2012    |   2011   |   2010   |   2009   |   2008   |   2007

2012

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis.
Breakfield NW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, Rubio-Somoza I, Weigel D, Ohler U and Benfey PN.
Genome Res. 2012; 22(1): 163-176. PMCID: PMC3246203. [Full Text Available 7/2012]

Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus.
Garfield D, Haygood R, Nielsen WJ and Wray GA.
Evolution & Development. 2012; 14(2): 152-167.

Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors.
Guo X, Bulyk ML and Hartemink AJ.
Pac Symp Biocomput. 2012; 104-115. [PDF]

Temporal transcriptional profiling of somatic and germ cells reveals lineage priming of sexual fate in the fetal mouse gonad.
Jameson S, Natarajan A, Cool J, De Falco T, Maatouk D, Mørk L, Munger S and Capel B.
PLoS Genet. 2012; 8(3): e1002575 [Full Text]

Frizzled1/2/7 signaling directs β-catenin nuclearisation and initiates endoderm specification in macromeres during sea urchin embryogenesis.
Lhomond G, McClay DR, Gache C and Croce JC.
Development. 2012; 139(4): 816-825. PMCID: PMC3265065. [Full Text Available 2/2013]

Integrative systems biology: an attempt to describe a simple weed.
Liberman LM, Sozzani R and Benfey PN.
Curr Opin Plant Biol. 2012; 15(2): 162-167.

Close encounters of the collaborative kind.
Mayhew MB, Guo X, Haase SB and Hartemink AJ.
Computer. 2012; 42(3): 24-30.

Transcriptional switches direct plant organ formation and patterning.
Moreno-Risueno MA, Van Norman JM and Benfey PN.
Curr Top Dev Biol. 2012; 98: 229-257. [Full Text]

The protein expression landscape of the Arabidopsis root.
Petricka JJ, Schauer M, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U and Benfey PN.
Proc Natl Acad Sci U S A. 2012; Mar 23. [Epub ahead of print]. [PDF]

Cell type-specific transcriptional profiling: implications for metabolite profiling.
Rogers ED, Jackson T, Moussaieff A, Aharoni A and Benfey PN.
Plant J. 2012; 70(1): 5-17. PMCID: PMC3315153. [Full Text Available 4/2013]

Cyclin-Dependent Kinases Are Regulators and Effectors of Oscillations Driven by a Transcription Factor Network.
Simmons Kovacs LA, Mayhew MB, Orlando DA, Jin Y, Li Q, Huang C, Reed SI, Mukherjee S and Haase SB.
Mol Cell. 2012; 45(5): 669-79.

Engineering microbial systems to explore ecological and evolutionary dynamics.
Tanouchi Y, Smith RP and You L.
Current Op Biotechnol. 2012; Feb 4. [Epub ahead of print].

Model-controlled flooding with applications to image reconstruction and segmentation.
Wang Q and West M.
Journal of Electronic Imaging. 2012; In press. [Full Text]

Perturbations to the Hh pathway in sea urchin embryos.
Warner J and McClay DR.
Methods Mol Bio. 2012; In press

Tension and robustness in multitasking cellular networks.
Wong JV, Li B and You L.
PLoS Comput Biol. 2012; 8(4): e1002491. [Full Text]

 

2011

Taking a developmental perspective on systems biology.
Benfey PN.
Dev Cell. 2011; 21(1): 27-28.

Bayesian learning from marginal data in bionetwork models.
Bonassi FV, You L and West M.
Stat Appl Genet Mol Biol. 2011; 10(1): Article 49.

