Full Text Journal Articles by
Author Joe W Gray

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Oligonucleotide conjugated antibodies permit highly multiplexed immunofluorescence for future use in clinical histopathology.

Nathan P McMahon, Jocelyn A Jones, Sunjong Kwon, Koei Chin, Michel A Nederlof, Joe W Gray, Summer L Gibbs,

SIGNIFICANCE:Advanced genetic characterization has informed cancer heterogeneity and the challenge it poses to effective therapy; however, current methods lack spatial context, which is vital to successful cancer therapy. Conventional immunolabeling, commonplace in the clinic, can provide spatial context to protein expression. However, these techniques are spectrally limited, resulting in inadequate ... Read more >>

J Biomed Opt (Journal of biomedical optics)
[2020, 25(5):1-18]

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How Machine Learning Will Transform Biomedicine.

Jeremy Goecks, Vahid Jalili, Laura M Heiser, Joe W Gray,

This Perspective explores the application of machine learning toward improved diagnosis and treatment. We outline a vision for how machine learning can transform three broad areas of biomedicine: clinical diagnostics, precision treatments, and health monitoring, where the goal is to maintain health through a range of diseases and the normal ... Read more >>

Cell (Cell)
[2020, 181(1):92-101]

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The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E Rood, Orr Ashenberg, Ethan Cerami, Robert J Coffey, Emek Demir, Li Ding, Edward D Esplin, James M Ford, Jeremy Goecks, Sharmistha Ghosh, Joe W Gray, Justin Guinney, Sean E Hanlon, Shannon K Hughes, E Shelley Hwang, Christine A Iacobuzio-Donahue, Judit Jané-Valbuena, Bruce E Johnson, Ken S Lau, Tracy Lively, Sarah A Mazzilli, Dana Pe'er, Sandro Santagata, Alex K Shalek, Denis Schapiro, Michael P Snyder, Peter K Sorger, Avrum E Spira, Sudhir Srivastava, Kai Tan, Robert B West, Elizabeth H Williams, ,

Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of ... Read more >>

Cell (Cell)
[2020, 181(2):236-249]

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A workflow for visualizing human cancer biopsies using large-format electron microscopy.

Jessica L Riesterer, Claudia S López, Erin S Stempinski, Melissa Williams, Kevin Loftis, Kevin Stoltz, Guillaume Thibault, Christian Lanicault, Todd Williams, Joe W Gray,

Recent developments in large format electron microscopy have enabled generation of images that provide detailed ultrastructural information on normal and diseased cells and tissues. Analyses of these images increase our understanding of cellular organization and interactions and disease-related changes therein. In this manuscript, we describe a workflow for two-dimensional (2D) ... Read more >>

Methods Cell Biol. (Methods in cell biology)
[2020, 158:163-181]

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RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging.

Young Hwan Chang, Koei Chin, Guillaume Thibault, Jennifer Eng, Erik Burlingame, Joe W Gray,

Recent advances in multiplexed imaging technologies promise to improve the understanding of the functional states of individual cells and the interactions between the cells in tissues. This often requires compilation of results from multiple samples. However, quantitative integration of information between samples is complicated by variations in staining intensity and ... Read more >>

Commun Biol (Communications biology)
[2020, 3(1):111]

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Fluorescent Imaging for In Situ Measurement of Drug Target Engagement and Cell Signaling Pathways.

Nathan P McMahon, Allison Solanki, Jocelyn Jones, Sunjong Kwon, Young-Hwan Chang, Koei Chin, Michel A Nederlof, Joe W Gray, Summer L Gibbs,

Successful cancer treatment continues to elude modern medicine and its arsenal of therapeutic strategies. Therapy resistance is driven by significant tumor heterogeneity, complex interactions between malignant, microenvironmental and immune cells and cross talk between signaling pathways. Advances in molecular characterization technologies such as next generation sequencing have helped unravel this ... Read more >>

Proc SPIE Int Soc Opt Eng (Proceedings of SPIE--the International Society for Optical Engineering)
[2020, 11219:]

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Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis.

