Carpenter Lab

Publications, Data, and Software

Publication lists and citation metrics also at: [Google Scholar] [PubMed] [ResearcherID]

[Additional platform papers]

Published Papers

119. McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE (2018). CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 16(7):e2005970 / doi: 10.1371/journal.pbio.2005970 PMID: 29969450 (Research article) [Github page]

118. Vasilevich AS, Mourcin F, Mentink A, Hulshof F, Beijer N, Zhao Y, Levers M, Papenburg B, Singh S, Carpenter AE, Stamatialis D, van Blitterswijk C, Tarte K, de Boer J (2018). Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells. Front Bioeng Biotechnol. 6:87 / doi: 10.3389/fbioe.2018.00087 PMCID: PMC6031747 (Research article)

117. Caicedo JC, McQuin C, Goodman A, Singh S, Carpenter AE (2018). Weakly supervised learning of single-cell feature embeddings. 2018 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) bioRxiv p. 293431. / doi: 10.1101/293431 (Conference paper) [Github page]

116. Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS (2018). Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface 15(141) / doi: 10.1098/rsif.2017.0387 PMCID: PMC5938574 (Research article)

115. Becker T, Caicedo JC, Singh S, Weckmann M, Carpenter AE (2018). Combining morphological and migration profiles of in vitro time-lapse data. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018). p. 965–968. (Conference paper)

114. Goldsborough P, Pawlowski N, Caicedo JC, Singh S, Carpenter AE (2018). CytoGAN: Generative Modeling of Cell Images / doi: 10.1101/227645. [link to biorxiv preprint]

113. Simm J, Klambauer G, Arany A, Steijaert M, Wegner JK, Gustin E, Chupakhin V, Chong YT, Vialard J, Buijnsters P, Velter I, Vapirev A, Singh S, Carpenter AE, Wuyts R, Hochreiter S, Moreau, Ceulemans H (2018). Repurposed High-Throughput Images Enable Biological Activity Prediction For Drug Discovery. doi: 10.1016/j.chembiol.2018.01.015 PMID: 29503208. PMCID: in process (Research article)

112. Doan M, Vorobjev I, Rees P, Filby A, Wolkenhauer O, Goldfeld AE, Lieberman J, Barteneva N, Carpenter AE, Hennig H (2018). Diagnostic Potential of Imaging Flow Cytometry. Trends Biotechnol 112:39-45 / doi: 10.1016/j.tibtech.2017.12.008 PMID: 29395345 (Review article)

111. Bray MA, Carpenter AE (2018). Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler. Methods Mol Biol 1683:89-112 / doi: 10.1007/978-1-4939-7357-6_7. PMID: 29082489. (Book chapter)

110. Hung J, Goodman A, Lopes S, Rangel G, Ravel D, Costa F, Duraisingh M, Marti M, Carpenter AE (2017). Applying Faster R-CNN for Object Detection on Malaria Images. 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). IEEE. p. 808–813. (Conference paper)

109. Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA (2017). Reconstructing cell cycle and disease progression using deep learning. Nat Commun 8(1):463 / doi: 10.1038/s41467-017-00623-3. PMID: 28878212; PMCID: PMC5587733. (Research article)

108. Caicedo JC, Cooper S, Heigwer F, Warchal S, Qiu P, Molnar C, Vasilevich AS, Barry JD, Bansal HS, Kraus O, Wawer M, Paavolainen L, Herrmann MD, Rohban M, Hung J, Hennig H, Concannon J, Smith I, Clemons PA, Singh S, Rees P, Horvath P, Linington RG, Carpenter AE (2017). Data-analysis strategies for image-based cell profiling. Nat Methods 14(9):849-863 / doi: 10.1038/nmeth.4397. PMID: 28858338. PMCID: N/A (Review article)

107. Hulshof FFB, Papenburg B, Vasilevich A, Hulsman M, Zhao Y, Levers M, Fekete N, de Boer M, Yuan H, Singh S, Beijer N, Bray MA, Logan DJ, Reinders M, Carpenter AE, van Blitterswijk C, Stamatialis D, de Boer J (2017). Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration. Biomaterials 137:49-60 / doi: 10.1016/j.biomaterials.2017.05.020. PMID: 28535442. PMCID: in process (Research article)

106. Barczak AK, Avraham R, Singh S, Luo SS, Zhang WR, Bray MA, Hinman AE, Thompson M, Nietupski RM, Golas A, Montgomery P, Fitzgerald M, Smith RS, White DW, Tischler AD, Carpenter AE, Hung DT (2017). Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. PLoS Pathog. 15;13(5):e1006363 / doi: 10.1371/journal.ppat.1006363. PMID: 28505176; PMCID: PMC5444860 (Research article)

105. Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, Carpenter AE (2016). Systematic morphological profiling of human gene and allele function via Cell Painting. eLife. 10.7554/eLife.24060 / doi: 10.7554/eLife.24060. PMID: 28315521. PMCID: PMC5386591 (Research article) [Github page]

