Papers

For our latest work, check out our preprints on bioRxiv! (Carpenter) (Singh)

Google Scholar pages (with citation metrics): (Carpenter) (Singh)

194. IGVF Consortium.(2024) Deciphering the impact of genomic variation on function. Nature 633, 47–57. https://doi.org/10.1038/s41586-024-07510-0 PMID: 39232149 PMCID: In process (Research article)

193. Weisbart, E, Kumar, A, Arevalo, J,  Carpenter AE, Cimini BA, Singh S. (2024) Cell Painting Gallery: an open resource for image-based profiling. Nature Methods. doi: 10.1038/s41592-024-02399-z  PMID: 39223397 PMCID: In process (Research article) 

192. Cimini, BA, Tromans-Coia C, Stirling, DR, Sivagurunathan S, Senft RA, Ryder PV, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE, (2024) A postdoctoral training program in bioimage analysis. Molecular Biology of the Cell. 35(9), pe2. https://doi.org/10.1091/mbc.E24-05-0214. PMID: 39105698 PMCID: In process (Research Article)

191. Arevalo J, Su E, Ewald JD, van Dijk R, Carpenter AE, Singh S. (2024) Evaluating batch correction methods for image-based cell profiling. Nature Communications. 2024;15(1):6516. doi:10.1038/s41467-024-50613-5. PMID: 39095341. PMCID: PMC11297288. (Research Article)

190. Chandrasekaran SN, Cimini BA, Goodale A, Miller L, Kost-Alimova M, Jamali N, Doench JG, Fritchman B, Skepner A, Melanson M, Kalinin AA, Arevalo J, Haghighi M, Caicedo JC, Kuhn D, Hernandez D, Berstler J, Abbasi HS, Root DE, Swalley SE, Singh S, Carpenter AE (2024). Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature Methods. 21, 1114–1121. PMID: 38594452. PMCID: PMC11166567. doi. pdf.  (Research article)

189. Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Conner L, Carpenter AE, Singh S, Nehme R, Raychaudhuri S. (2024). High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature Communications. 15: 347. PMID: 38184653 PMCID: PMC10771466 doi. pdf. (Research Article)

188. Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE (2024). Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. American Chemical Society. 26;64(4):1172-1186. PMID: 38300851 PMCID: PMC10900289 doi.  pdf. (Research Article)

187. Seal S, Carreras-Puigvert J, Singh S, Carpenter AE, Spjuth O, and Bender A (2024). From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability. Molecular Biology of the Cell. 1;35(3):mr2. PMID: 38170589 PMCID: PMC10916876. doi. pdf. (Research Article)

186. Moshkov N, Bornholdt M, Benoit S, Smith M, McQuin C, Goodman A,  Senft RA, Han Y, Babadi M, Horvath P, Cimini BA,  Carpenter AE, Singh S & Caicedo JC (2024). Learning representations for image-based profiling of perturbations. Nature Communications. 15(1):1594. PMID: 38383513 PMCID: PMC10881515  doi. pdf. (Research Article)

185. Carpenter AE, Singh S (2024). Bringing computation to biology by bridging the last mile. Nature Cell Biology. 26, 5–7. PMID: 38228822 PMCID: PMC10880119 doi. pdf. (Commentary paper)

184. Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, Rutter JC, Therrien M, Yoon H, Lai ZW, Baublis A, Subramanian R, Devkota R, Small J, Sreekanth V, Han M, Lim D, Carpenter AE, Flannick J, Finucane H, Haigis MC, Claussnitzer M, Sheu E, Stevens B, Wagner BK, Choudhary A, Shaw JL, Pablo JL, Greka A (2023). FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. Cell Metab. 35(5):887-905.e11. PMID: 37075753. PMCID: PMC10257950. doi. pdf. (Research Article) 

183. Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP (2023). High-content microscopy reveals a morphological signature of bortezomib resistance. Elife. 12:e91362. PMID: 37753907. PMCID: PMC10584373. doi. pdf. (Research Article) 

182. Tromans-Coia C, Jamali N, Abbasi HS, Giuliano KA, Hagimoto M, Jan K, Kaneko E, Letzsch S, Schreiner A, Sexton JZ, Suzuki M, Trask OJ, Yamaguchi M, Yanagawa F, Yang M, Carpenter AE, Cimini BA (2023). Assessing the performance of the Cell Painting assay across different imaging systems. Cytometry A. Epub ahead of print. PMID: 37789738. PMCID: awaiting assignment. doi. pdf. (Research Article) 

181. Haghighi M, Cruz MC, Weisbart E, Cimini BA, Singh A, Bauman J, Lozada ME, Kavari SL, Neal JT, Blainey PC, Carpenter AE, Singh S (2023). Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence. IJCAI-23. p. 4775–4784. doi. pdf. (Conference paper) 

180. Barnes CM, Power AL, Barber DG, Tennant RK, Jones RT, Lee GR, Hatton J, Elliott A, Zaragoza-Castells J, Haley SM, Summers HD, Doan M, Carpenter AE, Rees P, Love J (2023). Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry. New Phytol. 240(3):1305-1326. PMID: 37678361; PMCID: PMC10594409. doi. pdf. (Research Article)

