Publications

2014
Wählby C, Lee Conery A, Bray M-A, Kamentsky L, Larkins-Ford J, Sokolnicki KL, Veneskey M, Michaels K, Carpenter AE, and O'Rourke EJ. 2014. “High- and low-throughput scoring of fat mass and body fat distribution in C. elegans.” Methods 68(3):492-499. Publisher's Version
Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Siddiqi N, Rubin EJ, and Hung DT. 2014. “Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth.” PLoS Pathogens 10(2):e1003946. Publisher's Version
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, and Santagata S. 2014. “Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma.” Oncotarget 6(7):4704-16 . Publisher's Version
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Singh S, Carpenter AE, and Genovesio A. 2014. “Increasing the content of high-content screening: an overview.” Journal of Biomolecular Screening 19(5):640-650. Publisher's Version
Singh S, Bray M-A, Jones TR, and Carpenter AE. 2014. “Pipeline for illumination correction of images for high-throughput microscopy.” Journal of Microscopy 256(3):231-236. Publisher's Version
2013
Ljosa V, Caie PD, Horst ter R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, and 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. Publisher's Version
Shan J, Schwartz RE, Ross NT, Logan DJ, Thomas D, Duncan SA, North TE, Goessling W, Carpenter AE, and Bhatia SN. 2013. “Identification of small molecules for human hepatocyte expansion and iPS differentiation.” Nature Chemical Biology 9(8):514–520. Publisher's Version
March S, Ng S, Velmurugan S, Galstian A, Shan J, Logan DJ, Carpenter AE, Thomas D, Sim BK, Mota MM, Hoffman SL, and 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. Publisher's Version
Gustafsdottir SM**, Ljosa V**, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA*, Carpenter AE*, and Shamji AF*. 2013. “Multiplex cytological profiling assay to measure diverse cellular states.” PLoS One 8(12):e80999. Publisher's Version
Ishaq O, Negri J, Bray MA, Pacureanu A, Peterson RT, and Wählby C. 2013. “Automated quanitification of zebrafish tail deformation for high-throughput drug screening.” Protoc Int Symp Biomed Imaging: 902-905. Publisher's Version
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, and Yaffe MB. 2013. “The bromodomain protein Brd4 insulates chromatin from DNA damage signalling.” Nature 498(7453):246–250. Publisher's Version
Pardo-Martin C, Allalou A, Medina J, Eimon PM, Wählby C, and Faith Yanik M. 2013. “High-throughput hyperdimensional vertebrate phenotyping.” Nat. Commun., 4:1467. Publisher's Version
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, and Golub TR. 2013. “Niche-based screening identifies small-molecule inhibitors of leukemia stem cells.” Nature Chemical Biology 9(12):840-848. Publisher's Version
Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, and Ausubel FM. 2013. “Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death.” Cell Host Microbe, 13(4):406-16. Publisher's Version
2012
Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Carpenter AE, Wessling M, Post GF, Uetz M, Reinders MJT, Stamatialis D, Blitterswijk van CA, and Boer de J. 2012. “An algorithm-based topographical biomaterials library to instruct cell fate.” PNAS 108(40):16565. Publisher's Version
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, and Carpenter AE. 2012. “Biological imaging software tools.” Nature Methods 9(7):697-710. Publisher's Version
Carpenter AE, Kamentsky L, and Eliceiri KW. 2012. “A call for bioimaging software usability.” Nature Methods 9(7):666-70. Publisher's Version
Kitami T, Logan DJ, Negri J, Hasaka T, Tolliday NJ, Carpenter AE, Spiegelman BM, and Mootha VK. 2012. “A chemical screen probing the relationship between mitochondrial content and cell size.” PLoS ONE 7(3):e33755. Publisher's Version
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, and Carpenter AE. 2012. “An image analysis toolbox for high-throughput C. elegans assays.” Nature Methods 9(7):714-716. Publisher's Version
Bray, M-A, Fraser AN, Hasaka TP, and Carpenter AE. 2012. “Workflow and metrics for image quality control in large-scale high-content screens.” Journal of Biomolecular Screening 17(2):135-143. Publisher's Version

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