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Neural population control via deep image synthesis.

Bashivan P, Kar K, DiCarlo JJ.

Science. 2019 May 3;364(6439). pii: eaav9436. doi: 10.1126/science.aav9436.


Evidence that recurrent circuits are critical to the ventral stream's execution of core object recognition behavior.

Kar K, Kubilius J, Schmidt K, Issa EB, DiCarlo JJ.

Nat Neurosci. 2019 Jun;22(6):974-983. doi: 10.1038/s41593-019-0392-5. Epub 2019 Apr 29.


Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI.

Peng Q, Xu C, Kim D, Lewis M, DiCarlo J, Wang Y.

Sci Rep. 2019 Mar 18;9(1):4810. doi: 10.1038/s41598-019-41215-z.


Reversible Inactivation of Different Millimeter-Scale Regions of Primate IT Results in Different Patterns of Core Object Recognition Deficits.

Rajalingham R, DiCarlo JJ.

Neuron. 2019 Apr 17;102(2):493-505.e5. doi: 10.1016/j.neuron.2019.02.001. Epub 2019 Mar 13.


MRI and Dose Selection in a Phase II Trial of Baricitinib with Conventional Synthetic Disease-modifying Antirheumatic Drugs in Rheumatoid Arthritis.

Peterfy C, DiCarlo J, Emery P, Genovese MC, Keystone EC, Taylor PC, Schlichting DE, Beattie SD, Luchi M, Macias W.

J Rheumatol. 2019 Jan 15. pii: jrheum.171469. doi: 10.3899/jrheum.171469. [Epub ahead of print]


Neural dynamics at successive stages of the ventral visual stream are consistent with hierarchical error signals.

Issa EB, Cadieu CF, DiCarlo JJ.

Elife. 2018 Nov 28;7. pii: e42870. doi: 10.7554/eLife.42870.


Renal Replacement Therapy Modalities in Critically Ill Children.

Beltramo F, DiCarlo J, Gruber JB, Taylor T, Totapally BR.

Pediatr Crit Care Med. 2019 Jan;20(1):e1-e9. doi: 10.1097/PCC.0000000000001754.


Deep learning reaches the motor system.

Batista AP, DiCarlo JJ.

Nat Methods. 2018 Oct;15(10):772-773. doi: 10.1038/s41592-018-0152-6. No abstract available.


smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.

Xu C, Gu X, Padmanabhan R, Wu Z, Peng Q, DiCarlo J, Wang Y.

Bioinformatics. 2019 Apr 15;35(8):1299-1309. doi: 10.1093/bioinformatics/bty790.


Large-Scale, High-Resolution Comparison of the Core Visual Object Recognition Behavior of Humans, Monkeys, and State-of-the-Art Deep Artificial Neural Networks.

Rajalingham R, Issa EB, Bashivan P, Kar K, Schmidt K, DiCarlo JJ.

J Neurosci. 2018 Aug 15;38(33):7255-7269. doi: 10.1523/JNEUROSCI.0388-18.2018. Epub 2018 Jul 13.


Association Between Inherited Germline Mutations in Cancer Predisposition Genes and Risk of Pancreatic Cancer.

Hu C, Hart SN, Polley EC, Gnanaolivu R, Shimelis H, Lee KY, Lilyquist J, Na J, Moore R, Antwi SO, Bamlet WR, Chaffee KG, DiCarlo J, Wu Z, Samara R, Kasi PM, McWilliams RR, Petersen GM, Couch FJ.

JAMA. 2018 Jun 19;319(23):2401-2409. doi: 10.1001/jama.2018.6228.


Gene therapy and genome surgery in the retina.

DiCarlo JE, Mahajan VB, Tsang SH.

J Clin Invest. 2018 Jun 1;128(6):2177-2188. doi: 10.1172/JCI120429. Epub 2018 Jun 1. Review.


High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast.