179. Yu S, Kalinin AA, Paraskevopoulou MD, Maruggi M, Cheng J, Tang J, Icke I, Luo Y, Wei Q, Scheibe D, Hunter J, Singh S, Nguyen D, Carpenter AE, Horman SR (2023). Integrating inflammatory biomarker analysis and artificial intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis. Cell Chemical Biology. 30, 1-14. PMID: 37437569; PMCID: PMC10529501. doi. pdf. (Research Article)

178. Carpenter AE, Cimini BA, Eliceiri KW (2023). Smart microscopes of the future. Nature Methods. 20, 962-964. PMID: 37434001; PMCID: PMC10448787. doi. pdf. (Commentary paper)

177. Laber S, Strobel S, Mercader JM, Dashti H, R.C. dos Santos F, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, Kost-Alimova M, Deodato G, Harney A, Way GP, Saadat A, Harken S, Reibe-Pal S, Ebert H, Zhang Y, Calabuig-Navarro V, McGonagle E, Stefek A, Dupuis JE, Cimini BA, Hauner H, Udler MS, Carpenter AE, Florez JC, Lindgren C, Jacobs, Claussnitzer M (2023). Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genomics. 3, 100346. PMID: 37492099; PMCID: PMC10363917. doi. pdf. (Research Article)

176. Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan D, Concannon JB, Lardeau CH, Mouchet E, Singh S, Abbasi HS, Aspesi P Jr, Boyd JD, Gilbert T, Gnutt D, Hariharan S, Hernandez D, Hormel G, Juhani K, Melanson M, Mervin LH, Monteverde T, Pilling JE, Skepner A, Skepner SE, Vrcic A, Weisbart E, Williams G, Yu S, Zapiec B, Carpenter AE (2023). Optimizing the Cell Painting assay for image-based profiling. Nature Protocols. 18, 1981–2013. PMID: 37344608. doi. pdf. (Research Article)

175. Moshkov N, Becker T, Yang K, Horvath P, Dancik V, Wagner BK, Clemons PA, Singh S, Carpenter AE, Caicedo JC (2023). Predicting compound activity from phenotypic profiles and chemical structures. Nature Communications. 14, 1967. PMID: 37031208; PMCID: PMC10082762. doi. pdf. (Research Article)

174. Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, Calabuig-Navarro V, Skurk T, Ocvirk S, Stemmer K, Cimini BA, Carpenter AE, Dankel SN, Lindgren CM, Hauner H, Nobrega  MA, Claussnitzer M (2023). A non-coding variant linked to metabolic obesity with normal weight affects actin remodeling in subcutaneous adipocytes. Nature Metabolism. 5, 861–879. PMID: 37253881. doi. pdf. (Research Article)

173. Berryer MH, Rizki G, Nathanson A, Klein JA, Trendafilova D, Susco SG, Lam D, Messana A, Holton KM, Karhohs KW, Cimini BA, Pfaff K, Carpenter AE, Rubin LL, Barrett LE (2023). High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. Elife. 21;12:e80168. PMID: 37083703; PMCID: PMC10121225. doi. pdf. (Research Article)

172. Wakui T, Negishi M, Murakami Y, Tominaga S, Shiraishi Y, Carpenter AE, Singh S, Segawa H (2023). Predicting reprogramming-related gene expression from cell morphology in human induced pluripotent stem cells. Molecular Biology of the Cell. 1;34(5):ar45. PMID: 36947171; PMCID: PMC10162412. doi. pdf. (Research Article)

171. Garcia-Fossa F, Cruz MC, Haghighi M, Bispo de Jesus M, Singh S, Carpenter AE, Cimini BA (2023). Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Current Protocols, 3(3):e713. PMID: 36921124 PMCID: PMC10027367. doi. pdf. (Research Article)

170. Dahlin JL, Hua BK, Zucconi BE, Nelson SD  Jr, Singh S, Carpenter AE, Shrimp JH, Lima-Fernandes E, Wawer MJ, Chung LPW, Agrawal A, O’Reilly M, Barsyte-Lovejoy D, Szewczyk M, Li F, Lak P, Cuellar M, Cole PA, Meier JL, Thomas T, Baell JB, Brown PJ, Walters MA, Clemons PA, Schreiber SL, Wagner BK (2023). Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nature Communications, 14(1):1364. PMID: 36914634 PMCID: PMC10011410. doi. pdf. (Research Article) 

169. Way GP, Natoli T, Adeboye A. Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, Haghighi M, Weisbart E, Singh S, Subramanian A, Carpenter AE (2022). Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Systems, 13(11):911-923.e9.  PMID: 36395727 PMCID: in progress. doi. pdf. (Research Article) 

168. Haghighi M, Caicedo JC, Cimini BA, Carpenter AE, Singh S (2022). High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nature Methods, 19(12):1550-1557. PMID: 36344834 PMCID: PMC10012424. doi. pdf. (Research Article) 

167. Rees P, Summers HD, Filby A, Carpenter AE, Doan M (2022). Imaging flow cytometry: a primer. Nature Reviews Methods Primers, 2(86). doi. pdf. (Review Article) 

