Recent publications

Singh S*, Wang L*, Schaff DL, Sutcliffe MD, Koeppel AF, Kim J, Onengut-Gumuscu S, Park KS, Zong H, Janes KA. (2019) In situ 10-cell RNA sequencing in tissue and tumor biopsy samples. Sci Rep, 9, 4836. [Link]
Corliss BA, Ray HC, Patrie J, Mansour J, Kesting S, Park J, Rohde G, Yates PA, Janes KA, Peirce SM. (2019) CIRCOAST: A Statistical Hypothesis Test for Cellular Colocalization with Network Structures. Bioinformatics, 35, 506-14. [Link]
Borten MA*, Bajikar SS*, Sasaki N, Clevers H, Janes KA. (2018) Automated brightfield morphometry of 3D organoid populations by OrganoSeg. Sci Rep, 8, 5319. [Link]
  • Top 2% most downloaded in cell and molecular biology (2018)
Bajikar SS, Wang CC, Borten MA, Pereira EJ, Atkins KA, Janes KA. (2017) Tumor-suppressor inactivation of GDF11 occurs by precursor sequestration in triple-negative breast cancer. Dev Cell, 43, 418-35.e13. [Link]
  News release: UVA Today
Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA. (2017) An engineering design approach to systems biology. Integr Biol, 9, 574-83. [Link]
Shah M, Smolko CM, Kinicki S, Chapman ZD, Brautigan DL, Janes KA. (2017) Profiling subcellular phosphatase responses to coxsackievirus B3 infection of cardiomyocytes. Mol Cell Proteomics, 16, S244-S262. [Link]
Pereira EJ, Smolko CM, Janes KA. (2016) Computational models of reactive oxygen species as metabolic byproducts and signal-transduction modulators. Front Pharmacol, 7, 457. [Link]
Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pullikan 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. (2016) Small molecule inhibitors of CBFβ-RUNX binding for RUNX transcription factor driven cancers. EBioMedicine, 8, 117-31. [Link]
Chitforoushzadeh Z, Ye Z, Sheng Z, LaRue S, Fry RC, Lauffenburger DA, Janes KA. (2016) TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.  Sci Signal, 9, ra59.  [Full text] [PDF]
  Podcast:  Janes KA, VanHook AM. (2016) Science Signaling Podcast for 7 June 2016: Modeling signal integration.  Sci Signal, 9, pc13.  [Link]
  Editor’s Choice:  Gough NR. (2016) New connections:  Making discoveries in complex data sets.  Sci Signal, 9, ec132.  [Link]
Janes KA. (2016) Single-cell states versus single-cell atlases—two classes of heterogeneity that differ in meaning and method.  Curr Opin Biotechnol, 39, 120-5. [Link]
Jensen KJ*, Moyer CB*, Janes KA. (2016) Network architecture predisposes an enzyme to pharmacologic or genetic targeting.  Cell Syst, 2, 112-21.  [Link]
  Research Highlight:  Kostic M. (2016) Small Molecule Inhibitors versus Genetic Knockdown: Round One.  Cell Chem Biol, 23, 313.  [Link]
Janes KA. (2015) Cell-to-cell transcript variability:  seeing signal in the noise.  Cell, 163, 1566-8.  [Link]
Janes KA. (2015) An analysis of critical factors for quantitative immunoblotting.  Sci Signal, 8, rs2.  [Full text]
Janes KA, Wang CC. (2014) Bringing systems biology to cancer, immunology and infectious disease.  Genome Biol, 15, 407. [Link]
Wang CC, Janes KA. (2014) Non-genetic heterogeneity caused by differential single-cell adhesion.  Cell Cycle, 13, 2149-50. [Link]
Wang CC, Bajikar SS, Jamal L, Atkins KA, Janes KA. (2014) A time- and matrix-dependent TGFBR3–JUND–KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies. Nat Cell Biol, 16, 345-56. [Link]
  News and Views: Michor F, Weaver VM. (2014) Understanding tissue context influences on intratumor heterogeneity. Nat Cell Biol, 16, 301-2. [Link]
  Editor's Choice: Ferrarelli LK. (2014) Contact regulation of heterogeneity.  Sci Signal, 7, ec104.  [Link]
  News release:  UVA Today, BMES
Bajikar SS*, Fuchs C*, Roller A, Theis FJ†, Janes KA†. (2014) Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proc Natl Acad Sci, 111, E626-35. [Link] [Code]
  Extended PNAS Plus article
Research Highlight:  (2014) Unmixing gene expression in cell samples.  Nat Methods, 11, 229.  [Link]
News release: Helmholtz Center
Kang BH*, Jensen KJ*, Hatch JA, Janes KA. (2013) Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal, 6, rs13. [Full text]
Janes KA*, Lauffenburger DA*. (2013) Signalling networks and models – what cell biologists can gain from them and give to them. J Cell Sci, 126, 1913-21. [Link]
Bose AK, Janes KA. (2013) A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts. Mol Cell Proteomics, 12, 797-806. [Link]
Jensen KJ, Garmaroudi FS, Zhang J, Lin J, Boroomand S, Zhang M, Luo Z, Yang D, Luo H, McManus BM*, and Janes KA*. (2013) An ERK–p38
         subnetwork coordinates host-cell apoptosis and necrosis during coxsackievirus B3 infection. Cell Host Microbe, 13, 67-76. [Link]
Wang L, Janes KA. (2013) Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors, and cultured cells. Nat Protoc, 8, 282-301. [Link]
Jensen KJ, Janes KA. (2012) Modeling the latent dimensions of multivariate signaling datasets. Phys Biol, 9, 045004. [Link]
Bajikar SS, Janes KA. (2012) Multiscale models of cell signaling. Ann Biomed Eng, 40, 2319-27. [Link]