A stele-enriched gene regulatory network in the Arabidopsis root.
Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ and Benfey PN.
Mol Syst Biol. 2011; 7: 459. PMCID: PMC3049412. [Full Text] [Dataset]

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD and Ohler U.
Genome Biol. 2011; 12(8): R79. [Full Text] [Software]

Wnt6 activates endoderm in the sea urchin gene regulatory network.
Croce J, Range R, Wu SY, Miranda E, Lhomond G, Peng JC, Lepage T and McClay DR.
Development. 2011; 138(15): 3297-3306. PMCID: PMC3133919. [Full Text Available 8/2012]

Efficient classification-based relabeling in mixture models.
Cron AJ and West M.
Am Stat. 2011; 65(1): 16-20. PMCID: PMC3110018. [Full Text] [Software]

A potential role for glucose transporters in the evolution of human brain size.
Fedrigo O, Pfefferle AD, Babbitt CC, Haygood R, Wall CE and Wray GA.
Brain Behav Evol. 2011; 78(4): 315-326. PMCID: PMC3237107. [PDF]

Pleiotropic signaling pathways orchestrate yeast development.
Granek JA, Kayikçi Ö and Magwene PM.
Curr Opin Microbiol 2011; 14(6):676-81. [Full Text Available 12/2012]

Estimating variable structure and dependence in multi-task learning via gradients.
Guinney J, Wu Q and Mukherjee S.
Machine Learning. 2011; 84(3): 265-287. [PDF]

Computation of steady-state probability distributions in stochastic models of cellular networks.
Hallen M, Li B, Tanouchi Y, Tan CM, West M and You L.
PLoS Comput Biol. 2011; 7: e1002209. PMCID: PMC3192818. [Full Text]

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae.
Magwene PM, Kayikçi Ö, Granek JA, Reininga JM, Scholl Z and Murray D.
Proc Natl Acad Sci U S A. 2011; 108(5): 1987-1992. PMCID: PMC3033294. [Full Text]  [Datasets]

The statistics of bulk segregant analysis using next generation sequencing.
Magwene PM, Willis JH and Kelly JK.
PLoS Comput Biol. 2011; 7(11): e1002255. PMCID: PMC3207950 [Full Text]

A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.
Mayhew MB, Robinson JW, Jung B, Haase SB and Hartemink AJ.
Bioinformatics. 2011; 27(13): i295-303. PMCID: PMC3117372. [Full Text] [Software]

Visualizing fitness landscapes.
McCandlish DM.
Evolution. 2011; 65(6): 1544-1558.

Evolutionary crossroads in developmental biology: sea urchins.
McClay DR.
Development. 2011; 138(13): 2639-2648. PMCID: PMC3109595. [Full Text Available 7/2012]

Verification of systems biology research in the age of collaborative competition.
Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D and Stolovitzky G.
Nat Biotechnol. 2011; 29(9): 811-815. [Full Text]

Probability measures on the space of persistence diagrams.
Mileyko Y, Mukherjee S and Harer J.
Inverse Problems. 2011; 27: 124007. [Full text]

Time-based patterning in development: The role of oscillating gene expression.
Moreno-Risueno MA and Benfey PN.
Transcription. 2011; 2(3): 124-129. PMCID: PMC3149689. [Full Text]

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability.
Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M, Jr., Tuschl T, Ohler U and Keene JD.
Mol Cell. 2011; 43(3): 327-339. [Full Text]

Reconstructing regulatory network transitions.
Petricka JJ and Benfey PN.
Trends Cell Biol. 2011; 21(8): 442-451. PMCID: PMC3149721. [Full Text Availabe 8/2012]

Automatic annotation of spatial expression patterns via sparse Bayesian factor models.
Pruteanu-Malinici I, Mace DL and Ohler U.
PLoS Comput Biol. 2011; 7(7): e1002098. PMCID: PMC3140966. [Full Text]

The control of foxN2/3 expression in sea urchin embryos and its function in the skeletogenic gene regulatory network.
Rho HK and McClay DR.
Development. 2011; 138(5): 937-945. PMCID: PMC3035096. [Full Text]

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype.
Sozzani R and Benfey PN.
Genome Biol. 2011; 12(3): 219. PMCID: PMC3129668. [Full Text]

Intercellular communication during plant development.
Van Norman JM, Breakfield NW and Benfey PN.
Plant Cell. 2011; 23(3): 855-864. PMCID: PMC3082268. [Full Text]

Network calisthenics: Control of E2F dynamics in cell cycle entry.
Wong JV, Dong P, Nevins JR, Mathey-Prevot B and You L.
Cell Cycle. 2011; 10(18). [Full text Available 9/2012]

Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells.
Wong JV, Yao G, Nevins JR and You L.
Methods Enzymol. 2011; 497: 221-237.