Jennifer Eng, Guillaume Thibault, Shiuh-Wen Luoh, Joe W Gray, Young Hwan Chang, Koei Chin,

Immunotherapy harnesses the power of the adaptive immune system and has revolutionized the field of oncotherapy, as novel therapeutic strategies have been introduced into clinical use. The development of immune checkpoint inhibitors has led to durable control of disease in a subset of advanced cancer patients, such as those with ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2020, 2055:521-562]

Cited: 1 time

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Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop.

Mark E Lowe, Dana K Andersen, Richard M Caprioli, Jyoti Choudhary, Zobeida Cruz-Monserrate, Anil K Dasyam, Christopher E Forsmark, Fred S Gorelick, Joe W Gray, Mark Haupt, Kimberly A Kelly, Kenneth P Olive, Sylvia K Plevritis, Noa Rappaport, Holger R Roth, Hanno Steen, S Joshua Swamidass, Temel Tirkes, Aliye Uc, Kirill Veselkov, David C Whitcomb, Aida Habtezion,

A workshop on research gaps and opportunities for Precision Medicine in Pancreatic Disease was sponsored by the National Institute of Diabetes and Digestive Kidney Diseases on July 24, 2019, in Pittsburgh. The workshop included an overview lecture on precision medicine in cancer and 4 sessions: (1) general considerations for the ... Read more >>

Pancreas (Pancreas)
[2019, 48(10):1250-1258]

Cited: 1 time

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PLK1 and EGFR targeted nanoparticle as a radiation sensitizer for non-small cell lung cancer.

Moataz Reda, Worapol Ngamcherdtrakul, Shenda Gu, Daniel S Bejan, Natnaree Siriwon, Joe W Gray, Wassana Yantasee,

Radiation sensitizers that can selectively act on cancer cells hold great promise to patients who receive radiation therapy. We developed a novel targeted therapy and radiation sensitizer for non-small cell lung cancer (NSCLC) based on cetuximab conjugated nanoparticle that targets epidermal growth factor receptor (EGFR) and delivers small interfering RNA ... Read more >>

Cancer Lett. (Cancer letters)
[2019, 467:9-18]

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Targeting the Mevalonate Pathway to Overcome Acquired Anti-HER2 Treatment Resistance in Breast Cancer.

Vidyalakshmi Sethunath, Huizhong Hu, Carmine De Angelis, Jamunarani Veeraraghavan, Lanfang Qin, Nicholas Wang, Lukas M Simon, Tao Wang, Xiaoyong Fu, Agostina Nardone, Resel Pereira, Sarmistha Nanda, Obi L Griffith, Anna Tsimelzon, Chad Shaw, Gary C Chamness, Jorge S Reis-Filho, Britta Weigelt, Laura M Heiser, Susan G Hilsenbeck, Shixia Huang, Mothaffar F Rimawi, Joe W Gray, C Kent Osborne, Rachel Schiff,

Despite effective strategies, resistance in HER2+ breast cancer remains a challenge. While the mevalonate pathway (MVA) is suggested to promote cell growth and survival, including in HER2+ models, its potential role in resistance to HER2-targeted therapy is unknown. Parental HER2+ breast cancer cells and their lapatinib-resistant and lapatinib + trastuzumab-resistant ... Read more >>

Mol. Cancer Res. (Molecular cancer research : MCR)
[2019, 17(11):2318-2330]

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A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines.

Mario Niepel, Marc Hafner, Caitlin E Mills, Kartik Subramanian, Elizabeth H Williams, Mirra Chung, Benjamin Gaudio, Anne Marie Barrette, Alan D Stern, Bin Hu, James E Korkola, , Joe W Gray, Marc R Birtwistle, Laura M Heiser, Peter K Sorger,

Evidence that some high-impact biomedical results cannot be repeated has stimulated interest in practices that generate findable, accessible, interoperable, and reusable (FAIR) data. Multiple papers have identified specific examples of irreproducibility, but practical ways to make data more reproducible have not been widely studied. Here, five research centers in the ... Read more >>

Cell Syst (Cell systems)
[2019, 9(1):35-48.e5]

Cited: 2 times

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Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer.

