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Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora, by Morten O. A. Sommer, Gautam Dantas, and George M. Church, from Science (Aug 28, 2009)

Megan Riel-Mehan

Chemical Dissection of an Essential Redox Switch in Yeast Candice E. Paulsen1 and Kate S. Carroll1,2,3,* 1Chemical Biology Graduate Program 2Department of Chemistry 3Life Sciences Institute University of Michigan, Ann Arbor, MI 48109-2216, USA *Correspondence: katesc@umich.edu DOI 10.1016/j.chembiol.2009.01.003

Charlie Morgan

"Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators" Imamura, H., et al. PNAS Sept 15 2009.

Geoff Rollins

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Smith et al. Nature 459, 1122-1125 (2009)

Joanna Lipinski

"Programming cells by multiplex genome engineering and accelerated evolution" Wang H, Isaacs F, Carr P, Sun Z, Xu G, Forest C, Church G. Nature 460, 894-898 (13 August 2009)

Edwin Rodriguez

An Unfolded CH1 Domain Controls the Assembly and Secretion of IgG Antibodies Matthias J. Feige,1 Sandra Groscurth,1 Moritz Marcinowski,1 Yuichiro Shimizu,2 Horst Kessler,1 Linda M. Hendershot,2 and Johannes Buchner1,* Molecular Cell 34, 569–579, June 12, 2009

Idelisse Ortiz Torres

Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling Nature 461, 614-620 (1 October 2009) | doi:10.1038/nature08356;

Chris Fuller

"Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses" by Ido Amit, et al. It's in the October 9th issue of Science.

Dan Lu

Protein sectors: evolutionary units of three-dimensional structure. Najeeb Halabi, Olivier Rivoire, Stanislas Leibler, Rama Ranganathan. Cell vol. 138 (4) pp. 774-86 (August 21, 2009)

Dan Le

Inhibitors selective for mycobacterial versus human proteasomes Gang Lin et al Nature, Vol 461, 1 October 2009: pg 621-27

Henry Lin

I plan on doing my journal club (Nov 10th) talk on a paper titled: Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Erez Lieberman-Aiden, et al. Science 326: 5950. 289-293. Oct 9, 2009

Andrew Wiser

HDAC2 negatively regulates memory formation and synaptic plasticity" from Nature; vol 459; May 7, 2009

Emmanuel Yera

RNAi in Budding Yeast Ines A. Drinnenberg 1, David E. Weinberg 2, Kathleen T. Xie 2, Jeffrey P. Mower 3, Kenneth H. Wolfe 4, Gerald R. Fink 5, David P. Bartel 2*

Crystal Nyitray

A biological quarter-wave retarder with excellent achromacity in the visible wavelength region. Nature Photonics 3, 641 - 644 (2009) Published online: 25 October 2009 | doi:10.1038/nphoton.2009.189 N. W. Roberts1,2, T.-H. Chiou3, N. J. Marshall3 & T. W. Cronin4

Monica Tremont

Electron Relay in Proteins

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Michael Lopez

S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons

Nott, Alexi et al. S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons. Nature. Advanced online publication, (2008).

Noah Ollikainen

In vivo reprogramming of adult pancreatic exocrine cells to beta-cells

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Gabe Rocklin

Crowded, cell-like environment induces shape changes in aspherical protein

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Nicholas Hertz

A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms

Michael R. Sawaya, Wof M. Wojtowicz, Ingemar Andre, Bin Qian, Wei Wu, David Baker, David Eisenberg, S. Lawrence Zipursky (2008). A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms. Cell 134, 1007-1018

Adam Marko

It's all in your head: The Drosophila pheromone cVA activates a sexually dimorphic neural circuit

Sandeep Robert Datta, Maria Luisa Vasconcelos, Vanessa Ruta, Sean Luo, Allan Wong, Ebru Demir, Jorge Flores, Karen Balonze, Barry J. Dickson & Richard Axel. The Drosophila pheromone cVA activates a sexually dimorphic neural circuit. Nature 452, 473-477 (27 March 2008) doi:10.1038/nature06808.