Viral-mediated noisy gene expression reveals biphasic E2f1 response to MYC.
Wong JV, Yao G, Nevins JR and You L.
Mol Cell. 2011; 41(3): 275-285. PMCID: PMC3044932. [Full Text]

Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.
Xiong Q, Ancona N, Hauser ER, Mukherjee S and Furey TS.
Genome Res. 2011. [Full Text] [Software]

Origin of bistability underlying mammalian cell cycle entry.
Yao G, Tan C, West M, Nevins JR and You L.
Molecular Systems Biology. 2011; 7: 485. PMCID: PMC3101952. [Full Text]

Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution.
Yokoyama KD, Thorne JL and Wray GA.
Genome Biol Evol. 2011; 3: 66-74. PMCID: PMC3021792. [Full Text]

 

2010

Getting to the root of plant biology: Impact of the Arabidopsis genome sequence on root research.
Benfey PN, Bennett M and Schiefelbein J.
Plant J. 2010; 61(6): 992-1000. PMCID: PMC2967761. [Full Text]

Information processing without brains--the power of intercellular regulators in plants.
Busch W and Benfey PN.
Development. 2010; 137(8): 1215-1226. PMCID: PMC2847462. [Full Text]

Optimization of a highly standardized carboxyfluorescein succinimidyl ester flow cytometry panel and gating strategy design using discriminative information measure evaluation.
Chan C, Lin L, Frelinger J, Herbert V, Gagnon D, Landry C, Sekaly RP, Enzor J, Staats J, Weinhold KJ, Jaimes M and West M.
Cytometry A. 2010; 77(12): 1126-1136. PMCID: PMC3042236. [Full Text] [Data and MatLab Code]

Dynamics of Delta/Notch signaling on endomesoderm segregation in the sea urchin embryo.
Croce JC and McClay DR.
Development. 2010; 137(1): 83-91. PMCID: PMC2796929. [Full Text]

The evolution of gene regulatory interactions.
Garfield DA and Wray GA.
Bioscience. 2010; 60(1): 15-23.

Evidence-ranked motif identification.
Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S and Ohler U.
Genome Biol. 2010; 11(2): R19. PMCID: PMC2872879. [Full Text] [cERMIT Software and Dataset]

Finding regulatory DNA motifs using alignment-free evolutionary conservation information.
Gordan R, Narlikar L and Hartemink AJ.
Nucleic Acids Res. 2010; 38(6): e90. PMCID: PMC2847231. [Full Text] [Datasets]

Environmental and genetic determinants of colony morphology in yeast.
Granek JA and Magwene PM.
PLoS Genet. 2010; 6(1): e1000823. PMCID: PMC2809765. [Full Text]

Multiscale factor models for molecular networks.
Guinney J, Febbo PG, Maggioni M and Mukherjee S.
Proceedings of the Joint Statistics Meeting. 2010. [PDF]

Fluorescence-activated cell sorting in plant developmental biology.
Iyer-Pascuzzi AS and Benfey PN.
Methods Mol Biol. 2010; 655: 313-319. [Full Text]

Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems.
Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS and Benfey PN.
Plant Physiol. 2010; 152(3): 1148-1157. PMCID: PMC2832248. [Full Text]

Stochastic E2F activation and reconciliation of phenomenological cell-cycle models.
Lee TJ, Yao G, Bennett DC, Nevins JR and You L.
PLoS Biol. 2010; 8(9). PMCID: PMC2943438. [Full Text]