Guo X, Chavez A, Tung A, Chan Y, Kaas C, Yin Y, Cecchi R, Garnier SL, Kelsic ED, Schubert M, DiCarlo JE, Collins JJ, Church GM.

Nat Biotechnol. 2018 Jul;36(6):540-546. doi: 10.1038/nbt.4147. Epub 2018 May 21.


Minimally invasive multimode optical fiber microendoscope for deep brain fluorescence imaging.

Ohayon S, Caravaca-Aguirre A, Piestun R, DiCarlo JJ.

Biomed Opt Express. 2018 Mar 6;9(4):1492-1509. doi: 10.1364/BOE.9.001492. eCollection 2018 Apr 1.


Post-disaster agricultural transitions in Nepal.

DiCarlo J, Epstein K, Marsh R, Måren I.

Ambio. 2018 Nov;47(7):794-805. doi: 10.1007/s13280-018-1021-3. Epub 2018 Feb 19.


Magnetic resonance imaging of the hand and wrist in a randomized, double-blind, multicenter, placebo-controlled trial of infliximab for rheumatoid arthritis: Comparison of dynamic contrast enhanced assessments with semi-quantitative scoring.

Beals C, Baumgartner R, Peterfy C, Balanescu A, Mirea G, Harabagiu A, Popa S, Cheng A, Feng D, Ashton E, DiCarlo J, Vallee MH, Dardzinski BJ.

PLoS One. 2017 Dec 13;12(12):e0187397. doi: 10.1371/journal.pone.0187397. eCollection 2017.


Dissection of Human Retina and RPE-Choroid for Proteomic Analysis.

Cabral T, Toral MA, Velez G, DiCarlo JE, Gore AM, Mahajan M, Tsang SH, Bassuk AG, Mahajan VB.

J Vis Exp. 2017 Nov 12;(129). doi: 10.3791/56203.


Viral Vectors, Engineered Cells and the CRISPR Revolution.

DiCarlo JE, Deeconda A, Tsang SH.

Adv Exp Med Biol. 2017;1016:3-27. doi: 10.1007/978-3-319-63904-8_1. Review.


A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans.

Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ.

Nat Microbiol. 2018 Jan;3(1):73-82. doi: 10.1038/s41564-017-0043-0. Epub 2017 Oct 23.


CRISPR-Cas Genome Surgery in Ophthalmology.

DiCarlo JE, Sengillo JD, Justus S, Cabral T, Tsang SH, Mahajan VB.

Transl Vis Sci Technol. 2017 May 31;6(3):13. doi: 10.1167/tvst.6.3.13. eCollection 2017 May. Review.


Design of a synthetic yeast genome.

Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CL, Chandrasegaran S, Cai Y, Boeke JD, Bader JS.

Science. 2017 Mar 10;355(6329):1040-1044. doi: 10.1126/science.aaf4557.


CRISPR applications in ophthalmologic genome surgery.

Cabral T, DiCarlo JE, Justus S, Sengillo JD, Xu Y, Tsang SH.

Curr Opin Ophthalmol. 2017 May;28(3):252-259. doi: 10.1097/ICU.0000000000000359. Review.


Repeatability and response to therapy of dynamic contrast-enhanced magnetic resonance imaging biomarkers in rheumatoid arthritis in a large multicentre trial setting.

Waterton JC, Ho M, Nordenmark LH, Jenkins M, DiCarlo J, Guillard G, Roberts C, Buonaccorsi G, Parker GJM, Bowes MA, Peterfy C, Kellner H, Taylor PC.

Eur Radiol. 2017 Sep;27(9):3662-3668. doi: 10.1007/s00330-017-4736-9. Epub 2017 Jan 23.


Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

Xu C, Nezami Ranjbar MR, Wu Z, DiCarlo J, Wang Y.

BMC Genomics. 2017 Jan 3;18(1):5. doi: 10.1186/s12864-016-3425-4.


Short-term changes on MRI predict long-term changes on radiography in rheumatoid arthritis: an analysis by an OMERACT Task Force of pooled data from four randomised controlled trials.