Wang CC, Jamal L, Janes KA. (2012) Normal morphogenesis of epithelial tissues and progression of epithelial tumors.
         Wiley Interdiscip Rev Syst Biol Med, 4, 51-78. [Link]
Janes KA. (2011) RUNX1 and its understudied role in breast cancer. Cell Cycle, 10, 3461-5. [Link]
Wang L, Brugge JS, Janes KA. (2011) Intersection of FOXO and RUNX1 gene-expression programs in single breast epithelial cells during
         morphogenesis and tumor progression. Proc Natl Acad Sci, 108, E803-12. [Link]
  •  Extended PNAS Plus article
Garmaroudi FS, Marchant D, Si X, Khalili A, Bashashati A, Wong BW, Tabet A, Ng RT, Murphy K, Luo H, Janes KA*, McManus BM*. (2010)
         Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc Natl Acad Sci, 107, 17053-8. [Link]
Janes KA. (2010) Paring down signaling complexity. Nat Biotechnol, 28, 681-2. [Link]
Janes KA, Wang CC, Holmberg KJ, Cabral K, Brugge JS. (2010) Identifying single-cell molecular programs by stochastic profiling.
         Nat Methods, 7, 311-7.  [Link]
  •  News and Views: Quaranta V, Garbett SP. (2010) Not all noise is waste. Nat Methods, 7, 269-72. [Link]
•  Research Highlight:  Muers M. (2010) Gene expression: Standing out from the crowd. Nat Rev Genet, 11, 316-7. [Link]
•  Featured in: Gitig D. (2010) Transcriptomics: individuality in the cellular world. Biotechniques, 48, 439-43. [Link]
Janes KA*, Reinhardt HC*, Yaffe MB. (2008) Cytokine-induced signaling networks prioritize dynamic range over signal strength.
         Cell, 135, 343-54. [Link]
  •  Research Highlight:  Kritikou E.  (2008) Cell signaling: Range over strength. Nat Rev Mol Cell Biol 9, 922-3. [Link]
Janes KA. (2008) When microarrays Met epidermal-cell migration. Mol Syst Biol, 4, 200.  [Link]
Miller-Jensen K*, Janes KA*, Brugge JS, Lauffenburger DA. (2007) Common effector processing mediates cell-specific responses
         to stimuli. Nature, 448, 604-8.  [Link]
  •  Research Highlight:  Aschheim K. (2007) Signaling networks and cell type. Nat Biotechnol, 25, 999.  [Link]
Janes KA, Yaffe MB. (2006) Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol,7, 820-8.   [Link]
  •  Featured in:  Nat Rev Mol Cell Biol and Nat Cell Biol Podcast
Miller-Jensen K, Janes KA, Wong YL, Griffith LG, Lauffenburger DA. (2006) Adenoviral vector saturates Akt pro-survival signaling
         and blocks insulin-mediated rescue of tumor-necrosis-factor-induced apoptosis. J Cell Sci, 119, 3788-98.  [Link]
Kumar N, Hendriks BS, Janes KA, de Graaf D, Lauffenburger DA. (2006) Applying computational modeling to drug discovery
         and development. Drug Discov Today, 11, 806-11.  [Link]
Janes KA, Gaudet S, Albeck JG, Nielsen UB, Lauffenburger DA, Sorger PK. (2006) The Response of
         Human Epithelial Cells to TNF Involves an Inducible Autocrine Cascade. Cell, 124, 1225-39.   [Link]
  •  Commentary:  Loewer A, Lahav G. (2006) Cellular conference call: external feedback affects cell-fate decisions.
         Cell, 124, 1128-30.  [Link]
•  Editor’s Choice: (2006) Vacilating about a fateful decision. Sci STKE, tw107.  [Link]
•  Featured in:  MIT Tech Talk
•  Cited as landmark systems biology paper: Arkin AP, Schaffer DV. (2011) Network News: Innovations in 21st Century Systems Biology.
   Cell, 144, 844-9. [Link]
Janes KA, Lauffenburger DA. (2006) A biological approach to computational models of proteomic networks.
         Curr Opin Chem Biol, 10, 73-80.   [Link]
Janes KA*, Albeck JG*, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB. (2005) A systems model of signaling identifies a
         molecular basis set for cytokine-induced apoptosis. Science, 310, 1646-53.  [Link]
  •  Cited among top 10 breakthroughs of the year: (2005) Science, 310, 1880-5.  [Link]
•  Editor’s Choice:  (2005) Predicting responses on the death pathway.  Sci STKE, tw448.  [Link]
•  Cited as landmark systems biology paper: Arkin AP, Schaffer DV. (2011) Network News: Innovations in 21st Century Systems Biology.
   Cell, 144, 844-9. [Link]
Gaudet S, Janes KA, Albeck JG, Pace EA, Lauffenburger DA, Sorger PK. (2005) A Compendium of Signals and Responses
         Triggered by Prodeath and Prosurvival Cytokines. Mol Cell Proteomics, 4, 1569-1590.  [Link]
Shults MD, Janes KA, Lauffenburger DA, Imperiali B. (2005) A multiplexed homogeneous fluorescence-based assay for protein
         kinase activity in cell lysates. Nat Methods, 2, 277-284.  [Link]
  •  News and Views:  Turk BE. (2005) Measuring kinase activity: finding needles in a haystack. Nat Methods, 2, 251-2.  [Link]
Janes KA, Kelly JR, Gaudet S, Albeck JG, Sorger PK, Lauffenburger DA. (2004) Cue-signal-response analysis of TNF-induced apoptosis
         by partial least squares regression of dynamic multivariate data. J Comput Biol, 11, 544-61.  [Link]
Janes KA, Albeck JG, Peng LX, Sorger PK, Lauffenburger DA, Yaffe MB. (2003) A high-throughput quantitative multiplex kinase assay
        for monitoring information flow in signaling networks: application to sepsis-apoptosis. Mol Cell Proteomics, 2, 463-73.  [Link]
  •  Cover article