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Cheryl Tajon

The effect of particle design on cellular internalization pathways

Stephanie E. A. Gratton, Patricia A. Ropp, Patrick D. Pohlhaus, J. Christopher Luft, Victoria J. Madden, Mary E. Napier, and Joseph M. DeSimone. The effect of particle design on cellular internalization pathways. PNAS August 29, 2008
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Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

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David Burkhardt

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

S. Jhunjhunwala, M. van Zelm, M. Peak, S. Cutchin, R. Riblet, J. van Dongen, F. Grosveld, T. Knoch, C. Mur. The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions. Cell, Volume 133, Issue 2, Pages 265-279.

Rebecca Maglathlin

"An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms"

"An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms" Hiratsuka, et. al., Science, 321, 1670 (2008):DOI: 10.1126/science.1160446

Bethany Simmons

Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos

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Jaline Gerardin

A mechanism for asymmetric segregation of age during yeast budding

Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y. A mechanism for asymmetric segregation of age during yeast budding. Nature. 2008 Aug 7;454(7205):728-34.

Brandon Butler

Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation

EM Duncan, TL Muratore-Schroeder, RG Cook, BA Garcia, J Shabanowitz, DF Hunt, and CD Allis. Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation. Cell, Volume 135, Issue 2, 284-294, 17 October 2008. doi:10.1016/j.cell.2008.09.055

Elaine Kirschke

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

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Hannes Braberg

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNA

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Robin Aglietti

The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly

The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly. André Scheffel and Dirk Schüler. Journal of Bacteriology, September 2007, p. 6437-6446, Vol. 189, No. 17. doi:10.1128/JB.00421-07

Rand Miller

CASK Functions as a Mg2+-independent Neurexin Kinase

CASK Functions as a Mg2+-independent Neurexin Kinase. Mukherjee, M. et al. Cell, Vol. 133, No. 2, April 18, 2008, p. 328-339

Heather Newman

Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy

Christian W. Freudiger, Wei Min, Brian G. Saar, Sijia Lu, Gary R. Holtom, Chengwei He, Jason C. Tsai, Jing X. Kang, and X. Sunney Xie. Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy. Science 322 (5909), 1857. (19 December 2008) [DOI:10.1126/science.1165758]

Charlie Kehoe

Structure and function of an RNase H domain at the heart of the spliceosome

Vladimir Pena, Alexey Rozov, Patrizia Fabrizio, Reinhard Lührmann, and Markus C Wahl. Structure and function of an RNase H domain at the heart of the spliceosome. The EMBO Journal (2008) 27, 2929–2940, doi:10.1038/emboj.2008.209 Published online 9 October 2008

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George Peterson

Tomas-Loba A, Flores I, Fernandez-Marcos PJ, Cayuela ML, Maraver A, Tejera A, Borras C, Matheu A, Klatt P, Flores JM, Vina J, Serrano M, Blasco MA. Telomerase Reverse Transcriptase Delays Aging in Cancer-Resistant Mice. Cell 135 (2008), 609-622.

Xiuming Wong

Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry

Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry. P Li, MJ Plevin, M Ikura. Cell, Volume 135, Issue 1, 110-122, 3 October 2008

Peter Skewes-Cox

Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature. 2008 Dec 11;456(7223):750-4

Carrie Shiau

DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45. Rai, K. et al. Cell, Vol 135, No. 7, December 26, 2008, p. 1201-1212.

Joe Kliegman

Sun et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell (2008) vol. 135 (7) pp. 1251-62

Chris Wen

Ashok Prasada,Julie Zikhermanb, Jayajit Dasa, Jeroen P. Roosec, Arthur Weissbd1 and Arup K. Chakrabortyaef1. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. PNAS January 13, 2009 vol. 106 no. 2 528-533

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Scott Smukalla, Marina Caldara, Nathalie Pochet, Anne Beauvais, Stephanie Guadagnini, Chen Yan, Marcelo D. Vinces, An Jansen, Marie Christine Prevost, Jean-Paul Latge, Gerald R. Fink, Kevin R. Foster, and Kevin J. Verstrepen. (2008) FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast. Cell 135(4), 726-737.