166. Rueden CT, Hiner MC, Evans EL III, Pinkert MA, Lucas AM, Carpenter AE, Cimini BA, Eliceiri KW (2022). PyImageJ: A library for integrating ImageJ and Python. Nature Methods, 19(11):1326-1327. PMID: 36253645 PMCID: PMC9783691. doi. pdf. (Research Article) 

165. Carpenter AE (2022). Why I shrank my lab by half. eLife, 11:e82831. PMID: 36063089 PMCID: PMC9444239. doi. pdf. (Feature article)

164. Lemmel S, Weckmann M, Wohlers A, Jirmo AC, Grychtol R, Ricklefs I, Nissen G, Bachmann A, Singh S, Caicedo J, Bahmer T, Hansen G, Von Mutius E, Rabe KF, Fuchs O, DittrichA-M, SchaubB,HappleC, Carpenter AE, Kopp MV, Becker T and the ALLIANCE Study Group as part of the German Centre for Lung Research (DZL) (2022), In vitro neutrophil migration is associated with inhaled corticosteroid treatment and serum cytokines in pediatric asthma. Front. Pharmacol. 13:1021317. doi. pdf. (Research article)

163. Rohban MH, Fuller AM, Tan C, Goldstein JT, Syangtan D, Gutnick A, DeVine A, Nijsure MP, Rigby M, Sacher JR, Corsello SM, Peppler GB, Bogaczynska M, Boghossian A, Ciotti GE, Hands AT, Mekareeya A, Doan M, Gale JP, Derynck R, Turbyville T, Boerckel JD, Singh S, Kiessling LL, Schwarz TL, Varelas X, Wagner FF, Kafri R, Eisinger-Mathason TSK, Carpenter AE (2022). Virtual screening for small-molecule pathway regulators by image-profile matching. Cell Systems, 13(9), 724–736.e9. doi. pdf. (Research article)

162. Caicedo JC, Arevalo J, Piccioni F, Bray M.-A, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, Singh S. (2022). Cell Painting predicts impact of lung cancer variants. Molecular Biology of the Cell, 33(6), ar49. PMID: 35353015 PMCID: PMC9265158. doi. pdf. (Research article)

161. Filby A, Carpenter AE. (2022). A New Image for Cell Sorting. The New England Journal of Medicine, 386(18), 1755–1758. PMID: 35507488 PMCID: PMC10367913. doi. pdf. (Review Article)

160. Al-Janabi A, Carpenter AE. (2022, May 6) Ask the Experts: The impact of artificial intelligence in drug discovery, BioTechniques. article. pdf. (Commentary Interview)

159. Chow YL, Singh S, Carpenter AE, Way GP (2022). Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. PLoS Computational Biology, 18(2), e1009888. PMID: 35213530 PMCID: PMC8906577. doi. pdf. (Research Article)

158. Bagheri N, Carpenter AE, Lundberg E, Plant AL, Horwitz R. (2022). The new era of quantitative cell imaging—challenges and opportunities. Molecular Cell. PMID: 35063094 PMCID: PMC10339817. doi. pdf. (Review article)

157. Boivin B, Roet K, Huang X, Karhohs K, Rohban M, Sandoe J, Wiskow O, Maeda R, Grantham A, Dornon M, Shao J, Frost D, Baker D, Eggan K, Carpenter AE, Woolf C. (2021). A Multiparametric Activity Profiling Platform for Neuron Disease Phenotyping and Drug Screening. Molecular Biology Cell, in press. PMID: 34910584. doi. pdf. GitHub. Raw images.  (Research article)

156. (not peer reviewed) Way GP, Spitzer H, Burnham P, Raj A, Theis F, Singh S, Carpenter AE. (2022). Image-based profiling: a powerful and challenging new data type. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27, 407–411. PMID: 34890168. doi. pdf (Conference paper)

155. Jamali N, Dobson ETA, Eliceiri KW, Carpenter AE, Cimini BA (2022). 2021 BioImage Analysis Survey: Community experiences and needs for the future. Biological Imaging, 1–28. doi. pdf. GitHub. PMCID: PMC8982832. (Research article)

154. Stirling DR, Carpenter AE, Cimini BA (2021). CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics. / doi. pdf. PMID: 34478488. (Research article)

153. Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A (2021). CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics, 22 (1), 433. / doi. pdf. GitHub. PMID: 34507520 PMCID: PMC8431850. (Research article)

152. Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, Lȇ Cao K-A, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig, EJ (2021). A field guide to cultivating computational biology. PLoS Biology, 19(10), e3001419. / doi. pdf. PMID: 34618807 PMCID: PMC8525744. (Research article)

151. Ke W, Reed JN, Yang C, Higgason N, Rayyan L, Wählby C, Carpenter AE, Civelek M, O’Rourke EJ (2021). Genes in human obesity loci are causal obesity genes in C. elegans. PLoS Genetics, 17(9), e1009736. / doi. pdf. PMID: 34492009 PMCID: PMC8462697. (Research article)

150. Wills JW, Verma JR, Rees BJ, Harte DSG, Haxhiraj Q, Barnes CM, Barnes R, Rodrigues MA, Doan M, Filby A, Hewitt RE, Thornton CA, Cronin JG, Kenny JD, Buckley R, Lynch AM, Carpenter AE, Summers HD, Johnson GE, Rees P.(2021) Inter-laboratory automation of the in vitro micronucleus assay using imaging flow cytometry and deep learning. Archives of Toxicology / doi. pdf. PMID: 34245348. PMCID: PMC8380241 (Research article)