Peterfy C, Strand V, Tian L, Østergaard M, Lu Y, DiCarlo J, Countryman P, Deodhar A, Landewé R, Ranganath VK, Troum O, Conaghan PG.

Ann Rheum Dis. 2017 Jun;76(6):992-997. doi: 10.1136/annrheumdis-2016-210311. Epub 2016 Dec 14.


Neurophysiological Organization of the Middle Face Patch in Macaque Inferior Temporal Cortex.

Aparicio PL, Issa EB, DiCarlo JJ.

J Neurosci. 2016 Dec 14;36(50):12729-12745. Epub 2016 Nov 3.


Adoption of Information and Communication Technologies for Early Detection of Breast and Cervical Cancers in Low- and Middle-Income Countries.

DiCarlo JM, Gopakumar S, Dhillon PK, Krishnan S.

J Glob Oncol. 2016 Apr 13;2(4):222-234. doi: 10.1200/JGO.2015.002063. eCollection 2016 Aug. Review.


Eight open questions in the computational modeling of higher sensory cortex.

Yamins DL, DiCarlo JJ.

Curr Opin Neurobiol. 2016 Apr;37:114-120. doi: 10.1016/j.conb.2016.02.001. Epub 2016 Feb 26. Review.


Using goal-driven deep learning models to understand sensory cortex.

Yamins DL, DiCarlo JJ.

Nat Neurosci. 2016 Mar;19(3):356-65. doi: 10.1038/nn.4244. Review.


Explicit information for category-orthogonal object properties increases along the ventral stream.

Hong H, Yamins DL, Majaj NJ, DiCarlo JJ.

Nat Neurosci. 2016 Apr;19(4):613-22. doi: 10.1038/nn.4247. Epub 2016 Feb 22.


Sustained improvements in MRI outcomes with abatacept following the withdrawal of all treatments in patients with early, progressive rheumatoid arthritis.

Peterfy C, Burmester GR, Bykerk VP, Combe BG, DiCarlo JC, Furst DE, Huizinga TW, Wong DA, Conaghan PG, Emery P.

Ann Rheum Dis. 2016 Aug;75(8):1501-5. doi: 10.1136/annrheumdis-2015-208258. Epub 2016 Feb 10.


Safeguarding CRISPR-Cas9 gene drives in yeast.

DiCarlo JE, Chavez A, Dietz SL, Esvelt KM, Church GM.

Nat Biotechnol. 2015 Dec;33(12):1250-1255. doi: 10.1038/nbt.3412. Epub 2015 Nov 16.


Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance.

Majaj NJ, Hong H, Solomon EA, DiCarlo JJ.

J Neurosci. 2015 Sep 30;35(39):13402-18. doi: 10.1523/JNEUROSCI.5181-14.2015.


Comparison of Object Recognition Behavior in Human and Monkey.

Rajalingham R, Schmidt K, DiCarlo JJ.

J Neurosci. 2015 Sep 2;35(35):12127-36. doi: 10.1523/JNEUROSCI.0573-15.2015.


Optogenetic and pharmacological suppression of spatial clusters of face neurons reveal their causal role in face gender discrimination.

Afraz A, Boyden ES, DiCarlo JJ.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6730-5. doi: 10.1073/pnas.1423328112. Epub 2015 May 7.


Steven Hsiao: in memoriam.

Bensmaia SJ, DiCarlo JJ.

Neuron. 2015 Feb 4;85(3):458-61. No abstract available.


Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.

Reinecke F, Satya RV, DiCarlo J.

BMC Bioinformatics. 2015 Jan 28;16:17. doi: 10.1186/s12859-014-0428-5.


Deep neural networks rival the representation of primate IT cortex for core visual object recognition.

Cadieu CF, Hong H, Yamins DL, Pinto N, Ardila D, Solomon EA, Majaj NJ, DiCarlo JJ.

