C, Fordyce P, Greninger A, Li H, DeRisi JL.

Nucleic Acid Research, 2013 Jul 1; 41(12):5991-6004. [PubMed]



Global analysis of ubiquitylation and phosphorylation crosstalk in protein degradation

Swaney DL, Beltrao P, Starita L, Fields S, Krogan NJ, Villen J.

Nature Methods. 2013 Jul; 10(7):676-82. [PubMed]



Systematic triple mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation

Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Johnson JR, Bloom K, Krogan NJ.

Cell Reports. 2013 Jun 27; 3(6):2168-78. [PubMed]



Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS

Xin H, Fuller CK, Song Y, Meng Q, Zhang B, Yang X, Li H.

American Journal of Human Genetics, 2013 May 2; 92(5):667-80. [PubMed]



Dispersed Sites of HIV Vif-Dependent Polyubiquitination in the DNA Deaminase APOBEC3F

Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS.

J Mol Biol. 2013 Apr 12; 425(7):1172-82. [PubMed]



The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat

Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T. 

Elife. 2013 Mar 5; 2:e00327. [PubMed]



Cell-based therapeutics: the next pillar of medicine
Fischbach MA, Bluestone JA, Lim WA.

Science Translational Medicine. 2013 Apr 3; 5(179):179ps7. [PubMed]



Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA.
Cell. 2013 Feb 28; 152(5):1173-83.
[PubMed]


CBFβ Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression
Kim DY, Kwon E, Hartley PD, Crosby DC, Mann S, Krogan NJ, Gross JD.

Mol Cell. 2013 Feb 21; 49(4):632-44.
[PubMed]


Formation of Subnuclear Foci Is a Unique Spatial Behavior of Mating MAPKs during Hyperosmotic Stress

Vidal SE, Pincus D, Stewart-Ornstein J, El-Samad H.

Cell Rep. 2013 Feb 21; 3(2):328-34. [PubMed]

 

 

Quantitative genetic-interaction mapping in mammalian cells
Roguev A, Talbot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ.

Nat Methods. 2013 May; 10(5):432-7. [PubMed]

 

 

Design requirements for interfering particles to maintain coadaptive stability with HIV-1

Rouzine IM, Weinberger LS.

J Virol. 2013 Feb; 87(4):2081-93. [PubMed]



A gene ontology inferred from molecular networks
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. 

Nat Biotechnol. 2013 Jan; 31(1):38-45.[PubMed]


From systems to structure: bridging networks and mechanism
Fraser JS, Gross JD, Krogan NJ.

Mol Cell. 2013 Jan 24; 49(2):222-31.[PubMed]


Dissection of DNA damage responses using multiconditional genetic interaction maps

Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H.

Mol Cell. 2013 Jan 24; 49(2):346-58. [PubMed]



Design principles of regulatory networks: searching for the molecular algorithms of the cell
Lim WA, Lee CM, Tang C.

Mol Cell. 2013 Jan 24; 49(2):202-12. [PubMed]

Dispersed Sites of HIV Vif-Dependent Polyubiquitination in the DNA Deaminase APOBEC3F
Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS.
J Mol Biol 2013 Apr 12; 425(7):1172-82.
[PubMed]

 

HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold
Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ,Zhou Q, Alber T.
Proc Natl Acad Sci USA. 2013 Jan 8; 110(2):E123-31.
[PubMed]


Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins 

Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R.

Mol Cell Proteomics. 2013 Jan; 12(1):29-41. [PubMed]



COMPUTER SCIENCE CONFERENCE PUBLICATION

Rate-independent computation in mass-action chemical reaction networks
Chen HL, Doty D, Soloveichik D.

ITCS 2014: Proceedings of the 5th Innovations in Theoretical Computer Science Conference, (Princeton, New Jersey, USA, January 12-14, 2014), to appear.


 

2012


 

Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G
Stanley DJ, Bartholomeeusen K, Crosby DC, Kim DY, Kwon E, Yen L, Cartozo NC, Li M, Jäger S, Mason-Herr J, Hayashi F, Yokoyama S, Krogan NJ, Harris RS, Peterlin BM, Gross JD.

PLoS Pathog. 2012 Dec [Epub 2012 Dec 27]; 8(12):e1003085. doi: 10.1371/journal.ppat.1003085. [PubMed]


Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models

Armakola M, Higgins MJ, Figley MD, Barmada SJ, Scarborough EA, Diaz Z, Fang X, Shorter J, Krogan NJ, Finkbeiner S, Farese RV Jr, Gitler AD.

Nat Genet. 2012 Dec [Epub 2012 Oct 28]; 44(12):1302-9. doi: 10.1038/ng.2434. [PubMed]


The yeast SR-like protein Npl3 links chromatin modification to mRNA processing

Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C.

