Amgad M, Sarkar A, Srinivas C, Redman R, Ratra S, Bechert CJ, Calhoun BC, Mrazeck K, Kurkure U, Cooper LA, Barnes M. Joint region and nucleus segmentation for characterization of tumor infiltrating lymphocytes in breast cancer. InMedical Imaging 2019: Digital Pathology 2019 Mar 18 (Vol. 10956, p. 109560M). International Society for Optics and Photonics.

Yousefi S, Song C, Nauata N, Cooper L. Learning genomic representations to predict clinical outcomes in cancer. International Conference on Learning Representations; 2016 May; San Juan Puerto Rico. Available online.

Mobadersany P, Cooper LA, Goldstein JA. GestAltNet: aggregation and attention to improve deep learning of gestational age from placental whole-slide images. Laboratory Investigation. 2021 Mar 5:1-0.

Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W. An expanded universe of cancer targets. Cell. 2021 Mar 4;184(5):1142-55.

Lee S, Amgad M, Mobadersany P, McCormick M, Pollack BP, Elfandy H, Hussein H, Gutman DA, Cooper LAD. Interactive classification of whole-slide imaging data for cancer researchers. Cancer Research. 2021 Feb 15;81(4):1171-7.

Mobadersany P, Yousefi S, Amgad M, Gutman DA, Barnholtz-Sloan JS, Vega JE, Brat DJ, Cooper LA. Predicting cancer outcomes from histology and genomics using convolutional networks. Proceedings of the National Academy of Sciences. 2018 Mar 27;115(13):E2970-9.

Farris AB, Vizcarra J, Amgad M, Cooper LAD, Gutman D, Hogan J. Artificial Intelligence and Algorithmic Computational Pathology: Introduction with Renal Allograft Examples. Histopathology. 2020 Nov 19.

Sakamoto T, Furukawa T, Lami K, Pham HH, Uegami W, Kuroda K, Kawai M, Sakanashi H, Cooper LA, Bychkov A, Fukuoka J. A narrative review of digital pathology and artificial intelligence: focusing on lung cancer. Translational Lung Cancer Research. 2020 Oct;9(5):2255.

Bakas S, Ormond DR, Alfaro-Munoz KD, Smits M, Cooper LA, Verhaak R, Poisson LM. iGLASS: imaging integration into the Glioma Longitudinal Analysis Consortium. Neuro-oncology. 2020 Oct;22(10):1545-6.

Hudeček J, Voorwerk L, van Seijen M, Nederlof I, de Maaker M, van den Berg J, van de Vijver KK, Sikorska K, Adams S, Demaria S, Viale G. Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials. NPJ breast cancer. 2020 May 12;6(1):1-8.

Kos Z, Roblin E, Kim RS, Michiels S, Gallas BD, Chen W, van de Vijver KK, Goel S, Adams S, Demaria S, Viale G. Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer. NPJ breast cancer. 2020 May 12;6(1):1-6.

Amgad M, Stovgaard ES, Balslev E, Thagaard J, Chen W, Dudgeon S, Sharma A, Kerner JK, Denkert C, Yuan Y, AbdulJabbar K. Report on computational assessment of tumor infiltrating lymphocytes from the International Immuno-Oncology Biomarker Working group. NPJ breast cancer. 2020 May 12;6(1):1-3.

Chandradevan R, Aljudi AA, Drumheller BR, Kunananthaseelan N, Amgad M, Gutman DA, Cooper LA, Jaye DL. Machine-based detection and classification for bone marrow aspirate differential counts: initial development focusing on nonneoplastic cells. Laboratory Investigation. 2020 Jan;100(1):98-109.

Chandrasekaran S, Sasaki M, Scharer CD, Kissick HT, Patterson DG, Magliocca KR, Seykora JT, Sapkota B, Gutman DA, Cooper LA, Lesinski GB. Phosphoinositide 3-kinase signaling can modulate MHC class I and II expression. Molecular Cancer Research. 2019 Dec 1;17(12):2395-409.

Amgad M, Elfandy H, Hussein H, Atteya LA, Elsebaie MA, Abo Elnasr LS, Sakr RA, Salem HS, Ismail AF, Saad AM, Ahmed J. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019 Sep 15;35(18):3461-7.

Gurbani SS, Sheriff S, Maudsley AA, Shim H, Cooper LA. Incorporation of a spectral model in a convolutional neural network for accelerated spectral fitting. Magnetic resonance in medicine. 2019 May;81(5):3346-57.

