Journal Club Papers Archive

Week 2 - 10/5/18: "Extracellular Vesicles Provide a Means for Tissue Crosstalk during Exercise"

Week 3 - 10/12/18: "RNA velocity of single cells"

Week 4 - 10/19/18: "Atlas of Circadian metabolism reveals system-wide coordination and communication between clocks"

Week 5 - 10/26/18: "Three-dimensional intact-tissue sequencing of single-cell transcriptional states"

Week 6 - 10/29/18: " Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq "

Week 7 - 11/16/18: "Three-dimensional microbiome and Metabolome Cartography of a Diseased Human Lung"

Week 8 - 11/19/18: " Global, quantitative, and dynamic mapping of protein subcellular localization" 

Week 9 - 11/30/18: "Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns" 

Week 10 - 12/7/18: "Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq"

Week 2 - 4/11/18 - https://www.nature.com/articles/nature25168

Week 3 - 4/18/18 - https://www.nature.com/articles/nature25193

Week 4 - 4/25/18 - RIP Talks

Week 5 - 5/2/18 - http://www.pnas.org/content/111/52/18507

Week 6 - 5/9/18 - https://www.nature.com/articles/nature26000

Week 7 - 5/16/18 - http://www.cell.com/cell/fulltext/S0092-8674(18)30052-7

Week 8 - 5/23/18 - RIP Talks

Week 9 - 5/30/18 - http://www.cell.com/cell-systems/fulltext/S2405-4712(18)30053-X

Week 10 - 6/6/18 - http://www.cell.com/cell/fulltext/S0092-8674(17)31142-X

Week 11 - 6/13/18 - http://www.cell.com/cell/fulltext/S0092-8674(17)31319-3

Week 2 - 01/24/18 - https://www.ncbi.nlm.nih.gov/pubmed/29153838

Week 3 - 01/26/18 - https://www.ncbi.nlm.nih.gov/pubmed/26700852

Week 4 - 02/02/18 - https://www.nature.com/articles/nmat3777

Week 5 - 02/09/18 - https://www.ncbi.nlm.nih.gov/pubmed/?term=Engineered+Tissue+Folding+by+Mechanical+Compaction+of+the+Mesenchyme

Week 6 - 02/16/18 - https://www.nature.com/articles/s41551-017-0169-7

Week 7 - 02/23/18 - https://www.ncbi.nlm.nih.gov/pubmed/29186117

Week 8 - 03/02/18 - https://www.ncbi.nlm.nih.gov/pubmed/28874527

Week 9 - 03/09/18 - https://www.ncbi.nlm.nih.gov/pubmed/29293494

Week 10 - 03/16/18 - https://www.ncbi.nlm.nih.gov/pubmed/27764670

Week 2 - 10/06/17 - http://www.cell.com/cell/fulltext/S0092-8674(16)31660-9

Week 3 - 10/13/17 - http://www.cell.com/cell/fulltext/S0092-8674(17)30185-X

Week 4 - 10/20/17 - http://www.nature.com/ncb/journal/v19/n5/full/ncb3507.html?foxtrotcallback=true

Week 5 - 10/30/17 - http://www.nature.com/neuro/journal/v19/n12/full/nn.4394.html

Week 6 - 11/3/17 -   http://www.cell.com/cell-systems/fulltext/S2405-4712(17)30090-X

Week 7 - 11/17/17 - https://www.nature.com/articles/s41540-017-0009-0

Week 8 - 12/1/17 -  http://msb.embopress.org/content/13/3/921

Week 9 - 12/8/17 -  https://link.springer.com/article/10.1007/s11538-017-0294-1

Week 1 - 04/14/17 - https://www.ncbi.nlm.nih.gov/pubmed/27870831

Week 2 - 04/21/17 - https://www.ncbi.nlm.nih.gov/pubmed/27870831

Week 3 - 04/28/17 - https://www.ncbi.nlm.nih.gov/pubmed/28171748/

Week 4 - 05/05/17 - https://www.ncbi.nlm.nih.gov/pubmed/28215526

Week 5 - 05/12/17 - https://www.ncbi.nlm.nih.gov/pubmed/27870831

Week 6 - 05/19/17 - https://www.ncbi.nlm.nih.gov/pubmed/27870831

Week 7 - 05/26/17 - https://www.ncbi.nlm.nih.gov/pubmed/27870831

Weeks 8 & 9 - 06/09/17 - https://www.ncbi.nlm.nih.gov/pubmed/27870831
https://www.nature.com/ncb/journal/v15/n6/pdf/ncb2745.pdf