PLoS Genet. 2012 [Epub 2012 Nov 29]; 8(11):e1003101. doi: 10.1371/journal.pgen.1003101.[PubMed]


Mitochondrial network size scaling in budding yeast
Rafelski SM, Viana MP, Zhang Y, Chan YH, Thorn KS, Yam P, Fung JC, Li H, Costa Lda F, Marshall WF.

Science. 2012 Nov 9; 338(6108):822-4. doi: 10.1126/science.1225720. [PubMed]


Single cell analysis of yeast replicative aging using a new generation of microfluidic device

Zhang Y, Luo C, Zou K, Xie Z, Brandman O, Ouyang Q, Li H. 
PLoS One. 2012 [Epub 2012 Nov 8]; 7(11):e48275. doi: 10.1371/journal.pone.0048275.
[PubMed]


Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant

Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P.
Mol Cell Biol. 2012 Nov [Epub 2012 Aug 27]; 32(21):4445-54. doi: 10.1128/MCB.01062-12.
[PubMed]


Transcriptional burst frequency and burst size are equally modulated across the human genome

Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM, Cox CD, Simpson ML, Weinberger LS.
Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17454-9. doi: 10.1073/pnas.1213530109. [PubMed]


Organelle Size Equalization by a Constitutive Process

Ludington WB, Shi LZ, Zhu Q, Berns MW, Marshall WF.
Curr Biol. 2012 Oct 16. doi:pii: S0960-9822(12)01142-6. 10.1016/j.cub.2012.09.040.[Epub ahed of print]
[PubMed]


Designing synthetic regulatory networks capable of self-organizing cell polarization
Chau AH, Walter JM, Gerardin J, Tang C, Lim WA.
Cell. 2012 Oct 12; 151(2):320-32. doi: 10.1016/j.cell.2012.08.040. [PubMed]


Directing the assembly of spatially organized mulitcomponent tissues from the bottom up
Liu JS, Gartner ZJ.
Trends Cell Biol. 2012 Oct 12. doi:pii: S0962-8924(12)00169-9. 10.1016/j.tcb.2012.09.004. [PubMed]


Programmed Cell-to-Cell Variability in Ras Activity Triggers Emergent Behaviors during Mammary Epithelial Morphogenesis

Liu JS, Farlow JT, Paulson AK, Labarge MA, Gartner ZJ
Cell Rep. 2012 Oct 3. doi:pii: S2211-1247(12)00278-1. 10.1016/j.celrep.2012.08.037.
[PubMed]


Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles

Lu C, Luo Z, Jäger S, Krogan NJ, Peterlin BM.

J Virol. 2012 Oct [Epub 2012 Jul 18]; 86(19):10517-23. doi: 10.1128/JVI.00868-12.
[PubMed]


How cells know the size of their organelles

Chan YH, Marshall WF.
Science. 2012 Sep 7; 337(6099):1186-9. Review.
[PubMed]


Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation

Zaltan JG, Coyle SM, Rajan S, Sidhu SS, Lim WA.
Science. 2012 Sep 7; 377(6009): 1218-22. Epub 2012 Aug 9. [PubMed]


Organelle size control systems: from cell geometry to organelle-directed medicine

Marshall WF.

Bioessays. 2012 Sep [Epub 2012 Jul 4]; 34(9):721-4. doi: 10.1002/bies.201200043.
[PubMed]


Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh, A, Razooky, BS, Dar, RD, Weinberger, LS

Mol Syst Biol. 2012 Aug 28; 8:607 [PubMed]


Evolutionary Analysis of Heterochromatin Protein Compatibility by Interspecies Complementation in Saccharomyces
Zill OA, Scannell DR, Kuei J, Sadhu M, Rine J.
Genetics. 2012 Aug 24. [Epub ahead of print] [PubMed]


Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse
Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL 
Mol Cell Proteomics. 2012 Aug;11(8):215-29. Epub 2012 May 29 [PubMed]

 

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells
Wei P, Wong WW, Park JS, Corcoran EE, Peisajovich SG, Onuffer JJ, Weiss A, Lim WA.
Nature. 2012 Jul 22. doi: 10.1038/nature11259 [PubMed]


Systematic Functional Prioritization of Protein Post-translational Modifications
Beltrao, P., V. Albanese, L. R. Kenner, A. Burlingame, J. S. Fraser, W. A. Lim, J. Frydman and N. J. Krogan.,
Cell, 2012 Jul 20;150(2):413-25 [PubMed]


Hierarchical modularity and the evolution of genetic interactomes across species
Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu  H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C,  Espenshade PJ, Ideker T, Krogan NJ. 
Mol Cell. 2012 Jun 8;46(5):691-704 [PubMed]


SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains
Thompson KE, Bashor CJ, Lim WA, Keating AE 
ACS Synth Biol. 2012 Apr 20;1(4):118-129[PubMed]