Rebecca Smith, Kaylyn Devlin, David Kilburn, Sean Gross, Damir Sudar, Elmar Bucher, Michel Nederlof, Mark Dane, Joe W Gray, Laura Heiser, James E Korkola,

Understanding the impact of the microenvironment on the phenotype of cells is a difficult problem due to the complex mixture of both soluble growth factors and matrix-associated proteins in the microenvironment in vivo. Furthermore, readily available reagents for the modeling of microenvironments in vitro typically utilize complex mixtures of proteins ... Read more >>

J Vis Exp (Journal of visualized experiments : JoVE)
[2019, (147):]

Cited: 1 time

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Variational Autoencoding Tissue Response to Microenvironment Perturbation.

Geoffrey F Schau, Guillaume Thibault, Mark A Dane, Joe W Gray, Laura M Heiser, Young Hwan Chang,

This work applies deep variational autoencoder learning architecture to study multi-cellular growth characteristics of human mammary epithelial cells in response to diverse microenvironment perturbations. Our approach introduces a novel method of visualizing learned feature spaces of trained variational autoencoding models that enables visualization of principal features in two dimensions. We ... Read more >>

Proc SPIE Int Soc Opt Eng (Proceedings of SPIE--the International Society for Optical Engineering)
[2019, 10949:]

Cited: 0 times

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Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers.

Laura M Heiser, Gordon B Mills, Joe W Gray,

In this issue of Cancer Cell, Jiang et al. report a genomic and transcriptional analysis of triple negative breast cancers (TNBCs) from an East Asian population. Their study shows minor differences with published studies of European and North American populations and suggests a therapeutic decision tree for treatment of TNBC. ... Read more >>

Cancer Cell (Cancer cell)
[2019, 35(3):341-343]

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Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting.

Ellen M Langer, Brittany L Allen-Petersen, Shelby M King, Nicholas D Kendsersky, Megan A Turnidge, Genevra M Kuziel, Rachelle Riggers, Ravi Samatham, Taylor S Amery, Steven L Jacques, Brett C Sheppard, James E Korkola, John L Muschler, Guillaume Thibault, Young Hwan Chang, Joe W Gray, Sharon C Presnell, Deborah G Nguyen, Rosalie C Sears,

The tumor microenvironment plays a critical role in tumor growth, progression, and therapeutic resistance, but interrogating the role of specific tumor-stromal interactions on tumorigenic phenotypes is challenging within in vivo tissues. Here, we tested whether three-dimensional (3D) bioprinting could improve in vitro models by incorporating multiple cell types into scaffold-free tumor tissues ... Read more >>

Cell Rep (Cell reports)
[2019, 26(3):608-623.e6]

Cited: 4 times

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Implementing a comprehensive translational oncology platform: from molecular testing to actionability.

Zahi I Mitri, Swapnil Parmar, Brett Johnson, Annette Kolodzie, Jamie M Keck, Max Morris, Alexander R Guimaraes, Brooke R Beckett, Uma Borate, Charles D Lopez, Kathleen A Kemmer, Joshi J Alumkal, Tomasz M Beer, Christopher L Corless, Gordon B Mills, Joe W Gray, Raymond C Bergan,

BACKGROUND:In order to establish the workflows required to implement a real-time process involving multi-omic analysis of patient samples to support precision-guided therapeutic intervention, a tissue acquisition and analysis trial was implemented. This report describes our findings to date, including the frequency with which mutational testing led to precision-guided therapy and ... Read more >>

J Transl Med (Journal of translational medicine)
[2018, 16(1):358]

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Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution.

Jeffrey B Cheng, Andrew J Sedgewick, Alex I Finnegan, Paymann Harirchian, Jerry Lee, Sunjong Kwon, Marlys S Fassett, Justin Golovato, Matthew Gray, Ruby Ghadially, Wilson Liao, Bethany E Perez White, Theodora M Mauro, Thaddeus Mully, Esther A Kim, Hani Sbitany, Isaac M Neuhaus, Roy C Grekin, Siegrid S Yu, Joe W Gray, Elizabeth Purdom, Ralf Paus, Charles J Vaske, Stephen C Benz, Jun S Song, Raymond J Cho,

Perturbations in the transcriptional programs specifying epidermal differentiation cause diverse skin pathologies ranging from impaired barrier function to inflammatory skin disease. However, the global scope and organization of this complex cellular program remain undefined. Here we report single-cell RNA sequencing profiles of 92,889 human epidermal cells from 9 normal and ... Read more >>

Cell Rep (Cell reports)
[2018, 25(4):871-883]

Cited: 4 times

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Lack of acquired resistance in HER2-positive breast cancer cells after long-term HER2 siRNA nanoparticle treatment.