Week 1 - 01/20/17 - https://www.ncbi.nlm.nih.gov/pubmed/27984723

Week 2 - 01/27/17 - https://www.ncbi.nlm.nih.gov/pubmed/27849584

Week 3 - 02/03/17 - https://www.ncbi.nlm.nih.gov/pubmed/27708057

Week 4 - 02/10/17 - https://www.ncbi.nlm.nih.gov/pubmed/26712315

Week 5 - 02/17/17 - https://www.ncbi.nlm.nih.gov/pubmed/25809250

Week 6 - 02/24/17 - https://www.ncbi.nlm.nih.gov/pubmed/27768887

Week 7 - 03/03/17 - https://elifesciences.org/content/5/e17056

Week 8 - 03/10/17 - https://www.ncbi.nlm.nih.gov/pubmed/27641957

Week 9 - 03/17/17 - https://www.ncbi.nlm.nih.gov/pubmed/27965290

Week 1 - 09/30/16 - http://www.pnas.org/content/107/52/22534.full.pdf?sid=56a0bd47-3aaa-49f5-92cd-0a230696ed4b

Week 2 - 10/07/16 - http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000739

Week 3 - 10/14/16 - http://rsif.royalsocietypublishing.org/content/13/121/20160475

Week 4 - 10/21/16 - http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2008.06221.x/full

Week 5 - 10/28/16 - http://link.springer.com/article/10.1007/s11538-014-0023-y

Week 6 - 11/04/16 - http://msb.embopress.org/content/4/1/161

Week 7 - 11/18/16 - http://www.sciencedirect.com/science/article/pii/S002555641630147X

Week 8 - 12/02/16 - http://www.cell.com/cell-systems/pdf/S2405-4712%2816%2900005-3.pdf

Week 9 - 12/09/16 - http://www.pnas.org/content/107/2/565.full.pdf?sid=4c45655d-2a4d-405a-84b6-fdad515602d9 | http://www.pnas.org/content/early/2016/10/03/1608820113.full.pdf?sid=b23a4e57-fa41-476e-b5c5-ec4ede8c1ddd

Week 1 - 04/04/16 - Research in Progress (RIP) Talk - "The Role of EMT regulators in governing mammary epithelial plasticity"

Week 2 - 04/11/16 - http://www.cell.com/cell/fulltext/S0092-8674%2815%2900204-4

Week 3 - 04/18/16 - http://www.cell.com/cell/fulltext/S0092-8674%2815%2901108-3

Week 4 - 04/25/16 - http://www.cell.com/cell/fulltext/S0092-8674%2815%2900246-9

Week 5 - 05/02/16 - Research in Progress (RIP) Talk - "Mathematical modeling link Wnt signaling to emergent patterns of metabolism in colon cancer"

Week 6 - 05/09/16 - http://www.nature.com/ng/journal/v47/n11/full/ng.3414.html

Week 7 - 05/16/16 - http://www.ncbi.nlm.nih.gov/pubmed/26430121

Week 8 - 05/23/16 - http://www.cell.com/cell/fulltext/S0092-8674%2816%2930059-9#

Week 9 - 06/06/16 - http://www.ncbi.nlm.nih.gov/pubmed/26823433

Week 1 - 01/15/16 - http://www.sciencedirect.com/science/article/pii/S1534580714006832

Week 2 - 01/22/16 - http://science.sciencemag.org/content/342/6155/1238016.full

Week 3 - 01/29/16 - http://www.sciencedirect.com/science/article/pii/S0896627315007643
http://www.sciencedirect.com/science/article/pii/S0960982215014281

Week 4 - 02/05/16 - http://www.nature.com/nature/journal/v525/n7568/pdf/nature14971.pdf

http://www.nature.com/ni/journal/v15/n2/pdf/ni.2789.pdf

Week 5 - 02/12/16 - http://www.nature.com/nature/journal/v453/n7192/pdf/nature06879.pdf

Week 6 - 02/19/16 - http://msb.embopress.org/content/msb/4/1/195.full.pdf

Week 7 - 02/26/16 - http://www.nature.com/nature/journal/v529/n7587/full/nature16961.html