Molecular phenotyping of aging in single yeast cells using a novel microfluidic device
Xie Z, Zhang Y, Zou K, Brandman O, Luo C, Ouyang Q, Li H 
Aging Cell. 2012 Apr 12. doi: 10.1111/j.1474-9726.2012.00821.x.[Epub ahead of print] [PubMed]



Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T 
Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5277-82 [PubMed]


Regulatory architecture determines optimal regulation of gene expression in metabolic pathways
Chubukov V, Zuleta IA, Li H 
Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):5127-32 [PubMed]


Cell cycle synchronization by nutrient modulation
Tian Y, Luo C, Lu Y, Tang C, Ouyang Q 
Integr Biol (Camb). 2012 Mar;4(3):328-34 [PubMed]


RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36
Fuchs SM, Kizer KO, Braberg H, Krogan NJ, Strahl BD 
J Biol Chem. 2012 Jan 27;287(5):3249-56 [PubMed]


Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae
Stewart-Ornstein J, Weissman JS, El-Samad H 
Mol Cell. 2012 Feb 24;45:483-93 [PubMed]


Differential network biology
Ideker T, Krogan NJ 
Mol Syst Biol. 2012 Jan 17;8:565 [PubMed]

 

2011


 

Global landscape of HIV-human protein complexes
Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ 
Nature. 2011 Dec 21. 481(7381):365-70. [PubMed]


Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection

Jäger S, Kim DY, Hultquist JF, Shindo K, Larue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ 
Nature. 2011 Dec 21. 481(7381):371-5. [PubMed]


Light-based feedback for controlling intracellular signaling dynamics
Toettcher JE, Gong D, Lim WA, Weiner OD 
Nat Methods. 2011 Sep 11;8(10):837-9. [PubMed]


Key functional regions in the histone variant H2A.Z C-terminal docking domain
Wang AY, Aristizabal MJ, Ryan C, Krogan NJ, Kobor MS 
Mol Cell Biol. 2011 Sep;31(18):3871-84. [PubMed]


Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress
Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ 
Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10620-5. [PubMed]


Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase
Won AP, Garbarino JE, Lim WA 
Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9809-14. [PubMed]


Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information

Good MC, Zalatan JG, Lim WA
Science. 2011 May 6;332(6030):680-6. [PubMed]

Characterization of combinatorial patterns generated by multiple two-component sensors in E. coli that respond to many stimuli
Clarke E, Voigt, CA 
Biotechnology and Bioengineering. 2011 Mar;108(3):666-75. [PubMed]


Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli

Moon TS, Clarke EJ, Groban ES, Tamsir A, Clark RM, Eames M, Kortemme T, Voigt CA 
J Mol. Biol. 2011 Feb 18;406(2):215-27. [PubMed]


Multichromatic control of gene expression in Escherichia coli

Tabor JJ, Levskaya A, Voigt CA
J Mol Biol. 2011 Jan 14;405(2):315-24 [PubMed]


Robust multicellular computing using genetically-encoded NOR gates and chemical ‘wires’

Tamsir A, Tabor JJ, Voigt CA 
Nature. 2011 Jan 13;469(7329):212-5. [PubMed]

The promise of optogenetics in cell biology: interrogating molecular circuits in space and time
Toettcher JE, Voigt CA, Weiner OD, Lim WA 
Nat Methods. 2011 Jan;8(1):35-8 [PubMed]


2010


Cross-species chemogenomic profiling identifies evolutionarily conserved drug mode of action
Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, Babu MM, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ 
Molecular Systems Biology. 2010 Dec 21;6:451. [PubMed]


Build life to understand it
Elowitz M, Lim WA 
Nature. 2010 Dec 16;468(7326):889-90. [PubMed]


Rewiring of genetic networks in response to DNA damage
Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T
Science. 2010 Dec 3;330(6009):1385-9. [PubMed]


Epistatic relationships reveal the functional organization of yeast transcription factors

Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ
Molecular Systems Biology. 2010 Oct 5;6:420. [PubMed]


Phosphotyrosine signaling: evolving a new cellular communication system

Lim WA, Pawson T
Cell. 2010 Sep 3;142(5):661-7. [PubMed]

 


Feature publications


Biology by the numbers on the Hawaiian Islands
Bhatnagar R, Gordley R, Sevim S, Lee CM
Quantitative Biology. 2013, in press


Signalling change: signal transduction through the decades
Hynes NE, Ingham PW, Lim WA, Marshall CJ, Massague J, Pawson T
Nat Rev Mol Cell Biol. 2013 June; 14(6): 393-8 [PubMed]


Bridging cross-cultural gaps in scientific exchange through innovative team challenge workshops
Lee CM, Gong S, Tang C, Lim WA
Quantitative Biology. 2013 Mar; 1(1): 3-8. [DOI]


Can a systems perspective help us appreciate the biological meaning of small effects?
El-Samad H, Madhani HD
Dev Cell. 2011 Jul 19; 21(1):11-3. [PubMed]