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In reply to: Is Nodular Regenerative Hyperplasia an Immune-Mediated Phenomenon?

LoPiccolo J, Brener MI, Oshima K, Lipson EJ, Hamilton JP.

Hepatology. 2019 Feb 28. doi: 10.1002/hep.30595. [Epub ahead of print]


Deactivation of default mode network during touch.

Strauss T, Kämpe R, Hamilton JP, Olausson H, Rottstädt F, Raue C, Croy I.

Sci Rep. 2019 Feb 4;9(1):1293. doi: 10.1038/s41598-018-37597-1.


A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways.

Zhao D, Hamilton JP, Bhat WW, Johnson SR, Godden GT, Kinser TJ, Boachon B, Dudareva N, Soltis DE, Soltis PS, Hamberger B, Buell CR.

Gigascience. 2019 Mar 1;8(3). pii: giz005. doi: 10.1093/gigascience/giz005.


Identification of a bilirubin receptor that may mediate a component of cholestatic itch.

Meixiong J, Vasavda C, Green D, Zheng Q, Qi L, Kwatra SG, Hamilton JP, Snyder SH, Dong X.

Elife. 2019 Jan 21;8. pii: e44116. doi: 10.7554/eLife.44116.


An updated gene atlas for maize reveals organ-specific and stress-induced genes.

Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR.

Plant J. 2018 Dec 7. doi: 10.1111/tpj.14184. [Epub ahead of print]


Striatal dopamine deficits predict reductions in striatal functional connectivity in major depression: a concurrent 11C-raclopride positron emission tomography and functional magnetic resonance imaging investigation.

Hamilton JP, Sacchet MD, Hjørnevik T, Chin FT, Shen B, Kämpe R, Park JH, Knutson BD, Williams LM, Borg N, Zaharchuk G, Camacho MC, Mackey S, Heilig M, Drevets WC, Glover GH, Gambhir SS, Gotlib IH.

Transl Psychiatry. 2018 Nov 30;8(1):264. doi: 10.1038/s41398-018-0316-2.


Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement.

Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR, Fei Z.

Nat Commun. 2018 Nov 2;9(1):4580. doi: 10.1038/s41467-018-06983-8.


Coffee consumption and liver-related hospitalizations and deaths in the ARIC study.

Hu EA, Lazo M, Selvin E, Hamilton JP, Grams ME, Steffen LM, Coresh J, Rebholz CM.

Eur J Clin Nutr. 2018 Oct 19. doi: 10.1038/s41430-018-0346-0. [Epub ahead of print]


Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis.

Franke J, Kim J, Hamilton JP, Zhao D, Pham GM, Wiegert-Rininger K, Crisovan E, Newton L, Vaillancourt B, Tatsis E, Buell CR, O'Connor SE.

Chembiochem. 2019 Jan 2;20(1):83-87. doi: 10.1002/cbic.201800592. Epub 2018 Nov 13.


Nodular Regenerative Hyperplasia Associated With Immune Checkpoint Blockade.

LoPiccolo J, Brener MI, Oshima K, Lipson EJ, Hamilton JP.

Hepatology. 2018 Dec;68(6):2431-2433. doi: 10.1002/hep.30157. Epub 2018 Nov 5. No abstract available.


Reply to Huang et al.: Avoiding "one-size-fits-all" approaches to variant discovery.

Hardigan MA, Laimbeer FPE, Hamilton JP, Vaillancourt B, Douches DS, Farré EM, Veilleux RE, Buell CR.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6394-E6395. doi: 10.1073/pnas.1807622115. Epub 2018 Jun 22. No abstract available.


The salience of self, not social pain, is encoded by dorsal anterior cingulate and insula.

Perini I, Gustafsson PA, Hamilton JP, Kämpe R, Zetterqvist M, Heilig M.

Sci Rep. 2018 Apr 18;8(1):6165. doi: 10.1038/s41598-018-24658-8.


Distinct Neural-Functional Effects of Treatments With Selective Serotonin Reuptake Inhibitors, Electroconvulsive Therapy, and Transcranial Magnetic Stimulation and Their Relations to Regional Brain Function in Major Depression: A Meta-analysis.