Week 8 - 03/04/16 - http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001088

Week 9 - 03/11/16 - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478651/
http://genome.cshlp.org/content/25/12/1893.full

Week 1 - 10/02/15 - http://www.nature.com/nature/journal/v456/n7218/full/nature07331.html
http://www.nature.com/nature/journal/v427/n6976/full/nature02298.html

Week 2 - 10/09/15 - http://www.sciencemag.org/content/336/6085/1157.full.pdf?sid=5c7ab86f-9c00-4b5c-86fe-d211af12d475
http://www.pnas.org/content/103/23/8697.full.pdf?sid=3dae189f-ebf0-4c9b-8717-41d525236e8a

Week 3 - 10/16/15 - http://www.pnas.org/content/107/36/15995.full.pdf?sid=72c7937c-77ea-4e48-a1a8-f9796c8da567
http://www.sciencedirect.com/science/article/pii/S1046202313001643

Week 4 - 10/23/15 - http://www.sciencemag.org/content/327/5971/1389.full.pdf?sid=248e0b52-7a67-4c3e-82d3-ce5bd8750a86
http://www.esajournals.org/doi/pdf/10.1890/14-0417.1

Week 5 - 10/30/15 - http://www.nature.com/nature/journal/v428/n6983/full/nature02424.html
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004152

Week 6 - 11/06/15 - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568459/pdf/srep13910.pdf
http://bioinformatics.oxfordjournals.org/content/25/12/i101.full

Week 7 - 11/13/15 - http://genesdev.cshlp.org/content/28/1/71.full.pdf

Week 8 - 11/20/15 - http://www.sciencemag.org/content/314/5804/1447.full.pdf?sid=c190bbcb-0ab4-4951-9f0f-d79e9de20b2b
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000149

Week 9 -12/04/15 -  http://www.nature.com/ng/journal/v36/n2/pdf/ng1293.pdf
http://rsob.royalsocietypublishing.org/content/royopenbio/3/3/120179.full.pdf

Week 10 - 12/11/15 - http://www.nature.com/ng/journal/v38/n8/pdf/ng1847.pdf
http://epubs.siam.org/doi/pdf/10.1137/S0036139997330623
http://jb.oxfordjournals.org/content/157/3/121.full.pdf+html

Week 1 - 04/10/15 - http://www.sciencemag.org/content/347/6226/1259038.abstract; http://www.nature.com/nature/journal/v518/n7537/full/nature14128.html

Week 2 - 04/17/15 - http://www.nature.com/nature/journal/v519/n7542/full/nature13996.html; http://www.nature.com/nature/journal/v519/n7542/full/nature14279.html

Week 3 - 04/24/15 - http://www.nature.com/nature/journal/v519/n7542/full/nature14024.html; http://www.nature.com/nature/journal/v517/n7534/full/nature14045.html

Week 4 - 05/01/15 - http://www.sciencemag.org/content/347/6225/1010.abstract; http://www.sciencemag.org/content/347/6224/1257601.abstract

Week 5 - 05/08/15 - http://www.sciencemag.org/content/346/6216/1533.abstract; http://www.sciencemag.org/content/346/6215/1370.abstract

Week 6 - 05/15/15 - http://www.nature.com/nature/journal/v519/n7543/full/nature14187.html; http://www.nature.com/nature/journal/v518/n7538/full/nature14152.html

Week 7 - 05/22/15 - http://www.sciencemag.org/content/347/6228/1367.abstract; http://www.nature.com/nature/journal/v519/n7544/full/nature14318.html

Week 8 - 05/29/15 - http://www.sciencemag.org/content/347/6229/1446.full; http://www.nature.com/nature/journal/v518/n7537/full/nature14121.html; http://www.nature.com/nature/journal/v518/n7537/full/nature14095.html

Week 1 - 01/16/15 -http://www.nature.com/nbt/journal/v32/n7/full/nbt.2940.html; http://www.sciencemag.org/content/347/6217/78.full

Week 2 - 01/23/15 -http://www.cell.com/cell/fulltext/S0092-8674(14)01497-4; http://www.nature.com/nbt/journal/v32/n12/full/nbt.3044.html

Week 3 - 01/30/15 -http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html; http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html

Week 4 - 02/06/15 -http://www.sciencedirect.com/science/article/pii/S0092867414015189; http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3062.html