Older publications

Vila A, Sanchez A, Janes K, Behrens I, Kissel T, Vila Jato JL, Alonso MJ. (2004) Low molecular weightchitosan nanoparticles as new
         carriers for nasal vaccine delivery in mice. Eur J Pharm Biopharm, 57, 123-31.  [Link]
  •  Most cited paper award (2008)
•  Most cited paper award (2004)
Janes KA, Alonso MJ. (2003) Depolymerized chitosan nanoparticles for protein delivery: Preparation and characterization.
         J Appl Polym Sci, 88, 2769-2776.  [Link]
Janes KA, Calvo P, Alonso MJ. (2001) Polysaccharide colloidal particles as delivery systems for macromolecules.
         Adv Drug Deliv Rev, 47, 83-97. [Link]
Janes KA, Fresneau MP, Marazuela A, Fabra A, Alonso MJ. (2001) Chitosan nanoparticles as delivery systems for doxorubicin.
         J Control Release, 73, 255-67. [Link]
Mao HQ, Roy K, Troung-Le VL, Janes KA, Lin KY, Wang Y, August JT, Leong KW. (2001) Chitosan-DNAnanoparticles as gene carriers:
         synthesis, characterization and transfection efficiency. J Control Release, 70, 399-421. [Link]
  •  Highly downloaded paper award (2003)


Book chapters

Wang CC, Janes KA. (2016) Stochastic analysis of nongenetic cell-to-cell heterogeneity. In: Encyclopedia of Cell Biology
         (eds. RA Bradshaw, JD Stahl), pp 218-26.  Academic Press, Waltham.
Shah M, Chitforoushzadeh Z, Janes KA. (2016) Statistical data analysis and modeling.  In: Uncertainty in Biology – A Computational Modeling Approach
(eds. L Geris, D Gomez-Cabrero), pp 478.  Springer International.
Holmberg KJ*, Bose AK*, Janes KA. (2013) Systems-engineering principles in signal transduction and cell-fate choice. In: CRC Handbook of
         Biomedical Engineering
(eds. JD Bronzino and DR Peterson), pp 1642. CRC Press, Boca Raton.
Deppmann CD, Janes KA. (2012) Cytokine-cytokine crosstalk and cell-death decisions. In: Systems Biology of Apoptosis (ed. I Lavrik), pp 215.
         Springer-Verlag, New York.
Chowbina S, Janes KA, Peirce SM, Papin JA. (2011) Mathematical and computational models in cancer. In: Targeted Therapies: Mechanisms of Resistance
         (ed. D Gioeli), pp 201. Humana Press, New York.
Janes KA, Woolf PJ, Peirce SM. (2010) High-level modeling of biological networks. In: Systems Biomedicine (eds. ET Liu, DA Lauffenburger),
         pp 438. Academic Press, San Diego.
Janes KA, Reinhardt HC, Yaffe MB. (2009) The apoptotic signaling network dynamically interprets the outputs of individual signaling pathways
         in an early analog and late digital manner. In:  Systems Biology:  The Challenge of Complexity (eds. S Nakanishi, R Kageyama, S Watabe), pp 246.
         Springer, Tokyo.