149.  Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. (2021) Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging.Communications Biology 24:4,  786 / doi. pdf. GitHub. PMID: 34168275. PMCID: PMC8225800. (Research article)

148. Doan M, Barnes C, McQuin C, Caicedo JC, Goodman A, Carpenter AE, Rees P. (2021) Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry. Nature Protocols 16:7, 3572–3595 / doi. pdf. GitHub link 1. GitHub link 2. GitHub link 3. GitHub link 4. PMID: 34145434. PMCID: In progress. (Research article)

147.  Lundberg E, Funke J, Klemm AH, Uhlmann V, Gerlich D, Walter T, Carpenter AE, Coelho LP. (2021)Which image-based phenotypes are most promising for using AI to understand cellular functions and why?  Cell Systems 12:5, 384-387 / doi. pdf. PMID: 34015259. PMCID: Not applicable. (Feature article)

146. Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. (2021) ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Current Protocols 1:89, 789–798 / doi. pdf. PMID: 34038030. PMCID: PMC8450896. (Research article)

145. Levet F, Carpenter AE, Eliceiri KW, Kreshuk A, Bankhead P, Haase R (2021) Developing open-source software for bioimage analysis: opportunities and challenges[version 1; peer review: 2 approved]. F1000Research 10:302 / doi. pdf. PMID: 34249339 PMCID: PMC8226416 (Research article)

144. Lucas AM, Ryder PV, Li B, Cimini BA, Eliceiri KW, Carpenter AE (2021). Open-source deep-learning software for bioimage segmentation. Molecular Biology of the Cell 32:9, 823-829 / doi. pdf. PMID: 33872058 PMCID: PMC8108523 (Review article)

143. Way GP, Kost-Alimova M, Shibue T, Harrington WF, Gill S, Piccioni F, Becker T, Shafqat-Abbasi H, Hahn WC, Carpenter AE, Vazquez F, Singh S (2021). Predicting cell health phenotypes using image-based morphology profiling. Molecular Biology of the Cell 32:9, 995-1005 / doi. pdf. GitHub. IDR images. PMID: 33534641. PMCID:  PMC8108524 (Research article) 

142. Danielson E, de Arce KP, Cimini B, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M (2020). Molecular Diversity of Glutamatergic and GABAergic Synapses from Multiplexed Fluorescence Imaging. eNeuro 8(1) / doi. pdf. GitHub. PMID: 33355295. PMCID: PMC7877457 (Research article) 

141. Chandrasekaran SN, Ceulemans H, Boyd JD, Carpenter AE (2020). Image-based profiling for drug discovery: due for a machine-learning upgrade? Nature Reviews Drug Discovery 20: 145-159 / doi. pdf. PMID: 33353986. PMCID: PMC7754181  (Review article)

140. Carpenter AE (2020). A well-engineered path into cell biology and academia. Molecular Biology of the Cell 31(25): 2755–2756 / doi. pdf. PMID: 33253075. PMCID: PMC7851861 (Award essay)

139. Taga M, Petyuk VA, White C, Marsh G, Ma Y, Klein HU, Connor SM, Kroshilina A, Yung CJ, Khairallah A, Olah M, Schneider J, Karhohs K, Carpenter AE, Ransohoff R, Bennett DA, Crotti A, Bradshaw EM, De Jager PL (2020). BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology. BMC Molecular Neurodegeneration 15: 44 / doi. pdf. PMID: 32727516. PMCID: PMC7389646 (Research article) 

138. Hung J, Goodman A, Ravel D, Lopes SCP, Rangel GW, Nery OA, Malleret B, Nosten F, Lacerda MVG, Ferreira MU, Rénia L, Duraisingh MT, Costa FTM, Marti M, Carpenter AE (2020). Keras R-CNN: library for cell detection in biological images using deep neural networks. BMC Bioinformatics 21: 300 / doi. pdf. GitHub. BBBC022. BBBC041. PMID: 32652926. PMCID: PMC7353739 (Research article)

137. Vasilevich AS, Vermeulen S, Kamphuis M, Roumans N, Eroumé S, Hebels DGAJ, van de Peppel J, Reihs R, Beijer NRM, Carlier A, Carpenter AE, Singh S, de Boer J (2020). On the correlation between material-induced cell shape and phenotypical response of human mesenchymal stem cells. Scientific Reports 10: 18988 / doi. pdf. PMID: 33149200. PMCID: PMC7642380 (Research article)

136. French SL, Vijey P, Karhohs KW, Wilkie AR, Horin LJ, Ray A, Posorske B, Carpenter AE, Machlus KR, Italiano JE Jr (2020). High‐content, label‐free analysis of proplatelet production from megakaryocytes. Journal of Thrombosis and Haemostasis 18(10): 2701-2711 / doi. pdf. PMID: 32662223. PMCID: PMC7988437 (Research article)