Jennifer Liu

A tunable synthetic mammalian oscillator. Nature 457, 309-312 (15 January 2009)

David Booth

Byres E, et al. (4 Dec 2008) "Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin." Nature 456: 648-52.

Jonathan Choy

AMPK and PPARδ Agonists Are Exercise Mimetics.

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Daniel Le

Yamagata K, Daitoku H, Takahashi Y, Namiki K, Hisatake K, Kako K, Mukai H, Kasuya Y, Fukamizu A. Arginine methylation of FOXO transcription factors inhibits their phosphorylation by Akt. Mol Cell. 2008 Oct 24;32(2):221-31.

Chris Fuller

Genotype, haplotype and copy-number variation in worldwide human populations. Jakobsson, M. et al. Nature vol 451, 908-1002. 2008

Megan Riel-Mehan

Science 28 November 2008: Vol. 322. no. 5906, pp. 1387 - 1392. An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing. Julius Brennecke, Colin D. Malone, Alexei A. Aravin, Ravi Sachidanandam, Alexander Stark, Gregory J. Hannon.

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Intersubunit coordination in a homomeric ring ATPase. Moffitt et al. Nature 457, 446-450 (2009).

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ChIP-seq accurately predicts tissue-specific activity of enhancers. Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin & Len A. Pennacchio. Nature Vol 457| 12 February 2009| doi:10.1038/nature07730

Charles Morgan

Quantitive exploration of the catalytic landscape separating divergent plant sesquiterpene synthases". Nature Chemical Biology. October(2008) Vol. 4 Number 10. pg. 617-623. O'Maille et. al.

Russell Spitzer

A stress-responsive RNA switch regulates VEGFA expression. Partho Sarothi Ray, Jie Jia, Peng Yao, Mithu Majumder, Maria Hatzoglou & Paul L. Fox Nature. 457. 915-919. 2009

Edwin Rodriguez

Self-Sustained Replication of an RNA Enzyme. Science 323, 1229 (2009) Tracey A. Lincoln et al.

Emmanuel Yera

A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Sonia A Melo, Santiago Ropero, Catia Moutinho, Lauri A Aaltonen, Hiroyuki Yamamoto, George A Calin, Simona Rossi, Agustin F Fernandez, Fatima Carneiro, Carla Oliveira, Bibiana Ferreira, Chang-Gong Liu, Alberto Villanueva, Gabriel Capella, Simo Schwartz Jr, Ramin Shiekhattar & Manel Esteller. Nature Genetics 41, 365 - 370 (2009) Published online: 15 February 2009 | doi:10.1038/ng.317

Dan Lu

Julien F Ayroles et al. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet (2009) vol. 41 (3) pp. 299

Roxana Ordonez

Cohen et al. Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) vol. 322 (5907) pp. 1511-6

Andrew Wiser

"Monomeric fluorescent timers that change color from blue to red report on cellular trafficking". Subach et al. Nature Chemical Biology (2009) Volume 5 Number 2 February 2009 118-126

Henry Lin

Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site. Jenny Bostrom, Shang-Fan Yu, David Kan, Brent A. Appleton, Chingwei V. Lee, Karen Billeci, Wenyan Man, Franklin Peale, Sarajane Ross, Christian Wiesmann, Germaine Fuh. Science 323, 1610 (2009)

Samuel Myers

Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M. Mol Cell. 2009 Feb 27;33(4):417-27.

Anthony Shiver

Nature Structural & Molecular Biology. Helix Sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding Takashide Kon et al. Vol 16 numb 3 march 2009

Joanna Lipinski

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Sabrina L. Spencer, Suzanne Gaudet, John G. Albeck, John M. Burke & Peter K. Sorger. (doi:10.1038/nature08012)

Idelisse Ortiz Torres

Selective Erasure of a Fear Memory Jin-Hee Han, Steven A. Kushner, Adelaide P. Yiu, Hwa-Lin (Liz) Hsiang, Thorsten Buch, Ari Waisman, Bruno Bontempi, Rachael L. Neve, Paul W. Frankland, and Sheena A. Josselyn (13 March 2009) Science 323 (5920), 1492. [DOI: 10.1126/science.1164139]

Ryan Gile

Stretching Single Talin Rod Molecules Activates Vinculin Binding. Armando del Rio. Science (January 2009).

