How to cite this software in publications
Other papers describing the software
Papers using CellProfiler and/or CellProfiler Analyst

How to cite this software in publications- the project's survival depends on it!

It's also nice if you cite the website (www.cellprofiler.org) and email us so that we are aware of your publication, but these are much less critical than citing the publications.

Other papers describing the software and/or its methods:

Papers using CellProfiler and/or CellProfiler Analyst

  1. Wheeler DB, Bailey SN, Guertin DA, Carpenter AE, Higgins CO, Sabatini DM (2004) RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nature Methods 1(2):1-6. PMID: 15782175 [PDF]
  2. Bailey SN, Ali SM, Carpenter AE, Higgins CO, Sabatini DM (2006) Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nature Methods 3(2):117-22. PMID: 16432521 [PDF]
  3. Baltus AE, Menke DB, Hu YC, Goodheart ML, Carpenter AE, de Rooij DG, Page DC (2006) In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nature Genetics 38(12):1430_1434. PMID: 17115059 [PDF]
  4. Cowen LE, Carpenter AE, Matangkasombut O, Fink GR, Lindquist S (2006) Genetic architecture of Hsp90-dependent drug resistance. Eukaryotic Cell 5(12):2184-8. PMID: 17056742 [PDF]
  5. Hartwell KH, Muir B, Reinhardt F, Carpenter AE, Sgroi DC, Weinberg RA (2006) The Spemann Organizer gene, Goosecoid, promotes tumor metastasis. PNAS 103(50):18969-74 PMID: 17142318. [PDF]
  6. Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124(6):1283-98. PMID: 16564017 [PDF]
  7. Sigal A, Milo M, Cohen A, Geva-Zatorsky N, Klein Y, Alaluf I, Swerdlin N, Perzov N, Danon T, Liron Y, Raveh T, Carpenter AE, Lahav G, Alon U (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nature Methods 3(7):525-31. PMID 16791210. [PDF]
  8. Buth H, Buttigieg PL, Ostafe R, Rehders M, Dannenmann SR, Schaschke N, Stark HJ, Boukamp P, Brix K (2007) Cathepsin B is essential for regeneration of scratch-wounded normal human epidermal keratinocytes. European Journal of Cell Biology 86:747-761. PMID: 17651862
  9. Dai C, Whitesell L, Rogers AB, Lindquist S (2007) Heat shock factor 1 is a powerful multifaceted modifier of carcinogenesis. Cell 130:1005-1018. PMID: 17889646
  10. Kuijl C, Savage NDL, Marsman M, Tuin AW, Janssen L, Egan DA, Ketema M, van den Nieuwendijk R, van den Eeden SJF, Geluk A, Poot A, van der Marel G, Beijersbergen RL, Overkleeft H, Ottenhoff TH, Neefjes J (2007) Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1. Nature 450:725-U710. PMID: 18046412
  11. Li DD, Shao ZH, Vanden Hoek TL, Brorson JR (2007) Reperfusion accelerates acute neuronal death induced by simulated ischemia. Experimental Neurology 206:280-287. PMID: 17599834
  12. Lian S, Fritzler MJ, Katz J, Hamazaki T, Terada N, Satoh M, Chan EKL (2007) Small interfering RNA-mediated silencing induces target-dependent assembly of GW/P bodies. Molecular Biology of the Cell 18:3375-3387. PMID: 17596515
  13. Mu JJ, Wang Y, Luo H, Leng M, Zhang JL, Yang T, Besusso D, Jung SY, Qin J (2007) A proteomic analysis of ataxia telangiectasia-mutated (ATM)/ATM-Rad3-related (ATR) substrates identifies the ubiquitin-proteasome system as a regulator for DNA damage checkpoints. Journal of Biological Chemistry 282:17330-17334. PMID: 17478428
  14. Oh TI, Sung JH, Tatosian DA, Shuler ML, Kim D (2007) Real-time fluorescence detection of multiple microscale cell culture analog devices In situ. Cytometry Part A 71A:857-865. PMID: 17559134
  15. Pincus Z, Theriott JA (2007) Comparison of quantitative methods for cell-shape analysis.Journal of Microscopy-Oxford 227:140-156. PMID: 17845709
  16. Schlumberger MC, Kappeli R, Wetter M, Muller AJ, Misselwitz B, Dilling S, Kremer M, Hardt WD (2007) Two newly identified SipA domains (F1, F2) steer effector protein localization and contribute to Salmonella host cell manipulation. Molecular Microbiology 65:741-760. PMID: 17635190
  17. Wiley DJ, Rosqvist R, Schesser K (2007) Induction of the Yersinia type 3 secretion system as an all-or-none phenomenon. Journal of molecular biology 373:27-37. PMID: 17825321
  18. Bulosan M, Pauley KM, Yo K, Chan EK, Katz J, Peck AB, Cha S (2008) Inflammatory caspases are critical for enhanced cell death in the target tissue of Sjogren's syndrome before disease onset. Immunology and Cell Biology 87(1):81-90. PMID: 18936772
  19. Chiang S, Bazuine M, Lumeng CN, Geletka LM, Mowers J, White NM, Ma JT, Zhou J, Qi N, Westcott D, Delproposto JB, Blackwell TS, Yull FE, Saltiel AR (2009) The protein kinase IKK[var epsilon] regulates energy balance in obese mice. Cell 138(5):961-975. PMID: 19737522.