135. Doan M, Sebastian JA, Caicedo JC, Siegert S, Roch A, Turner TR, Mykhailova O, Pinto RN, McQuin C, Goodman A, Parsons MJ, Wolkenhauer O, Hennig H, Singh S, Wilson A, Acker JP, Rees P, Kolios MC, Carpenter AE (2020). Objective assessment of stored blood quality by deep learning. PNAS 117(35): 21381-21390 / doi. pdf. GitHub link 1. GitHub link 2. GitHub link 3. PMID: 32839303. PMCID: PMC7474613 (Research article)

134. Carpenter AE (2020). Bridging Domain and Data. Patterns 1(4): 100064 / doi. pdf. PMID: 33205116. PMCID: PMC7660377  

133. Boyd J, Fennell M, Carpenter AE (2020). Harnessing the power of microscopy images to accelerate drug discovery: what are the possibilities? Expert Opinion on Drug Discovery 15(6): 639-642 / doi. pdf. PMID: 32200648. PMCID: PMC7521136 (Research article)

132. Hollandi R, Szkalisity A, Toth T, Tasnadi E, Molnar C, Mathe B, Grexa I, Molnar J, Balind A, Gorbe M, Kovacs M, Migh E, Goodman A, Balassa T, Koos K, Wang W, Caicedo JC, Bara N, Kovacs F, Paavolainen L, Danka T, Kriston A, Carpenter AE, Smith K, Horvath P (2020). nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer. Cell Systems 10:453-458 / doi. pdf. GitHub. PMCID: PMC8247631 (Research article)

131. Doan M, Case M, Masic D, Hennig H, McQuin C, Caicedo J, Singh S, Goodman A, Wolkenhauer O, Summers HD, Jamieson D, Delft FV, Filby A, Carpenter AE, Rees P, Irving J (2020). Label‐free leukemia monitoring by computer vision. Cytometry 97: 407-414 / doi. pdf. GitHub. PMID: 32091180. PMCID: PMC7213640 (Research article)

130. Troyanskaya O, Trajanoski Z, Carpenter AE, Thrun S, Razavian N, Oliver, N (2020). Artificial intelligence and cancer. Nature Cancer 1:149–152 / doi. pdf. (Review article)

129. Lee CX, Cheah JH, Soule CK, Ding H, Whittaker CA, Karhohs K, Burds AA, Subramanyam KS, Carpenter AE, Eisner BH, Cima MJ (2019). Identification and local delivery of vasodilators for the reduction of ureteral contractions. Nature Biomedical Engineering 4:28-39 / doi. pdf. PMID: 31792422. PMCID: PMC7962136 (Research article)

128. Shlevkov E, Basu H, Bray MA, Sun Z, Wei W, Apaydin K, Karhohs KW, Chen PF, Smith JLM, Wiskow O, Roet K, Huang X, Eggan K, Carpenter, AE, Kleiman RJ, Schwarz TL (2019). A High-Content Screen Identifies TPP1 and Aurora B as Regulators of Axonal Mitochondrial Transport. Cell Reports. 28(12), 3224–3237.e5 / doi. pdf. PMID: 31533043. PMCID: PMC6937139 (Research article)

127. Caicedo JC, Goodman A, Karhohs KW, Cimini BA, Ackerman J, Haghighi M, Heng C, Becker T, Doan M, McQuin C, Rohban M, Singh S, Carpenter AE (2019). Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods 16:1247-1253 / doi. pdf. PMID: 31636459. PMCID: PMC6919559 (Research article)

126. Lafarge MW, Caicedo JC, Carpenter AE, Pluim JPW, Singh S, Veta M (2019). Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. Proceedings of Machine Learning Research, pdf. GitHub. 102: 315–325. (Conference paper)

125. Caicedo JC, Roth J, Goodman A, Becker T, Karhohs KW, Broisin M, Molnar C, McQuin C, Singh S, Theis F, Carpenter AE (2019). Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images. Cytometry, 95: 952-965. doi. pdf. GitHub. PMID: 31313519. PMCID: PMC6771982 (Research article)

124. Rueden CT, Ackerman J, Arena ET, Eglinger J, Cimini BA, Goodman A, Carpenter AE, Eliceiri KW (2019). Scientific Community Image Forum: A discussion forum for scientific image software. PLoS Biology / doi. pdf. PMID: 31216269. PMCID: PMC6602289 (PLoS Biology Community page)

123. Nassar M, Doan M, Filby A, Wolkenhauer O, Fogg DK, Piasecka J, Thornton CA, Carpenter AE, Summers HD, Rees P, Hennig H (2019). Label‐Free Identification of White Blood Cells Using Machine Learning. Cytometry / doi. pdf. GitHub. PMID: 31081599. PMCID: PMC6767740 (Research article)

122. Kulikov V, Guo SM, Stone M, Goodman A, Carpenter AE, Bathe M, Lempitsky V (2019). DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. PLoS Computational Biology 15(5): e1007012 / doi. pdf. GitHub. PMID: 31083649. PMCID: PMC6533009 (Research article)

121. Rohban MH, Shafqat-Abbasi H, Singh S, Carpenter AE (2019). Capturing single-cell heterogeneity via data fusion improves image-based profiling. Nature Communications. 10, 2082 / doi. pdf. GitHub. IDR images link 1. IDR images link 2. BBBC022. PMID: 31064985. PMCID: PMC6504923 (Research article)