Khosravi P, Kazemi E, Zhan Q, Malmsten JE, Toschi M, Zisimopoulos P, Sigaras A, Lavery S, Cooper LA, Hickman C, Meseguer M. Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization. NPJ digital medicine. 2019 Apr 4;2(1):1-9.

Gurbani S, Weinberg B, Cooper L, Mellon E, Schreibmann E, Sheriff S, Maudsley A, Goryawala M, Shu HK, Shim H. The Brain Imaging Collaboration Suite (BrICS): a cloud platform for integrating whole-brain spectroscopic MRI into the radiation therapy planning workflow. Tomography. 2019 Mar;5(1):184.

Halani SH, Yousefi S, Vega JV, Rossi MR, Zhao Z, Amrollahi F, Holder CA, Baxter-Stoltzfus A, Eschbacher J, Griffith B, Olson JJ. Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways. NPJ precision oncology. 2018 Nov 6;2(1):1-9.

Gurbani SS, Schreibmann E, Maudsley AA, Cordova JS, Soher BJ, Poptani H, Verma G, Barker PB, Shim H, Cooper LA. A convolutional neural network to filter artifacts in spectroscopic MRI. Magnetic resonance in medicine. 2018 Nov;80(5):1765-75.

Hou Y, Konen J, Brat DJ, Marcus AI, Cooper LA. TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics. Scientific reports. 2018 May 8;8(1):1-9.

Chittajallu DR, Siekierski N, Lee S, Gerber S, Beezley J, Manthey D, Gutman D, Cooper LAD. Vectorized persistent homology representations for characterizing glandular architecture in histology images. In 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) 2018 Apr 4 (pp. 232-235).

Cooper LAD, Sertel O, Kong J, Lozanski G, Huang K, Gurcan M. Feature-based registration of histopathology images with different stains: An application for computerized follicular lymphoma prognosis. Computer methods and programs in biomedicine. 2009 Dec 1;96(3):182-92.

Ruiz A, Ujaldon M, Cooper L, Huang K. Non-rigid registration for large sets of microscopic images on graphics processors. Journal of signal processing systems. 2009 Apr;55(1):229-50.

Mosaliganti K, Cooper LAD, Sharp R, Machiraju R, Leone G, Huang K, Saltz J. Reconstruction of cellular biological structures from optical microscopy data. IEEE Transactions on Visualization and Computer Graphics. 2008 Feb 2;14(4):863-76.

Cooper LA, Kong J, Gutman DA, Wang F, Cholleti SR, Pan TC, Widener PM, Sharma A, Mikkelsen T, Flanders AE, Rubin DL, Van Meir E, Kurc T, Moreno CS, Brat DJ, Saltz JH. An integrative approach for in silico glioma research. IEEE Transactions on Biomedical Engineering. 2010 Jul 23;57(10):2617-21.

Cooper LAD, Gutman DA, Long Q, Johnson BA, Cholleti SR, Kurc T, Saltz JH, Brat DJ, Moreno CS. The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas. PloS one. 2010 Sep 3;5(9):e12548.

Cork SM, Kaur B, Devi NS, Cooper LAD, Saltz JH, Sandberg EM, Kaluz S, Van Meir EG. A proprotein convertase/MMP-14 proteolytic cascade releases a novel 40 kDa vasculostatin from tumor suppressor BAI1. Oncogene. 2012 Dec;31(50):5144-52.

Cooper LA, Kong J, Gutman DA, Wang F, Gao J, Appin C, Cholleti S, Pan T, Sharma A, Scarpace L, Mikkelsen T, Kurc T, Moreno CS, Brat DJ, Saltz JH. Integrated morphologic analysis for the identification and characterization of disease subtypes. Journal of the American Medical Informatics Association. 2012 Mar 1;19(2):317-23.

Cooper LAD, Carter AB, Farris AB, Wang F, Kong J, Gutman DA, Widener P, Pan TC, Cholleti SR, Sharma A, Kurc TM, Brat DJ, Saltz JH. Digital pathology: Data-intensive frontier in medical imaging. Proceedings of the IEEE. 2012 Feb 17;100(4):991-1003.

Cooper LA, Gutman DA, Chisolm C, Appin C, Kong J, Rong Y, Kurc T, Van Meir EG, Saltz JH, Moreno CS, Brat DJ. The tumor microenvironment strongly impacts master transcriptional regulators and gene expression class of glioblastoma. The American journal of pathology. 2012 May 1;180(5):2108-19.