Shenda Gu, Worapol Ngamcherdtrakul, Moataz Reda, Zhi Hu, Joe W Gray, Wassana Yantasee,

Intrinsic and acquired resistance to current HER2 targeted therapies remains a challenge in clinics. We have developed a therapeutic HER2 siRNA delivered using mesoporous silica nanoparticles modified with polymers and conjugated with HER2 targeting antibodies. Our previous studies have shown that our HER2 siRNA nanoparticles could overcome intrinsic and acquired ... Read more >>

PLoS ONE (PloS one)
[2018, 13(6):e0198141]

Cited: 3 times

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CCR5 Governs DNA Damage Repair and Breast Cancer Stem Cell Expansion.

Xuanmao Jiao, Marco A Velasco-Velázquez, Min Wang, Zhiping Li, Hallgeir Rui, Amy R Peck, James E Korkola, Xuelian Chen, Shaohua Xu, James B DuHadaway, Sandra Guerrero-Rodriguez, Sankar Addya, Daniela Sicoli, Zhaomei Mu, Gang Zhang, Andres Stucky, Xi Zhang, Massimo Cristofanilli, Alessandro Fatatis, Joe W Gray, Jiang F Zhong, George C Prendergast, Richard G Pestell,

The functional significance of the chemokine receptor CCR5 in human breast cancer epithelial cells is poorly understood. Here, we report that CCR5 expression in human breast cancer correlates with poor outcome. CCR5+ breast cancer epithelial cells formed mammospheres and initiated tumors with >60-fold greater efficiency in mice. Reintroduction of CCR5 ... Read more >>

Cancer Res. (Cancer research)
[2018, 78(7):1657-1671]

Cited: 10 times

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Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Samuel W Brady, Jasmine A McQuerry, Yi Qiao, Stephen R Piccolo, Gajendra Shrestha, David F Jenkins, Ryan M Layer, Brent S Pedersen, Ryan H Miller, Amanda Esch, Sara R Selitsky, Joel S Parker, Layla A Anderson, Brian K Dalley, Rachel E Factor, Chakravarthy B Reddy, Jonathan P Boltax, Dean Y Li, Philip J Moos, Joe W Gray, Laura M Heiser, Saundra S Buys, Adam L Cohen, W Evan Johnson, Aaron R Quinlan, Gabor Marth, Theresa L Werner, Andrea H Bild,

The originally published version of this Article contained an error in Figure 4. In panel a, grey boxes surrounding the subclones associated with patients #2 and #4 obscured adjacent portions of the heatmap. This error has now been corrected in both the PDF and HTML versions of the Article. ... Read more >>

Nat Commun (Nature communications)
[2018, 9(1):572]

Cited: 0 times

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SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks.

Erik A Burlingame, Adam A Margolin, Joe W Gray, Young Hwan Chang,

Multiplexed imaging such as multicolor immunofluorescence staining, multiplexed immunohistochemistry (mIHC) or cyclic immunofluorescence (cycIF) enables deep assessment of cellular complexity in situ and, in conjunction with standard histology stains like hematoxylin and eosin (H&E), can help to unravel the complex molecular relationships and spatial interdependencies that undergird disease states. However, ... Read more >>

Proc SPIE Int Soc Opt Eng (Proceedings of SPIE--the International Society for Optical Engineering)
[2018, 10581:]