120. Doan M., Carpenter AE (2019). Leveraging machine vision in cell-based diagnostics to do more with less. Nature Materials 18, 414–418 / doi. pdf. PMID: 31000804 (Commentary paper)

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. pdf. GitHub. PMID: 29969450. PMCID: PMC6029841 (Research article)

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. pdf. PMID: 30003080. PMCID: PMC6031747 (Research article)

117. Caicedo JC, McQuin C, Goodman A, Singh S, & Carpenter AE (2018). Weakly Supervised Learning of Single-Cell Feature Embeddings. IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 9309–9318 / doi. pdf. GitHub. PMID: 30918435. PMCID: PMC6432648 (Conference paper)

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. pdf. GitHub. PMID: 29618526. 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). pdf. p. 965–968 / doi.  (Conference paper)

114. Goldsborough P, Pawlowski N, Caicedo JC, Singh S, Carpenter AE (2017). CytoGAN: Generative Modeling of Cell Images. Workshop on Machine Learning in Computational Biology, Neural Information Processing Systems (NeurIPS). bioRxiv. p. 227645 / doi. pdf. GitHub. (Conference paper)

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 Y, Ceulemans H (2018). Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery. Cell Chem Biol / doi. pdf. GitHub link 1. GitHub link 2. GitHub link 3. PMID: 29503208. PMCID: PMC6031326. (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. pdf. PMID: 29395345. PMCID: N/A (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. pdf. GitHub. BBBC. PMID: 29082489. PMCID: PMC6112602 (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 / doi. pdf. (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. pdf. GitHub. 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. pdf. PMID: 28858338. PMCID: PMC6871000 (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. pdf. PMID: 28535442. PMCID: N/A (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. pdf. PMID: 28505176. PMCID: PMC5444860 (Research article)

105. Rohban MH, Singh S, Wu X, Berthet JB, Bray MA, Shrestha Y, Varelas X, Boehm JS, Carpenter AE (2017). Systematic morphological profiling of human gene and allele function via Cell Painting. Elife / doi. pdf. GitHub. IDR images. PMID: 28315521. PMCID: PMC5386591 (Research article)

104. Pawlowski N, Caicedo JC, Singh S, Carpenter AE, Storkey A (2016). Automating Morphological Profiling with Generic Deep Convolutional Networks. Neural Information Processing Systems (NeurIPS) MLCB Workshop 2016 Conference / doi. pdf. GitHub. PMCID: N/A (Conference paper)

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. pdf. GitHub. PMID: 28327978. PMCID: PMC5721342 (Research article)

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. pdf. PMID: 27926723 PMCID: N/A (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. 112:201-210 / doi. pdf. 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. pdf. GitHub. PMID: 27560178. PMCID: PMC5223290. (Research article)

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. pdf. PMID: 28386206. PMCID: PMC5380232. (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. pdf. 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. pdf. 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. pdf. PMID: 27650791. PMCID: PMC6352718. (Research article)

95. Neves BJ, Dantas RF, Senger MR, Melo-Filho C, Valente W, de Almeida A, Rezende-Neto J, Lima E, Paveley R, Furnham N, Muratov E, Kamentsky L, Carpenter AE, Braga R, Silva-Jr F, Andrade C (2016). Discovery of new anti-schistosomal hits by integration of QSAR-based virtual screening and high content screening. Journal of Medicinal Chemistry 59(15):7075-88 / doi. pdf. PMID: 27119563. PMCID: PMC5844225. (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 147:50-56/ doi. pdf. 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. pdf. PMID: 27089218. PMCID: N/A. (Review article)

92. Uhlmann V, Shantanu S, Carpenter AE (2016). CP-CHARM: segmentation-free image classification made accessible. BMC Bioinformatics 17(1):51 / doi pdf. 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. Nature Communications 7:10256 / doi. pdf. PMID: 26739115. PMCID: PMC4729834. (Research article)

90. Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding MJ, 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. pdf. 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 96:6-11 / doi. pdf. 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. pdf. PMID: 26537300. PMCID: PMC4634901. (Research article)

87. Arbelle A, Drayman N, Bray MA, Alon U, Carpenter AE, Raviv-Riklin T (2015). Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics. Paper presented at MICCAI 2015 The 18th International Conference on Medical Image Computing and Computer Assisted Interventions. Lecture Notes in Computer Science (9351)218–225 / doi. pdf. PMID/PMCID: N/A. (Computational conference paper)

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): e0131370 / doi. pdf. PMID: 26197079. PMCID: PMCID4511418. (Research article)

85. Bray MA, 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. pdf. PMID: 25559103. PMCID: PMC4302752. (Research article) 

84. Metelo AM, Noonan HR, Li X, Jin Y, Kamentsky L, Baker R, Kamentsky L, Zhang Y, van Rooijen E, Shin J, Carpenter AE, Yeh JR, Peterson RT, Iliopoulos (2015). Pharmacological HIF2a inhibition improves VHL disease-associated phenotypes in zebrafish models. Journal of Clinical Investigation 125(5): 1987-97 / doi. pdf. PMID: 25866969. PMCID: PMC4463187. (Research article)