Teodoro G, Pan T, Kurc TM, Kong J, Cooper LAD, Saltz JH. Efficient irregular wavefront propagation algorithms on hybrid CPU–GPU machines. Parallel computing. 2013 Apr 1;39(4-5):189-211.

Gutman DA, Cooper LA, Hwang SN, Holder CA, Gao J, Aurora TD, Dunn Jr WD, Scarpace L, Mikkelsen T, Jain R, Wintermark M, Jilwan M, Raghavan P, Huang E, Clifford RJ, Mongkolwat P, Kleper V, Freymann J, Kirby J, Zinn PO, Moreno CS, Jaffe C, Colen R, Rubin DL, Saltz JH, Flanders A, Brat DJ. MR imaging predictors of molecular profile and survival: multi-institutional study of the TCGA glioblastoma data set. Radiology. 2013 May;267(2):560-9.

Rutledge WC, Kong J, Gao J, Gutman DA, Cooper LA, Appin C, Park Y, Scarpace L, Mikkelsen T, Cohen ML, Aldape KD, McLendon RE, Lehman NL, Miller CR, Schniederjan MJ, Brennan CW, Saltz JH, Moreno CS, Brat DJ. Tumor-infiltrating lymphocytes in glioblastoma are associated with specific genomic alterations and related to transcriptional class. Clinical Cancer Research. 2013 Sep 15;19(18):4951-60.

Gutman DA, Cobb J, Somanna D, Park Y, Wang F, Kurc T, Saltz JH, Brat DJ, Cooper LA, Kong J. Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data. Journal of the American Medical Informatics Association. 2013 Nov 1;20(6):1091-8.

Kong J, Cooper LA, Wang F, Gao J, Teodoro G, Scarpace L, Mikkelsen T, Schniederjan MJ, Moreno CS, Saltz JH, Brat DJ. Machine-based morphologic analysis of glioblastoma using whole-slide pathology images uncovers clinically relevant molecular correlates. PloS one. 2013 Nov 13;8(11):e81049.

Cooper LA, Kong J, Gutman DA, Dunn WD, Nalisnik M, Brat DJ. Novel genotype-phenotype associations in human cancers enabled by advanced molecular platforms and computational analysis of whole slide images. Laboratory investigation. 2015 Apr;95(4):366-76.

Cancer Genome Atlas Research Network. Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. New England Journal of Medicine. 2015 Jun 25;372(26):2481-98.

Gutman DA, Dunn WD, Grossmann P, Cooper LA, Holder CA, Ligon KL, Alexander BM, Aerts HJ. Somatic mutations associated with MRI-derived volumetric features in glioblastoma. Neuroradiology. 2015 Dec;57(12):1227-37.

Kurc T, Qi X, Wang D, Wang F, Teodoro G, Cooper L, Nalisnik M, Yang L, Saltz J, Foran DJ. Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies. BMC bioinformatics. 2015 Dec;16(1):1-21.

Hinrichs BH, Newman S, Appin CL, Dunn W, Cooper L, Pauly R, Kowalski J, Rossi MR, Brat DJ. Farewell to GBM-O: Genomic and transcriptomic profiling of glioblastoma with oligodendroglioma component reveals distinct molecular subgroups. Acta neuropathologica communications. 2016 Dec;4(1):1-9.

M Ceccarelli, FP Barthel, TM Malta, TS Sabedot, SR Salama, SM Pagnotta, BA Murray, O Mo- rozova, Y Newton, J Wang, DJ Brat, P Zoppoli, R Akbani, AD Cherniack, H Zhang, L Posson, T Mikelsen, WKA Yung, J Huse, CC Lau, A Rao, M Grifford, M Wrensch, R Beroukhim, LAD Cooper, R Rabadan, KD Aldape, PW Laird, DH Gutmann, H Noushmehr, A Iavarone, RGW Verhaak, The Cancer Genome Atlas Research Network, Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell. 2016 Jan 28;164(3):550-63.

Cordova JS, Shu HK, Liang Z, Gurbani SS, Cooper LA, Holder CA, Olson JJ, Kairdolf B, Schreibmann E, Neill SG, Hadjipanayis CG. Whole-brain spectroscopic MRI biomarkers identify infiltrating margins in glioblastoma patients. Neuro-oncology. 2016 Aug 1;18(8):1180-9.