Cited: 0 times

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The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Alexandra B Keenan, Sherry L Jenkins, Kathleen M Jagodnik, Simon Koplev, Edward He, Denis Torre, Zichen Wang, Anders B Dohlman, Moshe C Silverstein, Alexander Lachmann, Maxim V Kuleshov, Avi Ma'ayan, Vasileios Stathias, Raymond Terryn, Daniel Cooper, Michele Forlin, Amar Koleti, Dusica Vidovic, Caty Chung, Stephan C Schürer, Jouzas Vasiliauskas, Marcin Pilarczyk, Behrouz Shamsaei, Mehdi Fazel, Yan Ren, Wen Niu, Nicholas A Clark, Shana White, Naim Mahi, Lixia Zhang, Michal Kouril, John F Reichard, Siva Sivaganesan, Mario Medvedovic, Jaroslaw Meller, Rick J Koch, Marc R Birtwistle, Ravi Iyengar, Eric A Sobie, Evren U Azeloglu, Julia Kaye, Jeannette Osterloh, Kelly Haston, Jaslin Kalra, Steve Finkbiener, Jonathan Li, Pamela Milani, Miriam Adam, Renan Escalante-Chong, Karen Sachs, Alex Lenail, Divya Ramamoorthy, Ernest Fraenkel, Gavin Daigle, Uzma Hussain, Alyssa Coye, Jeffrey Rothstein, Dhruv Sareen, Loren Ornelas, Maria Banuelos, Berhan Mandefro, Ritchie Ho, Clive N Svendsen, Ryan G Lim, Jennifer Stocksdale, Malcolm S Casale, Terri G Thompson, Jie Wu, Leslie M Thompson, Victoria Dardov, Vidya Venkatraman, Andrea Matlock, Jennifer E Van Eyk, Jacob D Jaffe, Malvina Papanastasiou, Aravind Subramanian, Todd R Golub, Sean D Erickson, Mohammad Fallahi-Sichani, Marc Hafner, Nathanael S Gray, Jia-Ren Lin, Caitlin E Mills, Jeremy L Muhlich, Mario Niepel, Caroline E Shamu, Elizabeth H Williams, David Wrobel, Peter K Sorger, Laura M Heiser, Joe W Gray, James E Korkola, Gordon B Mills, Mark LaBarge, Heidi S Feiler, Mark A Dane, Elmar Bucher, Michel Nederlof, Damir Sudar, Sean Gross, David F Kilburn, Rebecca Smith, Kaylyn Devlin, Ron Margolis, Leslie Derr, Albert Lee, Ajay Pillai,

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of ... Read more >>

Cell Syst (Cell systems)
[2018, 6(1):13-24]

Cited: 43 times

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Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics.

Marc Hafner, Laura M Heiser, Elizabeth H Williams, Mario Niepel, Nicholas J Wang, James E Korkola, Joe W Gray, Peter K Sorger,

Traditional means for scoring the effects of anti-cancer drugs on the growth and survival of cell lines is based on relative cell number in drug-treated and control samples and is seriously confounded by unequal division rates arising from natural biological variation and differences in culture conditions. This problem can be ... Read more >>

Sci Data (Scientific data)
[2017, 4:170166]

Cited: 4 times

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Combating subclonal evolution of resistant cancer phenotypes.

Samuel W Brady, Jasmine A McQuerry, Yi Qiao, Stephen R Piccolo, Gajendra Shrestha, David F Jenkins, Ryan M Layer, Brent S Pedersen, Ryan H Miller, Amanda Esch, Sara R Selitsky, Joel S Parker, Layla A Anderson, Brian K Dalley, Rachel E Factor, Chakravarthy B Reddy, Jonathan P Boltax, Dean Y Li, Philip J Moos, Joe W Gray, Laura M Heiser, Saundra S Buys, Adam L Cohen, W Evan Johnson, Aaron R Quinlan, Gabor Marth, Theresa L Werner, Andrea H Bild,

Metastatic breast cancer remains challenging to treat, and most patients ultimately progress on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations (subclones) within heterogeneous tumors. Here, we track the genetic and phenotypic subclonal evolution of four breast cancers through years of treatment to better understand how breast ... Read more >>

Nat Commun (Nature communications)
[2017, 8(1):1231]

Cited: 11 times

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Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

James E Korkola, Eric A Collisson, Laura M Heiser, Chris Oates, Nora Bayani, Sleiman Itani, Amanda Esch, Wallace Thompson, Obi L Griffith, Nicholas J Wang, Wen-Lin Kuo, Brian Cooper, Jessica Billig, Safiyyah Ziyad, Jenny L Hung, Lakshmi Jakkula, Heidi Feiler, Yiling Lu, Gordon B Mills, Paul T Spellman, Claire Tomlin, Sach Mukherjee, Joe W Gray,

[This corrects the article DOI: 10.1371/journal.pone.0133219.]. ... Read more >>

PLoS ONE (PloS one)
[2017, 12(10):e0186551]

Cited: 0 times

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