104. Pawlowski N, Caicedo JC, Singh S, Carpenter AE, Storkey A (2016). Automating Morphological Profiling with Generic Deep Convolutional Networks. doi: 10.1101/085118 PMID: in process (Conference paper) [Github page]

103. Bray MA, Gustafsdottir SM, Ljosa V, Singh S, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancík V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, Carpenter AE (2017). A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay. Gigascience / doi: 10.1093/gigascience/giw014. PMID: 28327978. PMCID: in process (Research article) [link to bioRxiv preprint] [PDF] [Github page]

102. Meijering E, Carpenter AE, Peng H, Hamprecht F, Olivo-Marin, JC (2016). Imagining the future of bioimage analysis. Nature Biotechnology. 34(12)1250-55 / doi: 10.1038/nbt.3722. PMID: 27926723 PMCID: in process (Research article)

101. Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, Filby A (2016). An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods. pii: S1046-2023(16)30291-2 / doi: 10.1016/j.ymeth.2016.08.018. PMID: 27594698. PMCID: PMC5231320 (Research article)

100. Bray MA, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, Carpenter AE,(2016). Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nature Protocols. 11(9):1757-74 / doi: 10.1038/nprot.2016.105. PMID: 27560178. PMCID: PMC5223290 (Research article) [Github page]

99. Goodman A, Carpenter AE(2016). High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments. Microscopy and Microanalysis. 22(S3):538–539 / doi: 10.1017/S1431927616003548. NIHSMID: 838697. (Research article)

98. Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WC, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Silva-Junior FP, Andrade CH (2016). QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. Journal of Chemical Information and Modeling. 56(7):1357-72 / doi: 10.1021/acs.jcim.6b00055. PMID: 27253773. PMCID: PMC5283162. (Research article)

97. Dao D, Fraser AN, Hung J, Ljosa V, Singh S, Carpenter AE(2016). CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. Bioinformatics. 32(20):3210-3212 / doi: 10.1093/bioinformatics/btw390. PMID: 27354701. PMCID: PMC5048071. (Research article)

96. Shan J, Logan DJ, Root DE, Carpenter AE, Bhatia SN (2016). High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro. Journal of Biomolecular Screening. 21(9):897-911 / doi: 10.1177/1087057116660277. PMID: 27650791. PMCID: in process. (Research article)

95. Neves BJ, Dantas RF, Senger MR, Goes Valente WC, de Mello Rezende-Neto J, Chaves WT, Kamentsky L, Carpenter AE, Silva-Jr FP, Andrade CH (2016). The Antidepressant Drug Paroxetine as a New Lead Candidate in Schistosome Drug Discovery. MedChemComm / doi: 10.1039/C5MD00596E. PMID: 27119563. PMCID: PMC4903927.(Research article)

94. Dordea AC, Bray M-A, Allen K, Logan D, Fei F, Malhotra R, Gregory M, Carpenter AE, Buys ES (2016). An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. Experimental Eye Research / doi: 10.1016/j.exer.2016.04.012. PMID: 27119563. PMCID: PMC4903927. (Research article)

93. Caicedo JC, Singh S, Carpenter AE (2016). Applications in image-based profiling of perturbations. Current Opinion in Biotechnology 39:134-142 / doi: 10.1016/j.copbio.2016.04.003. PMID: 27089218. PMCID: In Process. (Review article)

92. Uhlmann V, Singh S, Carpenter AE (2016). CP-CHARM: segmentation-free image classification made accessible. BMC Bioinformatics 17(1):51 / doi: 10.1186/s12859-016-0895-y. PMID: 26817459. PMCID: PMC4729047. (Research article)

91. Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P (2016). Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nat Commun 7:10256 / doi: 10.1038/ncomms10256. PMID: 26739115. PMCID: PMC4729834. (Research article)

90. Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI (2016). A Genome-wide RNAi screen for microtubule network formation and lysosome motility regulation in Drosophila S2 cells. Cell Reports 14(3):611-20 / doi: 10.1016/j.celrep.2015.12.051. PMID: 26774481. PMCID: PMC4868501. (Research article)

89. Logan DJ, Shan J, Bhatia SN, Carpenter AE (2015). Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods pii: S1046-2023(15)30170-5 / doi: 10.1016/j.ymeth.2015.12.002. PMID: 26687239. PMCID: PMC4766037. (Research article)

88. Bray M-A, Carpenter AE (2015). CellProfiler Tracer: Exploring and Validating High-Throughput, Time-Lapse Microscopy Image Data. BMC Bioinformatics 16:368 / doi: 10.1186/s12859-015-0759-x. PMID: 26537300. PMCID: PMC4634901. (Research article)

87. Arbelle A, Drayman N, Bray M, Alon U, Carpenter AE, Riklin Raviv T. Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015. Springer International Publishing; 2015. p. 218–225. doi: 10.1007/978-3-319-24574-4_26. (Book chapter)

86. Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE (2015). Morphological profiles of RNAI-induced gene knockdown are highly reproducible but dominated by seed effects. PLoS One 10(7): e(0131370) / doi: 10.1371/journal.pone.0131370. PMID: 26197079. PMCID: PMC4511418. (Research article)

85. Bray M-A, Vokes MS, Carpenter AE (2015). Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images. Current Protocols in Molecular Biology. 109:14.17.1-14.17.13 / doi: 10.1002/0471142727.mb1417s109. PMID: 25559103. PMCID: PMC4302752 (Research article)

84. Metelo AM, Noonan HR, Li X, Jin Y, Baker R, Kamentsky L, Zhang Y, van Rooijen E, Shin J, Carpenter AE, Yeh JR, Peterson RT, Iliopoulous O (2015). Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model. Journal of Clinical Investigation. 125(5):1987-1997 / doi: 10.1172/JCI73665. PMID: 25866969 PMCID: PMC4463187 (Research article)

83. Gilad T, Bray MA, Carpenter AE, Riklin Raviv T (2015). Symmetry-Based Mitosis Detection in Time-Lapse Microscopy. Paper presented at ISBI 2015 2015 International Symposium on Biomedical Imaging: From Nano to Macro, 14:40-16:10; April 17-20, 2015; Brooklyn Bridge, NY. PMCID: not needed for computational conference papers (Conference paper)

82. Jeong Y-M, Duanting Z, Hennig H, Samanta A, Agrawalla BK, Bray M-A, Carpenter AE, Chang Y-T (2015). CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells. Chemistry and Biology.22(2):299-307 / doi: 10.1016/j.chembiol.2014.11.018. PMID: 25601075 PMCID: In Process (Research article)

81. Du Z, Abedalthagafi M, Aizer AA, McHenry AR, Sun HH, Bray MA, Viramontes O, Machaidze R, Brastianos PK, Reardon DA, Dunn IF, Freeman GJ, Ligon KL, Carpenter AE, Alexander BM, Agar NY, Rodig SJ, Bradshaw EM, Santagata S (2014). Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma. Oncotarget 6(7):4704-16 / doi: 10.18632/oncotarget.3082. PMID: PMC4467109 PMCID: PMC4467109 (Research article)[pdf]

80. Singh S, Bray M-A, Jones TR, Carpenter AE (2014). Pipeline for illumination correction of images for high-throughput microscopy. Journal of Microscopy 256(3):231-236 / doi: 10.1111/jmi.12178. PMID: 25228240 PMCID: PMC4359755 (Research article)

79. Rees P, Wills JW, Brown MR, Tonkin J, Holton MD, Hondow N, Brown AP, Brydson R, Millar V, Carpenter AE, Summers HD (2014). Nanoparticle vesicle encoding for imaging and tracking cell populations. Nature Methods 11:1177-1181 / doi: 10.1038/nmeth.3105. PMID: 25218182 PMCID: In Process (Research article)

78. Sheik-Khalil E, Bray M-A, Ozkaya S, Scarlatti G, Jansson M, Carpenter AE, Fenyo EM (2014). Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition. BMC Infectious Diseases 14:472 / doi: 10.1186/1471-2334-14-472. PMID: 25176034 PMCID: PMC4296150 (Research article)

77. Khan IA, Fraser A, Bray M-A, Smith PJ, White NS, Carpenter AE, Errington RJ (2014). ProtocolNavigator: emulation based software for the design, documentation and reproduction biological experiments. Bioinformatics 30(23):344--3442 / doi: 10.1093/bioinformatics/btu554. PMID: 25150250 PMCID: 4121832 (Research article)

76. Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSY, Duvall JR, Wilson JA, Bittker JA, Dančík V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, Clemons PA (2014). Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. PNAS. 111(30):10911-10916 / doi: 10.1073/pnas.1410933111. PMID: 25024206 PMCID: PMC4121832 (Research article) [Images in IDR]

75. Wählby C, Lee Conery A, Bray M-A, Kamentsky L, Larkins-Ford J, Sokolnicki KL, Veneskey M, Michaels K, Carpenter AE, O'Rourke EJ (2014). High- and low-throughput scoring of fat mass and body fat distribution in C. elegans. Methods 68(3):492-499 / doi: 10.1016/j.ymeth.2014.04.017. PMID: 24784529 PMCID: PMC4112171 (Research article)

74. Nieland TJF, Logan DJ, Saulnier J, Lam D, Johnson C, Root DE, Carpenter AE, Sabatini BL (2014). High Content Image Analysis Identifies Novel Regulators of Synaptogenesis in a High-Throughput RNAi Screen of Primary Neurons. PLoS ONE 9(3):e91744 / doi: 10.1371%2Fjournal.pone.0091744. PMID: 24633176 PMCID: PMC3954765 (Research article)

73. Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Siddiqi N, Rubin EJ, Hung DT (2014). Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathogens 10(2):e1003946 / doi: 10.1371/journal.ppat.1003946. PMID: 24586159 PMCID: PMC3930586 (Research article)

72. Chudnovsky Y, Kim D, Zheng S, Whyt WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Mitalipova M, Muffat J, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG (2014). ZFHX4 is a master regulator of NuRD core member CHD4 and regulates the glioblastoma tumor initiating cell state. Cell Reports 6(2):313-324 / doi: 10.1016/j.celrep.2013.12.032. PMID: 24440720 PMCID: PMC4041390 (Research article)

71. Singh S, Carpenter AE, Genovesio A (2014). Increasing the content of high-content screening: an overview. Journal of Biomolecular Screening 19(5):640-650 / doi: 10.1177/1087057114528537. PMID: 24710339 PMCID: PMC4230961 (Review article)

70. Gustafsdottir SM**, Ljosa V**, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA*, Carpenter AE*, Shamji AF* (2013). Multiplex cytological profiling assay to measure diverse cellular states. PLoS One 8(12):e80999 / doi: 10.1371/journal.pone.0080999. PMID: 24312513 PMCID: PMC3847047 (Research article)

**These authors contributed equally.

*These authors contributed equally.

69. Ljosa V, Caie PD, ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE (2013). Comparison of Methods for Image-Based Profiling of Cellular Morphological Responses to Small-Molecule Treatment. Journal of Biomolecular Screening 18:1321-1329 / doi: 10.1177/1087057113503553. PMID: 24045582 PMCID: PMC3884769 (Research article)

68. Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MAS, Scadden DT, Schreiber SL, Ebert BL, Golub TR (2013). Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nature Chemical Biology 9(12):840-848 / doi: 10.1038/nchembio.1367. PMID: 24161946 PMCID: PMC4009363 (Research article)

67. March S, Ng S, Velmurugan S, Galstian A, Shan J, Logan DJ, Carpenter AE, Thomas D, Sim BK, Mota MM, Hoffman SL, Bhatia SN (2013). A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax. Cell Host & Microbe 14(1):104–15 / doi: 10.1016/j.chom.2013.06.005. PMID: 23870318 PMCID: PMC3780791 (Research article)

66. Shan J, Schwartz RE, Ross NT, Logan DJ, Thomas D, Duncan SA, North TE, Goessling W, Carpenter AE, Bhatia SN (2013). Identification of small molecules for human hepatocyte expansion and iPS differentiation. Nature Chemical Biology 9(8):514–520 / doi: 10.1038/nchembio.1270. PMID: 23728495 PMCID: PMC3720805 (Research article)

65. Floyd SR, Pacold ME, Huang Q, Clarke SM, Lam FC, Cannell IG, Bryson BD, Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC, Maffa A, Del Rosario AM, Root DE, Carpenter AE, Hahn WC, Sabatini DM, Chen CC, White FM, Bradner JE, Yaffe MB (2013). The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature 498(7453):246–250 / doi: 10.1038/nature12147. PMID: 23728299 PMCID: PMC3683358 (Research article)

64. Bray MA and Carpenter AE (2012). Advanced Assay Development Guidelines for Image-Based High Content Screening and Analysis. In: Sittampalam GS et al., eds. Assay Guidance Manual. PMID: 23469374 (Book chapter) [NCBI Bookshelf link]

63. Wen Q, Goldenson B, Silver SJ, Schenone M, Dancik V, Huang Z, Wang LZ, Lewis TA, An WF, Li X, Bray MA, Thiollier C, Diebold L, Gilles L, Vokes MS, Moore CB, Bliss-Moreau M, Verplank L, Tolliday NJ, Mishra R, Vemula S, Shi J, Wei L, Kapur R, Lopez CK, Gerby B, Ballerini P, Pflumio F, Gilliland DG, Goldberg L, Birger Y, Izraeli S, Gamis AS, Smith FO, Woods WG, Taub J, Scherer CA, Bradner JE, Goh BC, Mercher T, Carpenter AE, Gould RJ, Clemons PA, Carr SA, Root DE, Schreiber SL, Stern AM, Crispino JD (2012). Identification of Regulators of Polyploidization Presents Therapeutic Targets for Treatment of AMKL. Cell 150(3):575-89 / doi:. PMID: 22863010 PMCID: PMC3613864 (Research article)

62. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE (2012). Biological imaging software tools. Nature Methods 9(7):697-710 / doi:. PMID: 22743775 PMCID: PMC3659807 (Review article)

61. Carpenter AE, Kamentsky L, Eliceiri KW (2012). A call for bioimaging software usability. Nature Methods 9(7):666-70 / doi: 10.1038/nmeth.2073. PMID: 22743771 PMCID: PMC3641581 (Review article)

