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Robust latent-variable interpretation of in vivo regression models by nested resampling.

Caulk AW, Janes KA.

Sci Rep. 2019 Dec 23;9(1):19671. doi: 10.1038/s41598-019-55796-2.


An ultrasensitive fiveplex activity assay for cellular kinases.

Smolko CM, Janes KA.

Sci Rep. 2019 Dec 19;9(1):19409. doi: 10.1038/s41598-019-55998-8.


In situ 10-cell RNA sequencing in tissue and tumor biopsy samples.

Singh S, Wang L, Schaff DL, Sutcliffe MD, Koeppel AF, Kim J, Onengut-Gumuscu S, Park KS, Zong H, Janes KA.

Sci Rep. 2019 Mar 20;9(1):4836. doi: 10.1038/s41598-019-41235-9.


CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures.

Corliss BA, Ray HC, Patrie JT, Mansour J, Kesting S, Park JH, Rohde G, Yates PA, Janes KA, Peirce SM.

Bioinformatics. 2019 Feb 15;35(4):720-721. doi: 10.1093/bioinformatics/bty797. No abstract available.


CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures.

Corliss BA, Ray HC, Patrie JT, Mansour J, Kesting S, Park JH, Rohde G, Yates PA, Janes KA, Peirce SM.

Bioinformatics. 2019 Feb 1;35(3):506-514. doi: 10.1093/bioinformatics/bty638. Erratum in: Bioinformatics. 2019 Feb 15;35(4):720-721.


Automated brightfield morphometry of 3D organoid populations by OrganoSeg.

Borten MA, Bajikar SS, Sasaki N, Clevers H, Janes KA.

Sci Rep. 2018 Mar 28;8(1):5319. doi: 10.1038/s41598-017-18815-8.


Tumor-Suppressor Inactivation of GDF11 Occurs by Precursor Sequestration in Triple-Negative Breast Cancer.

Bajikar SS, Wang CC, Borten MA, Pereira EJ, Atkins KA, Janes KA.

Dev Cell. 2017 Nov 20;43(4):418-435.e13. doi: 10.1016/j.devcel.2017.10.027.


Corrigendum to: "Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers" [EBioMedicine 8 (2016) 117-131].

Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH.

EBioMedicine. 2017 Nov;25:188. doi: 10.1016/j.ebiom.2017.10.029. Epub 2017 Oct 31. No abstract available.


An engineering design approach to systems biology.

Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA.

Integr Biol (Camb). 2017 Jul 17;9(7):574-583. doi: 10.1039/c7ib00014f. Review.


Profiling Subcellular Protein Phosphatase Responses to Coxsackievirus B3 Infection of Cardiomyocytes.

Shah M, Smolko CM, Kinicki S, Chapman ZD, Brautigan DL, Janes KA.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S244-S262. doi: 10.1074/mcp.O116.063487. Epub 2017 Feb 7.


Computational Models of Reactive Oxygen Species as Metabolic Byproducts and Signal-Transduction Modulators.

Pereira EJ, Smolko CM, Janes KA.

Front Pharmacol. 2016 Nov 29;7:457. eCollection 2016. Review.


Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers.

Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH.

EBioMedicine. 2016 Jun;8:117-131. doi: 10.1016/j.ebiom.2016.04.032. Epub 2016 Apr 29. Erratum in: EBioMedicine. 2017 Nov;25:188.


TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.

Chitforoushzadeh Z, Ye Z, Sheng Z, LaRue S, Fry RC, Lauffenburger DA, Janes KA.

Sci Signal. 2016 Jun 7;9(431):ra59. doi: 10.1126/scisignal.aad3373.


Science Signaling Podcast for 7 June 2016: Modeling signal integration.

Janes KA, VanHook AM.

Sci Signal. 2016 Jun 7;9(431):pc13. doi: 10.1126/scisignal.aag1902.


Single-cell states versus single-cell atlases - two classes of heterogeneity that differ in meaning and method.

Janes KA.