Huang K, Liu Y, Huang Y, Li L, Cooper L, Ruan J, Zhao Z. Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. 2016 Aug 22;524(17).

Kersh AE, Sasaki M, Cooper LA, Kissick HT, Pollack BP. Understanding the impact of ErbB activating events and signal transduction on antigen processing and presentation: MHC expression as a model. Frontiers in pharmacology. 2016 Sep 26;7:327.

Mo X, Qi Q, Ivanov AA, Niu Q, Luo Y, Havel J, Goetze R, Bell S, Moreno CS, Cooper LA, Johns MA, Khuri FR, Du Y, Fu H. AKT1, LKB1, and YAP1 revealed as MYC interactors with NanoLuc-based protein-fragment complementation assay. Molecular pharmacology. 2017 Apr 1;91(4):339-47.

Li Z, Ivanov AA, Su R, Gonzalez-Pecchi V, Qi Q, Liu S, Webber P, McMillan E, Rusnak L, Pham C, Chen X. The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies. Nature communications. 2017 Feb 16;8(1):1-4.

Wilkinson S, Hou Y, Zoine JT, Saltz J, Zhang C, Chen Z, Cooper LA, Marcus AI. Coordinated cell motility is regulated by a combination of LKB1 farnesylation and kinase activity. Scientific reports. 2017 Jan 19;7(1):1-6.

Harati S, Cooper LA, Moran JD, Giuste FO, Du Y, Ivanov AA, Johns MA, Khuri FR, Fu H, Moreno CS. MEDICI: mining essentiality data to identify critical interactions for cancer drug target discovery and development. PloS one. 2017 Jan 24;12(1):e0170339.

Yousefi S, Amrollahi F, Amgad M, Dong C, Lewis JE, Song C, Gutman DA, Halani SH, Vega JE, Brat DJ, Cooper LA. Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models. Scientific reports. 2017 Sep 15;7(1):1-1.

Patel SH, Poisson LM, Brat DJ, Zhou Y, Cooper L, Snuderl M, Thomas C, Franceschi AM, Griffith B, Flanders AE, Golfinos JG. T2–FLAIR mismatch, an imaging biomarker for IDH and 1p/19q status in lower-grade gliomas: a TCGA/TCIA project. Clinical cancer research. 2017 Oct 15;23(20):6078-85.

Ross JL, Cooper LA, Kong J, Gutman D, Williams M, Tucker-Burden C, McCrary MR, Bouras A, Kaluzova M, Dunn WD, Duong D. 5-Aminolevulinic acid guided sampling of glioblastoma microenvironments identifies pro-survival signaling at infiltrative margins. Scientific reports. 2017 Nov 15;7(1):1-1.

Gutman DA, Khalilia M, Lee S, Nalisnik M, Mullen Z, Beezley J, Chittajallu DR, Manthey D, Cooper LA. The digital slide archive: A software platform for management, integration, and analysis of histology for cancer research. Cancer research. 2017 Nov 1;77(21):e75-8.

Lazar AJ, McLellan MD, Bailey MH, Miller CA, Appelbaum EL, Cordes MG, Fronick CC, Fulton LA, Fulton RS, Mardis ER, Schmidt HK. Comprehensive and integrated genomic characterization of adult soft tissue sarcomas. Cell. 2017 Nov 2;171(4):950-65.

Nalisnik M, Amgad M, Lee S, Halani SH, Vega JE, Brat DJ, Gutman DA, Cooper LA. Interactive phenotyping of large-scale histology imaging data with HistomicsML. Scientific reports. 2017 Nov 6;7(1):1-2.

Ivanov AA, Revennaugh B, Rusnak L, Gonzalez-Pecchi V, Mo X, Johns MA, Du Y, Cooper LA, Moreno CS, Khuri FR, Fu H. The OncoPPi Portal: an integrative resource to explore and prioritize protein–protein interactions for cancer target discovery. Bioinformatics. 2018 Apr 1;34(7):1183-91.

Jordan J, Goldstein JS, Jaye DL, Gurcan M, Flowers CR, Cooper LA. Informatics approaches to address new challenges in the classification of lymphoid malignancies. JCO clinical cancer informatics. 2018 Feb;2:1-9.

Cooper LA, Demicco EG, Saltz JH, Powell RT, Rao A, Lazar AJ. PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective. The Journal of pathology (Annual Review Issue). 2018 Apr;244(5):512-24.