60. Ljosa V, Sokolnicki KL, Carpenter AE (2012). Annotated high-throughput microscopy image sets for validation. Nature Methods 9(7):637 / doi: 10.1038/nmeth.2083. PMID: 22743765 PMCID: PMC3627348 (Research article)

59. Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE (2012). An image analysis toolbox for high-throughput C. elegans assays. Nature Methods 9(7):714-716 / doi: 10.1038/nmeth.1984. PMID: 22522656 PMCID: PMC3433711 (Research article)

58. Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Carpenter AE, Wessling M, Post GF, Uetz M, Reinders MJT, Stamatialis D, van Blitterswijk CA, de Boer J (2012). An algorithm-based topographical biomaterials library to instruct cell fate. PNAS 108(40):16565/ doi: 10.1073/pnas.1109861108. PMID: 22454500 PMCID: PMC3326488 (Research article)

57. Kitami T, Logan DJ, Negri J, Hasaka T, Tolliday NJ, Carpenter AE, Spiegelman BM, Mootha VK (2012). A chemical screen probing the relationship between mitochondrial content and cell size. PLoS ONE 7(3):e33755/ doi:10.1371/journal.pone.0033755. PMID: 22479437 PMCID: PMC3315575 (Research article)

56. Bray, M-A, Fraser AN, Hasaka TP, Carpenter AE (2012) Workflow and metrics for image quality control in large-scale high-content screens. Journal of Biomolecular Screening 17(2):135-143/ doi: 10.1177/1087057111420292. PMID: 21956170 PMCID: PMC3593271 (Research article)

55. Pretorius AJ, Bray M-A, Carpenter AE, Ruddle R (2011) Visualization of parameter space for image analysis. In InfoVis 2011 (Proceedings of the 2011 IEEE Symposium on Information Visualization), 2402-11/ doi: 10.1109/TVCG.2011.253". PMID: 22034361 PMCID: PMC3598613 (Research article)

54. Peterson TR, Sengupta SS, Harris TE, Carmack AE, Balderas E, Guertin DA, Madden KL, Carpenter AE, Finck BN, Sabatini DM (2011) mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway. Cell 146(3):408-420/ doi: 10.1016/j.cell.2011.06.034. PMID: 21816276 PMCID: PMC3336367 (Research article)

53. Carpenter AE (2011) Extracting biomedically important information from large, automated imaging experiments. In ISBI 2011 (Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro), 1723-1726/ doi: 10.1109/ISBI.2011.5872737. PMID: 24525841 PMCID: PMC3920454 (Research article) [pdf]

52. Kamentsky L, Jones TR, Fraser A, Bray M, Logan D, Madden K, Ljosa V, Rueden C, Harris GB, Eliceiri K, Carpenter AE (2011) Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics 2011/ doi: 10.1093/bioinformatics/btr095. PMID: 21349861 PMCID: PMC3072555 (Research article) [pdf]

51. Elkabets M, Gifford AM, Scheel C, Nilsson B, Reinhardt F, Bray MA, Carpenter AE, Jirström K, Magnusson K, Ebert BL, Pontén F, Weinberg RA, McAllister SS (2011) Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice. Journal of Clinical Investigation 121(2): 784-99/ doi: 10.1172/JCI43757. PMID: 21266779 PMCID: PMC3026724 (Research article) [CellProfiler published pipeline]

50. Lindquist RA, Ottina KA, Wheeler DB, Hsu PP, Thoreen CC, Guertin DA, Siraj MA, Senguptal S, Shaul YD, Lamprecht MR, Madden KL, Papallo AR, Jones T, Sabatini DM, Carpenter AE (2011) Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1 - S6K pathway signaling. Genome Research 2011, 21:433-446/ doi: 10.1101/gr.111492.110. PMID: 21239477 PMCID: PMC3044857 (Research article)

49.♦ Kim K, Rowat AC. Carpenter AE (2010) Automated tracking of yeast cell lineages. Proceedings of SPIE 7798, 779823. doi: (Research article) [SPIE link]

48.♦ Carpenter AE (2010). High-content screening: Practical advice, tools and resources. SBS News 47:2, October 2010. [SBS news link ]

47.♦ Carpenter AE (2010). High-content screening: FAQs about trends, technologies, and outcomes. SBS News 47:2, August 2010. [SBS news link ]

46. Riklin-Raviv T, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C (2010) Morphology-guided graph search for untangling objects: C elegans analysis. In Medical Image Computing and Computer Assisted Intervention (MICCAI) 2010; 13(3):634-641/ doi: 10.1007/978-3-642-15711-0_79. PMID: 20879454 PMCID: PMC3050593 (Research article) [pdf]

45. Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE (2010) Resolving clustered worms via probabilistic shape models. In ISBI 2010 (Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro), 552-555/ doi: 10.1109/ISBI.2010.5490286. PMID: 21383863 PMCID: PMC3048333 (Research article) [pdf]