PLoS Comput Biol. 2014 Dec 18;10(12):e1003963. doi: 10.1371/journal.pcbi.1003963. eCollection 2014 Dec.


Pre-treatment whole blood gene expression is associated with 14-week response assessed by dynamic contrast enhanced magnetic resonance imaging in infliximab-treated rheumatoid arthritis patients.

MacIsaac KD, Baumgartner R, Kang J, Loboda A, Peterfy C, DiCarlo J, Riek J, Beals C.

PLoS One. 2014 Dec 12;9(12):e113937. doi: 10.1371/journal.pone.0113937. eCollection 2014.


Edge effects in calling variants from targeted amplicon sequencing.

Satya RV, DiCarlo J.

BMC Genomics. 2014 Dec 5;15:1073. doi: 10.1186/1471-2164-15-1073.


MRI assessment of suppression of structural damage in patients with rheumatoid arthritis receiving rituximab: results from the randomised, placebo-controlled, double-blind RA-SCORE study.

Peterfy C, Emery P, Tak PP, Østergaard M, DiCarlo J, Otsa K, Navarro Sarabia F, Pavelka K, Bagnard MA, Gylvin LH, Bernasconi C, Gabriele A.

Ann Rheum Dis. 2016 Jan;75(1):170-7. doi: 10.1136/annrheumdis-2014-206015. Epub 2014 Oct 29.


Performance-optimized hierarchical models predict neural responses in higher visual cortex.

Yamins DL, Hong H, Cadieu CF, Solomon EA, Seibert D, DiCarlo JJ.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8619-24. doi: 10.1073/pnas.1403112111. Epub 2014 May 8.


Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.

Xu H, DiCarlo J, Satya RV, Peng Q, Wang Y.

BMC Genomics. 2014 Mar 28;15:244. doi: 10.1186/1471-2164-15-244.


Total synthesis of a functional designer eukaryotic chromosome.

Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S.

Science. 2014 Apr 4;344(6179):55-8. doi: 10.1126/science.1249252. Epub 2014 Mar 27. Erratum in: Science. 2014 May 23;344(6186):816.


"Not your father's internet"*.

DiCarlo JV, Markovitz BP.

Pediatr Crit Care Med. 2014 Mar;15(3):266-7. doi: 10.1097/PCC.0000000000000063. No abstract available.


The effects of tocilizumab on osteitis, synovitis and erosion progression in rheumatoid arthritis: results from the ACT-RAY MRI substudy.

Conaghan PG, Peterfy C, Olech E, Kaine J, Ridley D, Dicarlo J, Friedman J, Devenport J, Troum O.

Ann Rheum Dis. 2014 May;73(5):810-6. doi: 10.1136/annrheumdis-2013-204762. Epub 2014 Feb 13.


A Conversation with James DiCarlo.

DiCarlo J, Stix G.

Cold Spring Harb Symp Quant Biol. 2014;79:271-4. doi: 10.1101/sqb.2014.79.09. No abstract available.


Neural Mechanisms Underlying Visual Object Recognition.

Afraz A, Yamins DL, DiCarlo JJ.

Cold Spring Harb Symp Quant Biol. 2014;79:99-107. doi: 10.1101/sqb.2014.79.024729. Review.


Cytokine and chemokine patterns across 100 days after hematopoietic stem cell transplantation in children.

DiCarlo J, Agarwal-Hashmi R, Shah A, Kim P, Craveiro L, Killen R, Rosenberg-Hasson Y, Maecker H.

Biol Blood Marrow Transplant. 2014 Mar;20(3):361-9. doi: 10.1016/j.bbmt.2013.11.026. Epub 2013 Dec 4.


Yeast oligo-mediated genome engineering (YOGE).

DiCarlo JE, Conley AJ, Penttilä M, Jäntti J, Wang HH, Church GM.

ACS Synth Biol. 2013 Dec 20;2(12):741-9. doi: 10.1021/sb400117c. Epub 2013 Nov 18.

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