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.
MacAlpine HK, Gordan R, Powell SK, Hartemink AJ and MacAlpine DM.
Genome Res. 2010; 20(2): 201-211. PMCID: PMC2813476. [Full Text] [Dataset 1] [Dataset 2] [Dataset 3] [Dataset 4]

Selection sampling from large data sets for targeted inference in mixture modeling.
Manolopoulou I, Chan C and West M.
Bayesian Anal. 2010; 5(3): 1-22. PMCID: PMC2943396. [Full Text] [Code]

Bayesian mixture of inverse regressions.
Mao K, Liang F and Mukherjee S.
Thirteenth International Conference on Artificial Intelligence and Statistics. 2010; Cambridge, MA, USA, MIT Press. [PDF]

Omics meet networks - using systems approaches to infer regulatory networks in plants.
Moreno-Risueno MA, Busch W and Benfey PN.
Curr Opin Plant Biol. 2010; 13(2): 126-131. PMCID: PMC2862083. [Full Text]

Learning gradients on manifolds.
Mukherjee S, Wu Q and Zhou DX.
Bernoulli. 2010; 16(1): 181-207.

Adaptive mixture modelling Metropolis methods for Bayesian analysis of non-linear state-space models.
Niemi J and West M.
J Comput Graph Stat. 2010; 19(2): 260-280. PMCID: PMC2887612. [Full Text] [Supplemental Material Including Code]

Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.
Oliver TA, Garfield DA, Manier MK, Haygood R, Wray GA and Palumbi SR.
Genome Biol Evol. 2010; 2: 800-814. PMCID: PMC2975446. [Full Text]

Detecting separate time scales in genetic expression data.
Orlando DA, Brady SM, Fink TM, Benfey PN and Ahnert SE.
BMC Genomics. 2010; 11: 381. PMCID: PMC3017766. [Full Text]

Reliability of transcriptional cycles and the yeast cell-cycle oscillator.
Sevim V, Gong X and Socolar JES.
PLoS Comput Biol. 2010; 6(7): e1000842. PMCID: PMC2900291. [Full Text]

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.
Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JA and Benfey PN.
Nature. 2010; 466(7302): 128-132. PMCID: PMC2967763. [Full Text]

Understanding GPU programming for statistical computation: Studies in massively parallel massive mixtures.
Suchard MA, Wang Q, Chan C, Frelinger J, Cron A and West M.
J Comput Graph Stat. 2010; 19(2): 419-438. PMCID: PMC2945379. [Full Text] [Dataset and code]

Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root.
Tsukagoshi H, Busch W and Benfey PN.
Cell 2010; 143(4): 606-616.

Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations.
Tung J, Alberts SC and Wray GA.
Trends Genet 2010; 26(8): 353-362. PMCID: PMC2933653. [Full Text]

Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.
Wang Q, Niemi J, Tan CM, You L and West M.
Cytometry A. 2010; 77(1): 101-110. PMCID: PMC2797831. [Full Text]

Learning gradients: Predictive models that infer geometry and dependence.
Wu Q, Guinney J, Maggioni M and Mukherjee S.
Journal of Machine Learning Research. 2010; 11: 2175-2198. [PDF]

Localized sliced inverse regression.
Wu Q, Liang F and Mukherjee S.
J Comput Graph Stat. 2010; 19(4): 843-860.