44. Cataldo AM, McPhie DL, Lange NT, Punzell S, Elmiligy, Ye NZ, Froimowitz MP, Hassinger LC, Menesale EB, Sargent LW, Logan DJ, Carpenter AE, Cohen BM (2010). Abnormalities in Mitochondrial Structure in Cells of Patients with Bipolar Disorder. American Journal of Pathology 177(2):575-85/ doi: 10.2353/ajpath.2010.081068. PMID: 20566748 PMCID: PMC2913344 (Research article) [American Journal of Pathology Link]

43. Logan DJ and Carpenter AE (2010). Screening Cellular Feature Measurements for Image-based Assay Development. Journal of Biomolecular Screening 15(7):840-6/ doi: 10.1177/1087057110370895. PMID: 20516293 PMCID: PMC3145348 (Research article)

42. Castoreno AB, Smurnyy Y, Torres AD, Vokes MS, Jones TR, Carpenter AE, Eggert US (2010). Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis. Nature Chemical Biology doi: 10.1038/nchembio.363. PMID: 20436488 PMCID: PMC2873065 (Research article)

41. Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché J-K (2010) Visualization of image data from cells to organisms. Nature Methods Supplement 7(3):S27-41/ doi: 10.1038/nmeth.1431. PMID: 20195255 PMCID: PMC3650473 (Review article) [Nature Methods Supplement Link]

40. Ljosa V, Carpenter AE (2009) Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening. PLoS Computational Biology 5(12):e1000603/ doi: 10.1371/journal.pcbi.1000603. PMID: 20041172 PMCID: PMC2791844 (Tutorial) [PLoS Computational Biology Link]

39. 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/ doi: 10.1371/journal.pone.0007339. PMID: 19802393 PMCID: PMC2752188 (Research article) [PLoS ONE Link]

38. 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 PMCID: PMC2745594 (Research article) [ACS Chemical Biology link] [pdf]

37. Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, Ebert BL (2009) Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinformatics 25(8):1078-79/ doi: 10.1093/bioinformatics/btp091. PMID: 19228802 (Research article) [pdf]

36. Jones TR**, Carpenter AE**, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, Sabatini DM (2009). Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. PNAS 106(6):1826-31/ doi: 10.1073/pnas.0808843106. PMID: 19188593 PMCID: PMC2634799 (Research article) [PNAS link]

     **These authors contributed equally.

35. Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (2008). CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 9(1):482/ doi: 10.1186/1471-2105-9-482. PMID: 19014601 PMCID: PMC2614436 (Research article) [BioMed Central link] [pdf]

34. 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 283(45):31087-9/ doi: 10.1074/jbc.M806592200. PMID: 18799457 PMCID: PMC2576541 (Research article) [pdf]

33♦. Vokes MS, Carpenter AE (2008) CellProfiler: Open-source software to automatically quantify images. Microscopy Today 16(5):38-39 (Short review article) [pdf]

32. Ljosa V, Carpenter AE (2008) High-throughput screens for fluorescent dye discovery. Trends in Biotechnology 10:527-30/ doi:. PMID: 18706725 (Review article) [pdf]

31. Vokes MS, Carpenter AE (2008) Using CellProfiler for automatic identification and measurement of biological objects in images. In: Ausubel, FM et al., eds. Current Protocols in Molecular Biology 82:14.17.1-14.17.12. PMID: 18425761 (Book chapter) [pdf]

30. Carpenter AE (2007) Image-based chemical screening. Nature Chemical Biology. 3:461-465 PMID: 17637778 (Review article) [NatChemBiology link] [pdf]

29. Carpenter AE (2007) Extracting rich information from images. In: Clemons PA et al., eds. Cell-Based Assays for High-Throughput Screening, Methods in Molecular Biology 486:14. New York, NY: Humana Press; 193-211. PMID: 19347625 (Book chapter) [pdf]

28♦. Jones TR, Carpenter AE (2007) Flexible Image Analysis. Biophotonics Journal. 14(7):31-32. (Short review article) [pdf] PMID-none

27♦. Carpenter AE (2007) Software opens the door to quantitative imaging. Nature Methods. 4(2):120-1. PMID: 17264858 (Short review article) [pdf]

26. Lamprecht MR, Sabatini DM, Carpenter AE (2007) CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 42(1):71-75. PMID: 17269487 PMCID: not needed prior to 2008(Research article) [pdf]

25. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology, 7:R100 / doi: 10.1186/gb-2006-7-10-r100. PMID: 17076895 (Research article) PMCID: PMC1794559

24. 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 / doi: 10.1073/pnas.0608636103. PMID: 17142318 PMCID: PMC1748161 (Research article)

23. Cowen LE, Carpenter AE, Matangkasombut O, Fink GR, Lindquist S (2006) Genetic architecture of Hsp90-dependent drug resistance. Eukaryotic Cell. 5(12):2184-8 / doi: 10.1128/EC.00274-06. PMID 17056742 PMCID: PMC1694807 (Research article)