Curr Opin Biotechnol. 2016 Jun;39:120-125. doi: 10.1016/j.copbio.2016.03.015. Epub 2016 Apr 1. Review.


Network Architecture Predisposes an Enzyme to Either Pharmacologic or Genetic Targeting.

Jensen KJ, Moyer CB, Janes KA.

Cell Syst. 2016 Feb 24;2(2):112-121.


Cell-to-Cell Transcript Variability: Seeing Signal in the Noise.

Janes KA.

Cell. 2015 Dec 17;163(7):1566-8. doi: 10.1016/j.cell.2015.12.010.


An analysis of critical factors for quantitative immunoblotting.

Janes KA.

Sci Signal. 2015 Apr 7;8(371):rs2. doi: 10.1126/scisignal.2005966.


Bringing systems biology to cancer, immunology and infectious disease.

Janes KA, Wang CC.

Genome Biol. 2014 Jul 31;15(7):407. doi: 10.1186/s13059-014-0407-1.


Non-genetic heterogeneity caused by differential single-cell adhesion.

Wang CC, Janes KA.

Cell Cycle. 2014;13(14):2149-50. doi: 10.4161/cc.29660. Epub 2014 Jun 23. No abstract available.


A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies.

Wang CC, Bajikar SS, Jamal L, Atkins KA, Janes KA.

Nat Cell Biol. 2014 Apr;16(4):345-56. doi: 10.1038/ncb2930. Epub 2014 Mar 23.


Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles.

Bajikar SS, Fuchs C, Roller A, Theis FJ, Janes KA.

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):E626-35. doi: 10.1073/pnas.1311647111. Epub 2014 Jan 21.


Simultaneous profiling of 194 distinct receptor transcripts in human cells.

Kang BH, Jensen KJ, Hatch JA, Janes KA.

Sci Signal. 2013 Aug 6;6(287):rs13. doi: 10.1126/scisignal.2003624.


Models of signalling networks - what cell biologists can gain from them and give to them.

Janes KA, Lauffenburger DA.

J Cell Sci. 2013 May 1;126(Pt 9):1913-21. doi: 10.1242/jcs.112045. Review.


An ERK-p38 subnetwork coordinates host cell apoptosis and necrosis during coxsackievirus B3 infection.

Jensen KJ, Garmaroudi FS, Zhang J, Lin J, Boroomand S, Zhang M, Luo Z, Yang D, Luo H, McManus BM, Janes KA.

Cell Host Microbe. 2013 Jan 16;13(1):67-76. doi: 10.1016/j.chom.2012.11.009. Epub 2013 Jan 16.


Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells.

Wang L, Janes KA.

Nat Protoc. 2013 Feb;8(2):282-301. doi: 10.1038/nprot.2012.158. Epub 2013 Jan 10.


A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts.

Bose AK, Janes KA.

Mol Cell Proteomics. 2013 Mar;12(3):797-806. doi: 10.1074/mcp.O112.024059. Epub 2012 Dec 11.


Modeling the latent dimensions of multivariate signaling datasets.

Jensen KJ, Janes KA.

Phys Biol. 2012 Aug;9(4):045004. doi: 10.1088/1478-3975/9/4/045004. Epub 2012 Aug 7.


Multiscale models of cell signaling.

Bajikar SS, Janes KA.

Ann Biomed Eng. 2012 Nov;40(11):2319-27. doi: 10.1007/s10439-012-0560-1. Epub 2012 Apr 3. Review.


RUNX1 and its understudied role in breast cancer.

Janes KA.

Cell Cycle. 2011 Oct 15;10(20):3461-5. doi: 10.4161/cc.10.20.18029. Epub 2011 Oct 15.


Normal morphogenesis of epithelial tissues and progression of epithelial tumors.

Wang CC, Jamal L, Janes KA.

Wiley Interdiscip Rev Syst Biol Med. 2012 Jan-Feb;4(1):51-78. doi: 10.1002/wsbm.159. Epub 2011 Sep 2. Review.


Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression.

Wang L, Brugge JS, Janes KA.

Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):E803-12. doi: 10.1073/pnas.1103423108. Epub 2011 Aug 22.


Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection.

Garmaroudi FS, Marchant D, Si X, Khalili A, Bashashati A, Wong BW, Tabet A, Ng RT, Murphy K, Luo H, Janes KA, McManus BM.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):17053-8. doi: 10.1073/pnas.1006478107. Epub 2010 Sep 10.


Paring down signaling complexity.

Janes KA.

Nat Biotechnol. 2010 Jul;28(7):681-2. doi: 10.1038/nbt0710-681. No abstract available.


Identifying single-cell molecular programs by stochastic profiling.

Janes KA, Wang CC, Holmberg KJ, Cabral K, Brugge JS.

Nat Methods. 2010 Apr;7(4):311-7. doi: 10.1038/nmeth.1442. Epub 2010 Mar 14.


Cytokine-induced signaling networks prioritize dynamic range over signal strength.

Janes KA, Reinhardt HC, Yaffe MB.

Cell. 2008 Oct 17;135(2):343-54. doi: 10.1016/j.cell.2008.08.034.


When microarrays Met epidermal-cell migration.

Janes KA.

Mol Syst Biol. 2008;4:200. doi: 10.1038/msb.2008.41. Epub 2008 Jul 1. No abstract available.


Common effector processing mediates cell-specific responses to stimuli.

Miller-Jensen K, Janes KA, Brugge JS, Lauffenburger DA.

Nature. 2007 Aug 2;448(7153):604-8. Epub 2007 Jul 18.


Data-driven modelling of signal-transduction networks.

Janes KA, Yaffe MB.

Nat Rev Mol Cell Biol. 2006 Nov;7(11):820-8. Review.


Adenoviral vector saturates Akt pro-survival signaling and blocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis.

Miller-Jensen K, Janes KA, Wong YL, Griffith LG, Lauffenburger DA.

J Cell Sci. 2006 Sep 15;119(Pt 18):3788-98. Epub 2006 Aug 29.


Applying computational modeling to drug discovery and development.

Kumar N, Hendriks BS, Janes KA, de Graaf D, Lauffenburger DA.

Drug Discov Today. 2006 Sep;11(17-18):806-11. Review.


The response of human epithelial cells to TNF involves an inducible autocrine cascade.

Janes KA, Gaudet S, Albeck JG, Nielsen UB, Lauffenburger DA, Sorger PK.

Cell. 2006 Mar 24;124(6):1225-39.


A biological approach to computational models of proteomic networks.

Janes KA, Lauffenburger DA.

Curr Opin Chem Biol. 2006 Feb;10(1):73-80. Epub 2006 Jan 6. Review.


A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB.

Science. 2005 Dec 9;310(5754):1646-53.


A compendium of signals and responses triggered by prodeath and prosurvival cytokines.

Gaudet S, Janes KA, Albeck JG, Pace EA, Lauffenburger DA, Sorger PK.

Mol Cell Proteomics. 2005 Oct;4(10):1569-90. Epub 2005 Jul 18.


A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates.

Shults MD, Janes KA, Lauffenburger DA, Imperiali B.

Nat Methods. 2005 Apr;2(4):277-83. Epub 2005 Mar 23.


Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data.

Janes KA, Kelly JR, Gaudet S, Albeck JG, Sorger PK, Lauffenburger DA.

J Comput Biol. 2004;11(4):544-61.


A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis-apoptosis.

Janes KA, Albeck JG, Peng LX, Sorger PK, Lauffenburger DA, Yaffe MB.

Mol Cell Proteomics. 2003 Jul;2(7):463-73. Epub 2003 Jun 26.


Chitosan nanoparticles as delivery systems for doxorubicin.

Janes KA, Fresneau MP, Marazuela A, Fabra A, Alonso MJ.

J Control Release. 2001 Jun 15;73(2-3):255-67.


Polysaccharide colloidal particles as delivery systems for macromolecules.

Janes KA, Calvo P, Alonso MJ.

Adv Drug Deliv Rev. 2001 Mar 23;47(1):83-97. Review.


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