83. Gilad T, Bray M-A, Carpenter AE, Riklin Raviv T (2015). Symmetry-Based Mitosis Detection in Time-Lapse Micoscopy. Paper presented at ISBI 2015. 2015 International Symposium on Biomedical Imaging: From Nano to Macro, 164-167 / doi. pdf. April 17-20, 2015; Brooklyn Bridge, NY. (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. 19;22(2):299-307 doi. pdf. PMID: 25601075. PMCID: N/A . (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. doi. pdf. PMID: 25609200. PMCID: PMC4467109. (Research article)

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. pdf. 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(11):1177-1181 / doi. pdf. PMID: 25218182. PMCID: N/A (Research article)

78. Sheik-Khalil E, Bray M-A, Özkaya ŞG, Scarlatti G, Jansson M, Carpenter AE, Fenyö EM (2014). Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition. BMC Infectious Diseases. 14:472 / doi. pdf. PMID: 25176034. PMCID: PMC4261578 (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):3440-2/ doi. pdf. PMID: 25150250. PMCID: PMC4121832 (Research article)

76. Wawer MJ, Li J, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CS, Duvall JR, Wilson JA, Bittker JA, Dancik 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):10911-6 / doi. pdf. Images in IDR. PMID: 25024206. PMCID: PMC4121832. (Research Article)

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. pdf. PMID: 24784529. PMCID: PMC4112171 (Research article)

74. Nieland TJ, 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. pdf. 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. pdf. 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. pdf. 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. pdf. PMID: 24710339. PMCID: PMC4230961 (Review article)

Winner of 2017 SLAS Discovery Authors’ Choice Award, reflecting popularity among authors (citations) throughout 2016.

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. pdf. PMID: 24312513. PMCID: PMC3847047 (Research article)

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. pdf. 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. pdf. 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. pdf. 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. pdf. 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. pdf. 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. pdf. PMID: 23469374 (Book chapter)

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. pdf. 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. pdf. 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. pdf. 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. pdf. 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):714-6 / doi. pdf. PMID: 22522656. PMCID: PMC3433711 (Research article)

58. Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller, 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):16565–70 / doi. pdf. 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. pdf. 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. pdf. 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. pdf. 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. pdf. PMID: 2186276. 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. pdf. PMID: 24525841. PMCID: PMC3920454 (Research article)

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. pdf. PMID: 21349861. PMCID: PMC3072555 (Research article)

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. pdf. PMID: 21266779. PMCID: PMC3026724 (Research article)

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 21(3):433–446 / doi. pdf. PMID: 21239477. PMCID: PMC3044857 (Research article)

49 (not peer-reviewed). Kim K, Rowat AC, Carpenter AE (2010). Automated tracking of yeast cell lineages. Proceedings of the Society of Photo-Optical Instrumentation Engineers (SPIE) 7798, 779823/ doi. pdf. PMID: N/A (Conference paper)

48 (not peer-reviewed). Carpenter AE (2010). High-content screening: Practical advice, tools and resources. SBS News 48:5, October 2010. pdf. PMID: None (Review article)

47 (not peer-reviewed). Carpenter AE (2010). High-content screening: FAQs about trends, technologies, and outcomes. SBS News 47:2, August 2010. pdf. PMID: None (Review article)

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. pdf. PMID: 20879454. PMCID: PMC3048333 (Research article)

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. pdf. PMID: 21383863. PMCID: PMC3048333 (Research article)

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) / doi. pdf. PMID: 20566748. PMCID: PMC2913344 (Research article)

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. pdf. 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. pdf. 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, Heriche JK (2010). Visualization of image data from cells to organisms. Nature Methods 7:S26–41 / doi. pdf. PMID: 20195255. PMCID: PMC3650473 (Review article)

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. pdf. PMID: 20041172. PMCID: PMC2791844 (Tutorial)

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. pdf. PMID: 19802393. PMCID: PMC2752188 (Research article)

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. pdf. PMID: 19572548. PMCID: PMC2745594 (Research article)

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):1078–1079 / doi. pdf. PMID: 19228802 (Research article)

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):1826–1831/ doi. pdf. PMID: 19188593. PMCID: PMC2634799 (Research article)

**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. pdf. PMID: 19014601. PMCID: PMC261443 (Research article)

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  / doi. pdf. PMID: 18799457. PMCID: PMC2576541 (Research article)

33 (not peer-reviewed). Vokes MS, Carpenter AE (2008). CellProfiler: Open-source software to automatically quantify images. Microscopy Today 16(5):38–39 / doi. pdf. PMID: None (Short review)

32. Ljosa V, Carpenter AE (2008). High-throughput screens for fluorescent dye discovery. Trends in Biotechnology 26(10):527–30 / doi. pdf. PMID: 18706725 (Review)

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. / doi. pdf. PMID: 18425761 (Book chapter)

30. Carpenter AE (2007). Image-based chemical screening. Nature Chemical Biology 3:461–465 / doi. pdf. PMID: 17637778 (Review article)

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 / doi. pdf. PMID: 19347625 (Book chapter)

28 (not peer-reviewed). Jones TR and Carpenter AE (2007). Flexible image analysis. Biophotonics International, 14(7):31–32. pdf. PMID: None (Short review)