22. 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 PMCID: not needed prior to 2008 (Research article) [pdf]

21. Jones TR, Carpenter AE, Sabatini DM, Golland P (2006) Methods for high-content, high-throughput image-based cell screening. Proceedings of the Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB). Metaxas DN, Whitaker RT, Rittcher J, Sebastian T (Eds). Copenhagen, Denmark, October 5, pp 65-72. (Research article) [pdf] PMID-none

Updated as a book chapter:

     Jones TR, Carpenter AE, Golland P, Sabatini DM (2008) Methods for high-content, high throughput image-based cell screening. In: Rittscher J, Machiraju R, Wong STC , editors. Microscopic Image Analysis for Life Science Applications. Norwood, MA: Artech House Publishers, pp. 209-221 (Book chapter)

20. 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 PMCID: not needed prior to 2008 (Research article) [pdf]

19. Chuang CH, Carpenter AE, Fuchsova B, Johnson T, de Lanerolle P, Belmont AS (2006) Long-Range Directional Movement of an Interphase Chromosome Site. Current Biology, 16:1-7 / doi: 10.1016/j.cub.2006.03.059. PMID 16631592 (Research article) PMCID: not needed prior to 2008

18. 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 / doi: 10.1016/j.cell.2006.01.040. PMID 16564017 PMCID: not needed prior to 2008 (Research article)

17. 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 PMCID: not needed prior to 2008 (Research article) [pdf]

16. Jones TR, Carpenter AE, Golland P (2005) Voronoi-based segmentation of cells on image manifolds. Proceedings of the Workshop on Computer Vision for Biomedical Image Applications (CVBIA). Yanxi Liu, Tianzi Jiang, Changshui Zhang (Eds.). Beijing, China, October 21. Lecture Notes in Computer Science 3765. Published by Springer-Verlag, Berlin, p. 535-543, ISBN 3-540-29411-2 (Research article) [pdf] PMID-none

15. Wheeler DB, Carpenter AE, Sabatini DM (2005) Cell microarrays and RNA interference chip away at gene function. Nature Genetics, 37 Supplement: S25-30. PMID 15920526 (Review article) PMCID: not needed prior to 2008 [pdf]

14. Verschure PJ, van der Kraan I, de Leeuw W, van der Vlag J, Carpenter AE, Belmont AS, van Driel R (2005) In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. Molecular and Cellular Biology, 25(11):4552-64 / doi: 10.1128/MCB.25.11.4552-4564.2005. PMID 15899859 PMCID: PMC1140641 (Research article)

13. Rai D, Frolova A, Frasor J, Carpenter AE, Katzenellenbogen BS (2005) Distinctive actions of membrane-targeted versus nuclear localized estrogen receptors in breast cancer cells. Molecular Endocrinology, 19(6):1606-17. PMID 15831524 PMCID: not needed prior to 2008 (Research article) [pdf]

12. 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):127-32. PMID 15782175 PMCID: not needed prior to 2008 (Research article) [pdf][download News&Views article referring to this work][download blurb referring to this work]

11. Carpenter AE, Memedula S, Plutz MJ, Belmont AS. Common effects of acidic activators on large-scale chromatin structure and transcription (2005) Molecular and Cellular Biology, 25(3):958-968 / doi: 10.1128/MCB.25.3.958-968.2005. PMID 15657424 PMCID: PMC544008 (Research article)

10. Carpenter AE, Ashouri A, Belmont AS (2004) Automated microscopy identifies estrogen receptor subdomains with large-scale chromatin structure unfolding activity. Cytometry A, 58A(2):157-166 / doi: 10.1002/cyto.a.10113. PMID 15057969 PMCID: not needed prior to 2008 (Research article)

9. Carpenter AE, Sabatini DM (2004) Systematic genome-wide screens of gene function. Nature Reviews Genetics, 5(1):11-22. PMID 14708012 PMCID: not needed prior to 2008 (Review article) [pdf]

8♦. Carpenter AE, Belmont AS (2004) Direct visualization of transcription factor-induced chromatin remodeling and cofactor recruitment in vivo. Methods in Enzymology, 375:366-81. PMID 14870678 PMCID: not needed prior to 2008 (A methods paper which includes substantial unpublished research) [pdf]

(please note name change in 2003 from AC Nye to AE Carpenter)

___7.5 ---- Ph.D. thesis ---> [download Word document]

7. Nye AC, Rajendran RR, Belmont AS (2003) Chromosomes and Chromatin. In: Cooper DN (ed.) Nature Encyclopedia of the Human Genome, vol. 1:766-773. London: Nature Publishing Group. PMID-none (Review article) [pdf]

6. Rajendran RR, Nye AC, Frasor J, Balsara RD, Martini PGV, Katzenellenbogen BS (2003) Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97). Journal of Biological Chemistry, 278(7):4628-38 / doi: 10.1074/jbc.M210066200. PMID 12466272 PMCID: not needed prior to 2008 (Research article)