  20. Chariot D, Campa V, Azimi B, Mercola M, Ingermanson R, McDonough PM, Price, JH (2008) Automated calcium measurements in live cardiomyocytes. Fifth IEEE International Symposium on Biomedical Imaging: From Nero to Macro, doi:10.1109/ISBI.2008.4540996.
  21. Dobbelaere J, Josué F, Suijkerbuijk S, Baum B, Tapon N, Raff J (2008) A Genome-Wide RNAi Screen to Dissect Centriole Duplication and Centrosome Maturation in Drosophila. PLoS Biology 6(9):e224 PMID: 18798690
  22. Hasegawa Y, Murph M, Yu S, Tigyi G, Mills GB (2008) Lysophosphatidic acid (LPA)-induced vasodilator-stimulated phosphoprotein mediates lamellipodia formation to initiate motility in PC-3 prostate cancer cells. Molecular Oncology 2(1): 54-69. PMID: none
  23. Liberali P, Ramo P, Pelkmans L (2008) Protein kinases: starting a molecular systems view of endocytosis. Annual Review Pelkmans, L. Annual Review of Cell and Developmental Biology 24:501-523. PMID: 18598215.
  24. Mayer K, Iolyeva M E, Meyer-Grahle U, Brix K (2008) Intestine-specific expression of green fluorescent protein-tagged cathepsin B: proof-of-principle experiments. Biological Chemistry 389(8):1085-1096. PMID: 18690773
  25. Pan H, Yu J, Zhang L, Carpenter AE, Zhu, H, Li L, Ma D, Yuan J (2008) A novel small molecule regulator of guanine nucleotide exchange activity of ARF and golgi membrane trafficking. Journal of Biological Chemistry 10.1074/jbc.M806592200. PMID: 18799457
  26. Sacher R, Stergiou L, Pelkmans L (2008) Lessons from genetics: interpreting complex phenotypes in RNAi screens. Current Opinion in Cell Biology 20(4):483-489. PMID: 18602470.
  27. Sumiyoshi M, Ricciuto J, Tisdale A, Gipson IK, Mantelli F, Argueso P (2008) Antiadhesive character of mucin O-glycans at the apical surface of corneal epithelial cells. Investigative Ophthalmology & Visual Science 49:197-203. PMID: 18172093
  28. Tognarini I, Sorace S, Zonefrati R, Galli G, Gozzini A, Carbonell Sala SC, Thyrion GD, Carossino AM, Tanini A, Mavilia C, Azzari C, Sbaiz F, Facchini A, Capanna R, Brandi ML (2008) In vitro differentiation of human mesenchymal stem cells on Ti6Al4V surfaces. Biomaterials 29:809-824. PMID: 18022689
  29. Handel N, Brockel A, Heindl M, Klein E, Uhlig HH (2009) Cell-cell-neighborhood relations in tissue sections—a quantitative model for tissue cytometry. Cytometry Part A 75(4):356-61. PMID: 19184996
  30. Ilg K, Endt K, Misselwitz B, Stecher B, Aebi M, Hardt WD (2009) O-antigen-negative Salmonella enterica serovar Typhimurium is attenuated in intestinal colonization but elicits colitis in streptomycin-treated mice. Infection and Immunity 77(6):2568-75 PMID: 19364844. PMCID: PMC2687356.
  31. Kalany NY, Sabatini DM (2009) Tumours with PI3K activation are resistant to dietary restriction. Nature 458(7239):725-31. PMID: 19279572. PMCID: PMC2692085.
  32. Lai FPL, Szczodrak M, Oelkers JM, Ladwein M, Acconcia F, Benesch S, Auinger S, Faix J, Small JV, Polo S, Stradal TEB, Rottner K (2009) Cortactin promotes migration and platelet-derived growth factor-induced actin reorganization by signaling to rho-GTPases. Molecular Biology of the Cell 20(14):3209-3223. PMID: 19458196. PMCID: PMC2710823.
  33. Moy TI, Conery AL, Larkins-Ford J, Wu G, Mazitschek R, Casadei G, Lewis K, Carpenter AE, Ausubel FM (2009) High throughput screen for novel antimicrobials using a whole animal infection model. ACS Chemical Biology 4/doi:10.1021/cb900084v. PMID: 19572548
  34. Ramo P, Sacher R, Snijder B, Begemann B, Pelkmans L (2009) CellClassifier: supervised learning of cellular phenotypes. Bioinformatics 25(22):3028-3030. PMID: 19729371.
  35. Rocha N, Kuijl C, van der Kant R, Janssen L, Houben D, Janssen H, Zwart W, Neefjes J (2009) Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7-RILP-p150 glued and late endosome positioning. Journal of Cell Biology 185(7):1209-25. PMID: 19564404. PMCID: PMC2712958.
  36. Rodier F, Coppé JP, Patil CK, Hoeijmakers WA, Muñoz DP, Raza SR, Freund A, Campeau E, Davalos AR, Campisi J (2009) Persistent DNA damage signalling triggers senescence-associated inflammatory cytokine secretion. Nature Cell Biology 11(8):973-79. PMID: 19597488.
  37. Snijder B, Sacher R, Ramo P, Damm E, Liberali P, Pelkmans L (2009) Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 461(7263):520-523. PMID: 19710653.
  38. Tsui M, Xie T, Orth JD, Carpenter AE, Rudnicki S, Kim S, Shamu CE, Mitchison TJ (2009) An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor. PLoS ONE 4(10):e7339. PMID: 19802393. PMCID: PMC2752188.
  39. Zunder ER, Knight ZA, Houseman BT, Apsel B, Shokat KM T (2009) Discovery of drug-resistant and drug-sensitizing mutations in the oncogenic PI3K isoform p110 alpha. Cancer Cell 14(2):180-192. PMID: 18691552. PMCID: PMC2720137.