 

2009

Chordin is required for neural but not axial development in sea urchin embryos.
Bradham CA, Oikonomou C, Kuhn A, Core AB, Modell JW, McClay DR and Poustka AJ.
Dev Biol. 2009; 328(2): 221-233. PMCID: PMC2700341. [Full Text] [Dataset 1] [Dataset 2]

Cortex proliferation: simple phenotype, complex regulatory mechanisms.
Cui H and Benfey PN.
Plant Signal Behav. 2009; 4(6): 551-553. PMCID: PMC2688310. [Full Text]

Comparative embryology without a microscope: using genomic approaches to understand the evolution of development.
Garfield DA and Wray GA.
J Biol. 2009; 8(7): 65. PMCID: PMC2736668. [Full Text]

Distinguishing direct versus indirect transcription factor-DNA interactions.
Gordan R, Hartemink AJ and Bulyk ML.
Genome Res. 2009; 19(11): 2090-2100. PMCID: PMC2775597. [Full Text]

Domain-oriented edge-based alignment of protein interaction networks.
Guo X and Hartemink AJ.
Bioinformatics. 2009; 25(12): i240-246. PMCID: PMC2687956. [Full Text] [Supplementary material and Code]

Functional genomics of root growth and development in Arabidopsis.
Iyer-Pascuzzi A, Simpson J, Herrera-Estrella L and Benfey PN.
Curr Opin Plant Biol. 2009; 12(2): 165-171. PMCID: PMC2683257. [Full Text]

Transcriptional networks in root cell fate specification.
Iyer-Pascuzzi AS and Benfey PN.
Biochim Biophys Acta. 2009; 1789(4): 315-325. PMCID: PMC2691893. [Full Text]

Spatial mixture modelling for unobserved point processes: Examples in immunofluorescence histology.
Ji C, Merl D, Kepler TB and West M.
Bayesian Anal. 2009; 4(2): 297-316. PMCID: PMC2965046. [Full Text] [Code] [Dataset]

Cleavage and gastrulation in the sea urchin.
McClay D.
In "Encyclopedia of Life Sciences"; 2009. Wylie.

A transcription factor affinity-based code for mammalian transcription initiation.
Megraw M, Pereira F, Jensen ST, Ohler U and Hatzigeorgiou AG.
Genome Res. 2009; 19(4): 644-656. PMCID: PMC2665783. [Full Text] [Software]

Sequential Monte Carlo in model comparison: Example in cellular dynamics in systems biology.
Mukherjee C and West M.
JSM Proceedings, Section on Bayesian Statistical Science. Alexandria, VA: American Statistical Association 2009: 1274-1287. [PDF]

Elucidation of the transcription network governing mammalian sex determination by exploiting strain-specific susceptibility to sex reversal.
Munger SC, Aylor DL, Syed HA, Magwene PM, Threadgill DW and Capel B.
Genes Dev 2009; 23(21): 2521-2536. PMCID: PMC2779749. [Full Text] [Dataset]

Boolean modeling of collective effects in complex networks.
Norrell J and Socolar JES.
Phys Rev E Stat Nonlin Soft Matter Phys. 2009; 79(6): nihpa131303. PMCID: PMC2718684. [Full Text]

A branching process model for flow cytometry and budding index measurements in cell synchrony experiments.
Orlando DA, Iversen ES, Jr., Hartemink AJ and Haase SB.
Ann Appl Stat. 2009; 3(4): 1521-1541. PMCID: PMC3156593. [Full Text] [Software]

Engineering multicellular systems by cell-cell communication.
Pai A, Tanouchi Y, Collins CH and You L.
Curr Opin Biotechnol. 2009; 20(4): 461-470. PMCID: PMC2763981. [Full Text]

Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis.
Petricka JJ, Van Norman JM and Benfey PN.
Cold Spring Harb Perspect Biol. 2009; 1(5): a000497. PMCID: PMC2773642. [Full Text]

Emergent bistability by a growth-modulating positive feedback circuit.
Tan C, Marguet P and You L.
Nat Chem Biol. 2009; 5(11): 842-848. PMCID: PMC2908482. [Full Text]

Decoding biological principles using gene circuits.
Tanouchi Y, Pai A and You L.
Molecular Biosystems. 2009; 5(7): 695-703.

Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation.
Tung J, Fedrigo O, Haygood R, Mukherjee S and Wray GA.
Mol Biol Evol. 2009; 26(9): 2047-2059. PMCID: PMC2734157. [Full Text] [Dataset]

Arabidopsis thaliana as a model organism in systems biology.
Van Norman JM and Benfey PN.
Wiley Interdiscip Rev Syst Biol Med. 2009; 1(3): 372-379. PMCID: PMC2836806. [Full Text]

Hedgehog signaling patterns mesoderm in the sea urchin.
Walton KD, Warner J, Hertzler PH and McClay DR.
Dev Biol. 2009; 331(1): 26-37. PMCID: PMC2702090. [Full Text]

An ensemble model of competitive multi-factor binding of the genome.
Wasson T and Hartemink AJ.
Genome Res. 2009; 19(11): 2101-2112. PMCID: PMC2775586. [Full Text] [Software]

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.
Yokoyama KD, Ohler U and Wray GA.
Nucleic Acids Res. 2009; 37(13): e92. PMCID: PMC2715254. [Full Text]

 

2008

Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.
Colinas J, Schmidler SC, Bohrer G, Iordanov B and Benfey PN.
PLoS One. 2008; 3(11): e3670. PMCID: PMC2576458. [Full Text]

Evolution of the Wnt pathways.
Croce JC and McClay DR.
Methods Mol Biol. 2008; 469: 3-18. PMCID: PMC3052202. [Full Text]

Systems approaches to identifying gene regulatory networks in plants.
Long TA, Brady SM and Benfey PN.
Annu Rev Cell Dev Biol. 2008; 24: 81-103. PMCID: PMC2739012. [Full Text]

Global control of cell-cycle transcription by coupled CDK and network oscillators.
Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JES, Iversen ES, Hartemink AJ and Haase SB.
Nature. 2008; 453(7197): 944-947. PMCID: PMC2736871. [Full Text] [Dataset]

Root layers: complex regulation of developmental patterning.
Petricka JJ and Benfey PN.
Curr Opin Genet Dev. 2008; 18(4): 354-361. PMCID: PMC2605625. [Full Text]

LvNumb works synergistically with Notch signaling to specify non-skeletal mesoderm cells in the sea urchin embryo.
Range RC, Glenn TD, Miranda E and McClay DR.
Development. 2008; 135(14): 2445-2454. [Full Text]

FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis and regulate gastrulation during sea urchin development.
Rottinger E, Saudemont A, Duboc V, Besnardeau L, McClay D and Lepage T.
Development. 2008; 135(2): 353-365. [Full Text]

Transcription networks and cyclin/CDKs: the yin and yang of cell cycle oscillators.
Simmons Kovacs LA, Orlando DA and Haase SB.
Cell Cycle. 2008; 7(17): 2626-2629. [PDF]

A whole more than the sum of its synthetic parts.
Wong JV, Song H and You L.
ACS Chem Biol. 2008; 3(1): 27-29. [Full Text]

Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo.
Wu SY, Yang YP and McClay DR.
Dev Biol. 2008; 319(2): 406-415. PMCID: PMC2517249. [Full Text]

A bistable Rb-E2F switch underlies the restriction point.
Yao G, Lee TJ, Mori S, Nevins JR and You L.
Nat Cell Biol. 2008; 10(4): 476-482.

 

2007

A high-resolution root spatiotemporal map reveals dominant expression patterns.
Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U and Benfey PN.
Science. 2007; 318(5851): 801-806. [Full Text]

Noise-limited frequency signal transmission in gene circuits.
Tan C, Reza F and You L.
Biophys J. 2007; 93(11): 3753-3761. PMCID: PMC2084236. [Full Text]

A synthetic biology challenge: Making cells compute.
Tan C, Song H, Niemi J and You L.
Molecular Biosystems. 2007; 3(5): 343-353. [Full Text]

The evolutionary significance of cis-regulatory mutations.
Wray GA.
Nat Rev Genet. 2007; 8(3): 206-216.