2022

Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. (2022) Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors.  Cell Rep, 38, 110361.  [Link]
Janes KA. (2022) Systems virology at every scale.  Cell Syst, 13, 946.  [Link] [Link to Article]
Wang L*, Paudel BB*, McKnight RA, Janes KA. (2023) Escape from the HER2-activated DCIS-like state is skewed by divergent nucleocytoplasmic transport.   Nat Commun 14, 2110 [Link to Article]
Zeng J, Alvarez-Yela AC, Casarez E, Jiang Y, Wang L, Kelly BE, Ke E, Jenkins T, Atkins KA, Janes KA, Slack-Davis JK, Zong H. Quantitative clonal analysis reveals vast heterogeneity among fallopian tube cells for ovarian cancer-initiation and progression.  bioRxiv doi: https://doi.org/10.1101/2022.01.23.477434.  

2021

Janes KA. (2021) Ten Simple Rules for Being a Faculty Advocate of First-Year Graduate Students.  PLoS Comput Biol, 17, e1009379.  [Link]
Griffiths CD, Sweatt AJ, Janes KA. (2021) Simulating coxsackievirus B3 infection with an accessible computational model of its complete kinetics.  STAR Protoc, 2, 100940.  [Link]
Griffiths CD, Sweatt AJ, Janes KA. Simulating coxsackievirus B3 infection with an accessible computational model of its complete kinetics. STAR Protoc. 2021 Nov 5;2(4):100940.
[Link to Article]
Lopacinski AB*, Sweatt AJ*, Smolko CM, Gray-Gaillard E, Borgman CA, Shah M†, Janes KA†. (2021) Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback. Cell Syst, 12, 304-23.e1-e13. [Link to Article]
Sutcliffe MD, Galvao RP, Wang L, Kim J, Singh S, Zong H†, Janes KA†. (2021) Premalignant oligodendrocyte precursor cells stall in a heterogeneous state of replication stress prior to gliomagenesis.  Cancer Res, 81, 1868-82. [Link to Article]
Singh S, Sutcliffe MD, Repich K, Atkins KA, Harvey JA, Janes KA. (2021) Pan-cancer drivers are recurrent transcriptional regulatory heterogeneities in early-stage luminal breast cancer.  Cancer Res, 81, 1840-52. [Link to Article]
Schaff DL*, Singh S*, Kim K-B, Sutcliffe MD, Park K-S, Janes KA. (2021) Fragmentation of small-cell lung cancer regulatory states in heterotypic microenvironments. Cancer Res, 81, 1853-67. [Link to Article]

2020

Enriquez-Hesles E, Smith DL Jr, Maqani N, Wierman MB, Sutcliffe MD, Fine RD, Kalita A, Santos SM, Muehlbauer MJ, Bain JR, Janes KA, Hartman JL 4th, Hirschey MD, Smith JS. (2020) A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism, J Biol Chem, 296, 100125. [Link to Article]
Pereira EJ, Burns JS, Lee CY, Marohl T, Calderon D, Wang L, Atkins KA, Wang CC, Janes KA. (2020) Sporadic activation of an oxidative stress-dependent NRF2–p53 signaling network in breast epithelial spheroids and premalignancies, Sci Signal, 13, 627. [Link to Article]
Nye DMR, Albertson RM, Weiner AT, Hertzler JI, Shorey M, Goberdhan DCI, Wilson C, Janes KA, Rolls MM. (2020) The receptor tyrosine kinase Ror is required for dendrite regeneration in Drosophila neurons. PLoS Biol, 18, e3000657. [Link to Article]
Janes KA. (2020) Fragile epitopes-Antibody's guess is as good as yours. Sci Signal, 13, 616. [Link to Article]
Yao M, Ventura PB, Jiang Y, Rodriguez FJ, Wang L, Perry JSA, Yang Y, Wahl K, Crittenden RB, Bennett ML, Qi L, Gong CC, Li XN, Barres BA, Bender TP, Ravichandran KS, Janes KA, Eberhart CG, Zong H. (2020) Astrocytic trans-Differentiation Completes a Multicellular Paracrine Feedback Loop Required for Medulloblastoma Tumor Growth. Cell, 180, 502. [Link to Article]

2019

Smolko CM, Janes KA. (2019) An ultrasensitive fiveplex activity assay for cellular kinases. Sci Rep, 9, 19409. [Link to Article]
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 to Article]
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 to Article]
Caulk AW, Janes KA. (2019) Robust latent-variable interpretation of in vivo regression models by nested resampling. Sci Rep, 9, 19671. [Link to Article]

2018

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 to Article]

2017

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 to Article]
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 to Article]
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 to Article]

2016

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 to Article]
Jensen KJ*, Moyer CB*, Janes KA. (2016) Network architecture predisposes an enzyme to pharmacologic or genetic targeting. Cell Syst, 2, 112-21. [Link to Article]
  • Research Highlight: Kostic M. (2016) Small Molecule Inhibitors versus Genetic Knockdown: Round One. Cell Chem Biol, 23, 313.
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 to Article]
llendula 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 to Article]
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
  • Podcast: Janes KA, VanHook AM. (2016) Science Signaling Podcast for 7 June 2016: Modeling signal integration. Sci Signal, 9, pc13.
  • Editor’s Choice: Gough NR. (2016) New connections: Making discoveries in complex data sets. Sci Signal, 9, ec132.