Linh Ho

Linh Ho: AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity Nature 458, 1056-1060, 2009.

James Kraemer

Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules. Jan Philipp Junker, Fabian Ziegler, and Matthias Rief. Science 30 January 2009: 633-637.

Rocco Varela

Rocco Varela: An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer Nature. 2009 Apr 9;458(7239):732-6

Maya Chandru

Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion.

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Aptamer Displacement Identifies Alternative Small-Molecule Target Sites that Escape Viral Resistance

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Seelig B, Szostak JW. Nature. 2007 Aug 16;448(7155):828-31.

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Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis.

Ortlund, Bridgham, Redinbo, Thornton. Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.

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Rebeca Choy

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Charles Biddle-Snead

Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits

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Splicing factor SF3b as a target of the antitumor natural product pladienolide

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Daniele Canzio

A motor that makes his own track: helicase unwinding of DNA: Single-Molecule Studies Reveal Dynamics of DNA unwinding by the Ring-Shaped T7 Helicase

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David Stanley

Dynamic Scaffolding of a G Protein-Coupled Signaling System

Prashant Mishra, Michael Socolich, Mark A. Wall, Jennifer Graves, ZiFen Wang, and Rama Ranganathan. Cell, Vol 131, 80-92, 05 October 2007

Kris Kuchenbecker

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Ordered phosphorylation governs oscillation of a three-protein circadian clock

Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. Science. 2007 Nov 2;318(5851):809-12. Epub 2007 Oct 4.

Jonathan Choy

Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity

Steven W. Millward, Stephen Fiacco, Ryan J. Austin, and Richard W. Roberts (2007) ACS Chem. Biol. 2, 625-634.

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A Simple DNA-Based Translation System

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Retroposons: DNA parasites or facilitators? A CORE-SINE retroposon as a highly conserved neuronal enhancer.

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Functional specificity among ribosomal proteins regulates gene expression.

Komili S, Farny NG, Roth FP, Silver PA.Cell. 2007 Nov 2;131(3):450-1.

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Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin

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Joseph Kliegman

Minor Details of Transcription Factor Specificity

Rohit Joshi, Jonathan M. Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, Aneel K. Aggarwal, Barry Honig and Richard S. Mann. Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure, CellVolume 131, Issue 3, , 2 November 2007, Pages 530-543.

Michael Lopez

A GluR1-cGKII Interaction Regulates AMPA Receptor Trafficking

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Somewhere over the brainbow

Jean Livet, Tamily A. Weissman, Hyuno Kang, Ryan W. Draft, Ju Lu, Robyn A. Bennis, Joshua R. Sanes & Jeff W. Lichtman. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 450, 56-62 (2007).

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George Peterson

Nicotinamide Riboside Promotes Sir2 Silencing and Extends Lifespan via Nrk and Urh1/Pnp1/Meu1 Pathways to NAD+

Belenky P, Racette FG, Bogan KL, McClure JM, Smith JS, Brenner C. Cell 129: 473-84 (2007)

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Rebecca Maglathlin

Structural Rearrangements of NR1/NR2A NMDA Receptors during Allosteric Inhibition

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Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes

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Peter Skewes-Cox

Will newly identified host factors exploited by HIV make good drug targets?

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Switching from repression to activation: microRNAs can up-regulate translation.

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High-content single-cell drug screening with phosphospecific flow cytometry

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Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target

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A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol

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Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain

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Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

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Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin.

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A beta-arrestin 2 Signalling Complex Mediates Lithium Action on Behavior

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Direct observation of hierarchical folding in single riboswitch aptamers

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Transcriptional repression mediated by repositioning of genes to the nuclear lamina

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Computational Enzyme Design

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Hydrodynamic Flow-Mediated Protein Sorting on the Cell Surface of Trypanosomes

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Integrating high-content screening and ligand-target prediction to identify mechanism of action

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Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy

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