27 (not peer-reviewed). Carpenter AE (2007). Software opens the door to quantitative imaging. Nature Methods, 4(2):120–1 / doi. pdf. PMID: 17264858 (Short review article)

26. Lamprecht MR, Sabatini DM, Carpenter AE (2007). CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 42(1):71–75 / doi. pdf. PMID: 17269487 (Research article)

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. pdf. PMID: 17076895. PMCID: PMC1794559 (Research article)

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. pdf. 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. pdf. 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 / doi. pdf. PMID: 17115059 (Research article)

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. pdf. PMID: None (Research article)

Updated as a book chapter:

Jones TR, Carpenter AE, Sabatini DM, Golland P (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 / doi. pdf. PMID: 16791210 (Research article)

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(8):825–31 / doi. pdf. PMID: 16631592 (Research article)

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. pdf. PMID: 16564017 (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 / doi. pdf. PMID: 16432521 (Research article)

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 / doi. pdf. PMID: None (Research article)

15. Wheeler DB, Carpenter AE, Sabatini DM (2005). Cell microarrays and RNA interference chip away at gene function. Nature Genetics, 37 Supplement: S25–30 / doi. pdf. PMID: 15920526 (Review)

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. pdf. 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 / doi. pdf. PMID: 15831524 (Research article)

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 / doi. pdf. PMID: 15782175 (Research article)

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. pdf. 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. pdf. PMID: 15057969 (Research article)

9. Carpenter AE, Sabatini DM (2004). Systematic genome-wide screens of gene function. Nature Reviews Genetics, 5(1):11–22 / doi. pdf. PMID: 14708012 (Review)

8 (not peer-reviewed). Carpenter AE, Belmont AS (2004). Direct visualization of transcription factor-induced chromatin remodeling and cofactor recruitment in vivo. Methods in Enzymology, 375:366–81 / doi. pdf. PMID: 14870678 (A methods paper which includes substantial unpublished research)

7. Nye AC (= Carpenter AE), 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 / doi. pdf. PMID: None (Review)

6. Rajendran RR, Nye AC (= Carpenter AE), 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. pdf. PMID: 12466272 (Research article)

5. Nye AC (= Carpenter AE), 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. pdf. PMID: 11971975. PMCID: PMC133805 (Research article)

4. Ye Q, Hu YF, Zhong H, Nye AC (= Carpenter AE), 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. pdf. PMID: 11739404 PMCID: PMC2150890 (Research article)

3. Stenoien DL, Nye AC (= Carpenter AE), 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 / doi. pdf. PMID: 11390668. PMCID: PMC87100 (Research article)

2 (not peer-reviewed). Nye AC (= Carpenter AE), 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. doi. PMID: None (Movie & caption)

1 (not peer-reviewed). Belmont AS, Dietzel SD, Nye AC (= Carpenter AE), Tumbar T, Strukov Y (1999). Large scale chromatin structure and function. Current Opinion in Cell Biology, 11(3):307–311 / doi. pdf. PMID: 10395564 (Review)

Additional Carpenter lab papers before 2020 (Carpenter is not a co-author)

 

15. Garcia Ortegon M, Seal S, Singh S, Bender A, Bacallado S. (2024) Calibrated prediction of scarce adverse drug reaction labels with conditional neural processes, 2024 Workshop on Data-centric Machine Learning Research, International Conference of Machine Learning, bioRxiv,  doi: https://doi.org/10.1101/2024.06.07.598036 (Conference proceedings)

14. Wilson S L, Way G P, Bittremieux W, Armache J-P, Haendel M A, Hoffman M M (2021). Sharing biological data: why, when, and how. FEBS Letters, 595(7), 847–863. doi. pdf. PMID: 33843054 

13. Vasilevich A, Carlier A, Winkler DA, Singh S, de Boer J (2020). Evolutionary design of optimal surface topographies for biomaterials. Scientific Reports 10(1):22160 / doi. PMID: 33335124. PMCID: PMC7746696 (Research article)

12. Carey KL, Paulus GLC, Wang L, Balce DR, Luo JW, Bergman P, Ferder IC, Kong L, Renaud N, Singh S, Kost-Alimova M, Nyfeler B, Lassen KG, Virgin HW, Xavier RJ (2020). TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Reports 33(6):108371 / doi. PMID: 33176151. PMCID: PMC7686957 (Research article)

11. Ravindranathan A, Diolaiti ME, Cimini BA, Stohr BA (2019). In situ visualization of telomere length, telomere elongation, and TERT expression in single cells. Current Protocols in Cell Biology 85, e97 / doi. PMID: 31763768 (Research article)

10. Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O’Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR (2018). Genetic and transcriptional evolution alters cancer cell line drug response. Nature 560(7718):325–330 / doi. PMID: 30089904. PMCID: PMC6522222 (Research article)

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. GitHub. PMID: 29540156. PMCID: PMC5853029 (Research article)

8. Doan M (2017). Zooming in on adipocytes: High and deep. Cytometry A.;91(11):1051–1054 / doi. 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. 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. 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 SB, GoT2D Consortium, NHGRI JHS/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: 25157153. PMCID: PMC4246964 (Research article)

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

2. 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)

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