2024

Przanowska RK*, Labban N*, Przanowski P, Hawes RB, Atkins KA, Showalter SL†, Janes KA†. (2024) Patient-derived response estimates from zero-passage organoids of luminal breast cancer. Breast Cancer Res, Vol 26, 192. [Article]
Cameron D. Griffiths, Millie Shah, William Shao, Cheryl A. Borgman, and Kevin A. Janes (2024) Three modes of viral adaptation by the heart. Science Advances, Vol 10 (46), eadp6303
[Article]
Sweatt AJ, Griffiths CD, Paudel BB, Janes KA. (2024) Proteome-wide copy-number estimation from transcriptomics.  Mol Syst Biol, 20, 1230-1256 [Pubmed] [Article]
Nguyen YTM, Sibley L, Przanowski P, Zhao XY, Kovacs M, Wang S, Jones MK, Cowan M, Liu W, Merchak AR, Gaultier A, Janes K, Zang C, Harris T, Ewald SE, Zong H. (2024) Toxoplasma gondii infection supports the infiltration of T cells into brain tumors.  J Neuroimmunol, 393, 578402 [Pubmed] [Article]
Hsu J*, Nguyen KT*, Bujnowska M, Janes KA, Fallahi-Sichani M. (2024) Protocol for iterative indirect immunofluorescence imaging in cultured cells, tissue sections, and metaphase chromosome spreads.  STAR Protoc, 5, 103190 [Pubmed] [Article]
Paudel BB, Tan SF, Fox TE, Ung J, Golla U, Shaw J, Dunton W, Lee I, Fares WA, Patel S, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Feith DJ, Claxton D, Janes KA*, Loughran TP*.  (2024) Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes.  Blood Adv, 8, 1137-1142 [Pubmed]

2023

Zeng J, Alvarez-Yela AC, Casarez E, Jiang Y, Wang L, Kelly BE, Jenkins T, Ke E, Atkins KA, Janes KA, Slack-Davis JK, Zong H. (2023) Dichotomous ovarian cancer-initiating potential of Pax8+ cells revealed by a mouse genetic mosaic model.  iScience, 26, 106742. [Article]
Netterfield TS, Ostheimer GJ, Tentner AR, Joughin BA, Dakoyannis AM, Sharma CD, Sorger PK, Janes KA, Lauffenburger DA, Yaffe MB. (2023) Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition.  Cell Syst, 14, 582-604.e10. [Article]
Zeng J, Singh S, Zhou X, Jiang Y, Casarez E, Atkins KA, Janes KA, Zong H. (2023) A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer.  Dis Model Mech, 16, dmm050219. [Article]
  • Editor’s Choice:  Blyth, K. (2023) Lighting the way to track early progression of basal-like breast cancer.  Dis Model Mech, 16, dmm050565.  [Link]
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 [Article]

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. [Article]
Janes KA. (2022) Systems virology at every scale.  Cell Syst, 13, 946. [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.   [Article]

2021

Janes KA. (2021) Ten Simple Rules for Being a Faculty Advocate of First-Year Graduate Students.  PLoS Comput Biol, 17, e1009379. [Article]
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.
[Pubmed] [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. [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. [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. [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. [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. [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. [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. [Article]
Janes KA. (2020) Fragile epitopes-Antibody's guess is as good as yours. Sci Signal, 13, 616. [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. [Article]

2019

Smolko CM, Janes KA. (2019) An ultrasensitive fiveplex activity assay for cellular kinases. Sci Rep, 9, 19409. [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. [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. [Article]
Caulk AW, Janes KA. (2019) Robust latent-variable interpretation of in vivo regression models by nested resampling. Sci Rep, 9, 19671. [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. [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. [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. [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. [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. [Article]
Jensen KJ*, Moyer CB*, Janes KA. (2016) Network architecture predisposes an enzyme to pharmacologic or genetic targeting. Cell Syst, 2, 112-21. [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. [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. [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 [Article]
Janes KA. (2015) Cell-to-cell transcript variability: seeing signal in the noise. Cell, 163, 1566-8. [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. [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. [Article]
Wang CC, Janes KA. (2014) Non-genetic heterogeneity caused by differential single-cell adhesion. Cell Cycle, 13, 2149-50. [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. [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. [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. [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. [Article]
Kang BH*, Jensen KJ*, Hatch JA, Janes KA. (2013) Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal, 6, rs13. [Article]
Wang L, Janes KA. (2013) Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors, and cultured cells. Nat Protoc, 8, 282-301. [Article]

2012

Jensen KJ, Janes KA. (2012) Modeling the latent dimensions of multivariate signaling datasets. Phys Biol, 9, 045004. [Article]
Bajikar SS, Janes KA. (2012) Multiscale models of cell signaling. Ann Biomed Eng, 40, 2319-27. [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. [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. [Article]
Janes KA. (2011) RUNX1 and its understudied role in breast cancer. Cell Cycle, 10, 3461-5. [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. [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 [Article]
Janes KA. (2010) Paring down signaling complexity. Nat Biotechnol, 28, 681-2. [Article]

2009

2008

Janes KA*, Reinhardt HC*, Yaffe MB. (2008) Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell, 135, 343-54. [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. [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. [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. [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. [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 [Article]
Janes KA, Yaffe MB. (2006) Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol,7, 820-8. [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. [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. [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 [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. [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. [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. [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. [Article]
  • Cover Article
Janes KA, Alonso MJ. (2003) Depolymerized chitosan nanoparticles for protein delivery: Preparation and characterization. J Appl Polym Sci, 88, 2769-2776. [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. [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. [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. [Article]