Week 5 - 02/13/15 -http://www.sciencemag.org/content/347/6218/1254806.full; http://www.sciencedirect.com/science/article/pii/S0092867414015177

Week 6 - 02/20/15 -http://www.nature.com/nature/journal/v515/n7527/full/nature13992.html; http://www.nature.com/nbt/journal/v32/n9/full/nbt.2957.html

Week 7 - 02/27/15 - http://www.sciencedirect.com/science/article/pii/S0092867414014494; http://www.nature.com/nbt/journal/v32/n11/full/nbt.3027.html

Week 8 - 03/06/15 - http://www.sciencedirect.com/science/article/pii/S0092867414012264; http://www.cell.com/cell/abstract/S0092-8674(14)00471-1

Week 1 - 10/10/14 - http://www.ncbi.nlm.nih.gov/pubmed/25214630; http://www.ncbi.nlm.nih.gov/pubmed/25124443

Week 2 - 10/17/14 - http://www.ncbi.nlm.nih.gov/pubmed/25043035; http://www.ncbi.nlm.nih.gov/pubmed/25186725

Week 3 - 10/24/14 - http://www.ncbi.nlm.nih.gov/pubmed/24990743; http://www.ncbi.nlm.nih.gov/pubmed/25146290

Week 4 - 10/31/14 - http://www.ncbi.nlm.nih.gov/pubmed/24522532; http://www.ncbi.nlm.nih.gov/pubmed/25104393

Week 5 - 11/7/14 - http://www.ncbi.nlm.nih.gov/pubmed/24717442; http://www.ncbi.nlm.nih.gov/pubmed/24598544

Week 6 - 11/14/14 - http://www.ncbi.nlm.nih.gov/pubmed/24948735; http://www.ncbi.nlm.nih.gov/pubmed/24529478

Week 7 - 11/21/14 - http://www.ncbi.nlm.nih.gov/pubmed/24739965; http://www.ncbi.nlm.nih.gov/pubmed/25171416

Week 8 - 12/5/14 - http://www.ncbi.nlm.nih.gov/pubmed/25082703; http://www.ncbi.nlm.nih.gov/pubmed/25079331

Week 1: October 5, 2012 - Paper: An expansive human regulatory lexicon encoded in transcription factor footprints

Paper: Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Week 2: October 12, 2012 - Paper: Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Paper: Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

Week 3: October 26, 2012 -  Paper: The developmental transcriptome of Drosophila melanogaster

Week 4: November 2, 2012 - Paper: Structure-based prediction of protein–protein interactions on a genome-wide scale

Paper: Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs

Week 5: November 9, 2012 - Paper: Architecture of the human regulatory network derived from ENCODE data

Week 6: November 16, 2012 - Paper: Identification of Anchor Genes during Kidney Development Defines Ontological Relationships, Molecular Subcompartments and Regulatory Pathways

Paper: Atlas of Gene Expression in the Developing Kidney at Microanatomic Resolution

Paper: An integrated map of genetic variation from 1,092 human genomes

Week 7: November 30, 2012 - Paper: Tug-of-War in Motor Protein Ensembles Revealed with a Programmable DNA Origami Scaffold

Paper: Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Week 1: January 11, 2012 – Paper: Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

Week 2: January 18, 2012 – Paper: Increasing adult hippocampal neurogenesis is sufficient to improve pattern separation

Week 3: January 25, 2012 – Paper: Quantifying the Role of Angiogenesis in Malignant Progression of Gliomas: In Silico Modeling Integrates Imaging and Histology

Week 4: February 1, 2012 – Paper: Pathogenic huntingtin inhibits fast axonal transport by by activating JNK3 and phosphorylating kinesin

Week 5: February 8, 2012 – Paper: "Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays

Week 6: February 15, 2012 – Paper: Environmental and genetic perturbations reveal different networks of metabolic regulation

Week 7: February 22, 2012 – Paper: MicroRNA Predictors of Longevity in Caenorhabditis Elegans

Week 8 : February 29, 2012 – Paper: Inactivation of Pmel Alters Melanosome Shape But Has Only a Subtle Effect on Visible Pigmentation AND Mutations in or near the Transmembrane Domain Alter PMEL Amyloid Formation from Functional to Pathogenic

Week 9: March 7, 2012 - Paper: Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism

Week 10: March 14, 2012 – Paper: Depth Perception from Image Defocus in a Jumping Spider