5. Nye AC, Rajendran RR, Stenoien DL, Mancini MA, Katzenellenbogen BS, Belmont AS (2002) Alteration of large-scale chromatin structure by estrogen receptor. Molecular and Cellular Biology, 22(10):3437-49 / doi: 10.1128/MCB.22.10.3437-3449.2002. PMID 11971975 PMCID: PMC133805(Research article)

4. Ye Q, Hu YF, Zhong H, Nye AC, Belmont AS, Li R (2001) BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations. Journal of Cell Biology, 155(6):911-21 / doi: 10.1083/jcb.200108049. PMID 11739404 PMCID: PMC2150890 (Research article)

3. Stenoien DL, Nye AC, Mancini MG, Patel K, Dutertre M, O’Malley BW, Smith CL, Belmont AS, Mancini MA (2001) Ligand-mediated assembly and real-time cellular dynamics of estrogen receptor alpha-coactivator complexes in living cells. Molecular and Cellular Biology, 21(13):4404-12 / PMID 11390668 PMCID: PMC87100 [link to paper] (Research article)

2♦. Nye AC, Rajendran RR, Katzenellenbogen BS, Belmont AS (2000) The estrogen receptor alters large-scale chromatin structure. Trends in Cell Biology GFP in Motion CD-ROM, volume 2, ed. B Ludin and A Matus. PMID-none (Movie & caption) [movie (sorry, it doesn't always work)][abstract][background]

1. Belmont AS, Dietzel SD, Nye AC, Tumbar T, Strukov Y (1999) Large scale chromatin structure and function. Current Opinion in Cell Biology, 11(3):307-311. PMID 10395564 PMCID: not needed prior to 2008 (Review article) [pdf]

All are peer-reviewed except those marked with ♦.

Additional Carpenter lab papers (Carpenter not listed as a co-author)

9. Yang SJ, Berndl M, Michael Ando D, Barch M, Narayanaswamy A, Christiansen E, Hoyer S, Roat C, Hung J, Rueden CT, Shankar A, Finkbeiner S, Nelson P (2018). Assessing microscope image focus quality with deep learning. BMC Bioinformatics 19(1):28962 / doi: 10.1186/s12859-018-2087-4 (Research article) [Github page]

8. Doan M (2017). Zooming in on adipocytes: High and deep. Cytometry A.;91(11):1051–1054 / doi 10.1002/cyto.a.23269 PMID: 29072805 (Commentary paper)

7. Vasilevich AS, Carlier A, de Boer J, Singh S (2017). How Not To Drown in Data: A Guide for Biomaterial Engineers. Trends in Biotechnology, 35(9):743-755 / doi: 10.1016/j.tibtech.2017.05.007. PMID: 28693857 (Review article)

6. Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS (2016). High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell, 30(2):214-28 / doi: 10.1016/j.ccell.2016.06.022. PMID: 27478040. PMCID: PMC5003022. (Research article)

5. Arganda-Carreras I, Turaga SC, Berger DR, Cireşan D, Giusti A, Gambardella LM, Schmidhuber J, Laptev D, Dwivedi S, Buhmann JM, Liu T, Seyedhosseini M, Tasdizen T, Kamentsky L, Burget R, Uher V, Tan X, Sun C, Pham TD, Bas E, Uzunbas MG, Cardona A, Schindelin J, Seung HS (2015) Crowdsourcing the creation of image segmentation algorithms for connectomics. Frontiers in Neuroanatomy 9:00142 / doi:. PMID: 26594156. PMCID: PMC4633678. (Conference paper)

4. Majithia AR, Flannick J, Shahinian P, Guo M, Bray MA, Fontanillas P, Gabriel SE, GoT2D Consortium, NHGRI/FHS Allelic Spectrum Project, SIGMA T2D Consortium, T2D-GENES Consortium, Rosen ED, Altshuler D (2014). Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes. PNAS 111(36):13127-13132 / doi:. PMID: 1410428111 PMCID: PMC25157153 (Research article)

3. Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM (2013) Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death. Cell Host Microbe, 13(4):406-16 / doi:. PMID: 23601103. PMCID: PMC3641844. (Research article)

2. Pardo-Martin C, Allalou A, Medina J, Eimon PM, Wählby C, Faith Yanik M (2013) High-throughput hyperdimensional vertebrate phenotyping. Nat. Commun., 4:1467 / doi:. PMID: 23403568. PMCID: PMC3573763 (Research article)

1. Ishaq O, Negri J, Bray MA, Pacureanu A, Peterson RT, Wählby C (2013) Automated quanitification of zebrafish tail deformation for high-throughput drug screening. Protoc Int Symp Biomed Imaging: 902-905 / doi: PMID: 24499782. PMCID: PMC3909804 (Research article)