2015

Janes KA. (2015) An analysis of critical factors for quantitative immunoblotting. Sci Signal, 8, rs2 [Link to Article]
Janes KA. (2015) Cell-to-cell transcript variability: seeing signal in the noise. Cell, 163, 1566-8. [Link to Article]

2014

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 to Article]
  • News and Views: Michor F, Weaver VM. (2014) Understanding tissue context influences on intratumor heterogeneity. Nat Cell Biol, 16, 301-2.
  • Editor’s Choice: Ferrarelli LK. (2014) Contact regulation of heterogeneity. Sci Signal, 7, ec104. News release:
  • UVA Today: BMES
Janes KA, Wang CC. (2014) Bringing systems biology to cancer, immunology and infectious disease. Genome Biol, 15, 407. [Link to Article]
Wang CC, Janes KA. (2014) Non-genetic heterogeneity caused by differential single-cell adhesion. Cell Cycle, 13, 2149-50. [Link to Article]
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 to Article]

2013

Bose AK, Janes KA. (2013) A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts. Mol Cell Proteomics, 12, 797-806. [Link to Article]
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 to Article]
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 to Article]
Kang BH*, Jensen KJ*, Hatch JA, Janes KA. (2013) Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal, 6, rs13. [Link to Article]
Wang L, Janes KA. (2013) Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors, and cultured cells. Nat Protoc, 8, 282-301. [Link to Article]

2012

Jensen KJ, Janes KA. (2012) Modeling the latent dimensions of multivariate signaling datasets. Phys Biol, 9, 045004. [Link to Article]
Bajikar SS, Janes KA. (2012) Multiscale models of cell signaling. Ann Biomed Eng, 40, 2319-27. [Link to Article]
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 to Article]

2011

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 to Article]
Janes KA. (2011) RUNX1 and its understudied role in breast cancer. Cell Cycle, 10, 3461-5. [Link to Article]

2010

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 to Article]
  • News and Views: Quaranta V, Garbett SP. (2010) Not all noise is waste. Nat Methods, 7, 269-72.
  • Research Highlight: Muers M. (2010) Gene expression: Standing out from the crowd. Nat Rev Genet, 11, 316-7.
  • Featured in: Gitig D. (2010) Transcriptomics: individuality in the cellular world. Biotechniques, 48, 439-43.
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 to Article]
Janes KA. (2010) Paring down signaling complexity. Nat Biotechnol, 28, 681-2. [Link to Article]

2009

2008

Janes KA*, Reinhardt HC*, Yaffe MB. (2008) Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell, 135, 343-54. [Link to Article]
  • Research Highlight: Kritikou E. (2008) Cell signaling: Range over strength. Nat Rev Mol Cell Biol 9, 922-3.
Janes KA. (2008) When microarrays Met epidermal-cell migration. Mol Syst Biol, 4, 200. [Link to Article]

2007

Miller-Jensen K*, Janes KA*, Brugge JS, Lauffenburger DA. (2007) Common effector processing mediates cell-specific responses to stimuli. Nature, 448, 604-8. [Link to Article]
  • Research Highlight: Aschheim K. (2007) Signaling networks and cell type. Nat Biotechnol, 25, 999.

2006

Janes KA, Lauffenburger DA. (2006) A biological approach to computational models of proteomic networks. Curr Opin Chem Biol, 10, 73-80. [Link to Article]
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. [Link to Article]
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 to Article]
Janes KA, Yaffe MB. (2006) Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol,7, 820-8. [Link to Article]
  • Featured in: Nat Rev Mol Cell Biol and Nat Cell Biol Podcast.
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 to Article]

2005

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 to Article]
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 to Article]
  • News and Views: Turk BE. (2005) Measuring kinase activity: finding needles in a haystack. Nat Methods, 2, 251-2.
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 to Article]

2004

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 to Article]
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 to Article]
  • Most Cited Paper Award (2008)
  • Most Cited Paper Award (2004)

2003

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 to Article]
  • Cover Article
Janes KA, Alonso MJ. (2003) Depolymerized chitosan nanoparticles for protein delivery: Preparation and characterization. J Appl Polym Sci, 88, 2769-2776. [Link to Article]

2001

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 to Article]
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 to Article]
  • Highly Downloaded Paper Award (2003)
Janes KA, Calvo P, Alonso MJ. (2001) Polysaccharide colloidal particles as delivery systems for macromolecules. Adv Drug Deliv Rev, 47, 83-97. [Link to Article]