Chau DT, Fogelman P, Nordanskog P, Drevets WC, Hamilton JP.

Biol Psychiatry Cogn Neurosci Neuroimaging. 2017 May;2(4):318-326. doi: 10.1016/j.bpsc.2017.01.003. Epub 2017 Jan 26.


The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.

Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N.

Nucleic Acids Res. 2018 Mar 16;46(5):2700. doi: 10.1093/nar/gky091. No abstract available.


Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

Leisner CP, Hamilton JP, Crisovan E, Manrique-Carpintero NC, Marand AP, Newton L, Pham GM, Jiang J, Douches DS, Jansky SH, Buell CR.

Plant J. 2018 May;94(3):562-570. doi: 10.1111/tpj.13857. Epub 2018 Mar 22. Erratum in: Plant J. 2018 Oct;96(2):482.


Role of nucleoside/nucleotide analogues and low-dose hepatitis B immune globülin in prophylaxis of hepatitis B recurrence among cadaveric liver transplant recipients.

Ajayi T, Luu H, Saberi B, Hamilton JP, Konduk BT, Özşeker B, Al Khalloufi K, Pustavoitau A, Philosophe B, Cameron AM, Gürakar A.

Turk J Gastroenterol. 2018 Jan;29(1):61-66. doi: 10.5152/tjg.2018.17595.


The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.

Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N.

Nucleic Acids Res. 2018 Mar 16;46(5):2380-2397. doi: 10.1093/nar/gky025.


Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides.

Hoopes GM, Hamilton JP, Kim J, Zhao D, Wiegert-Rininger K, Crisovan E, Buell CR.

G3 (Bethesda). 2018 Feb 2;8(2):385-391. doi: 10.1534/g3.117.300331.


Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato.

Hardigan MA, Laimbeer FPE, Newton L, Crisovan E, Hamilton JP, Vaillancourt B, Wiegert-Rininger K, Wood JC, Douches DS, Farré EM, Veilleux RE, Buell CR.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9999-E10008. doi: 10.1073/pnas.1714380114. Epub 2017 Oct 30.


Pregnancy in Wilson disease.

Rabiee A, Hamilton JPA.

Hepatology. 2018 Apr;67(4):1201-1203. doi: 10.1002/hep.29619. Epub 2018 Feb 20. No abstract available.


De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin.

Zhao D, Hamilton JP, Pham GM, Crisovan E, Wiegert-Rininger K, Vaillancourt B, DellaPenna D, Buell CR.

Gigascience. 2017 Sep 1;6(9):1-7. doi: 10.1093/gigascience/gix065.


Utilization of hepatitis C virus RNA-positive donor liver for transplant to hepatitis C virus RNA-negative recipient.

Saberi B, Hamilton JP, Durand CM, Li Z, Philosophe B, Cameron AM, Sulkowski MS, Gurakar A.

Liver Transpl. 2018 Jan;24(1):140-143. doi: 10.1002/lt.24838. No abstract available.


Statistical differences in the white matter tracts in subjects with depression by using different skeletonized voxel-wise analysis approaches and DTI fitting procedures.

Bergamino M, Farmer M, Yeh HW, Paul E, Hamilton JP.

Brain Res. 2017 Aug 15;1669:131-140. doi: 10.1016/j.brainres.2017.06.013. Epub 2017 Jun 16.


Targeted inactivation of copper transporter Atp7b in hepatocytes causes liver steatosis and obesity in mice.

Muchenditsi A, Yang H, Hamilton JP, Koganti L, Housseau F, Aronov L, Fan H, Pierson H, Bhattacharjee A, Murphy R, Sears C, Potter J, Wooton-Kee CR, Lutsenko S.

Am J Physiol Gastrointest Liver Physiol. 2017 Jul 1;313(1):G39-G49. doi: 10.1152/ajpgi.00312.2016. Epub 2017 Apr 20.


The GABAB Positive Allosteric Modulator ADX71441 Attenuates Alcohol Self-Administration and Relapse to Alcohol Seeking in Rats.

Augier E, Dulman RS, Damadzic R, Pilling A, Hamilton JP, Heilig M.

Neuropsychopharmacology. 2017 Aug;42(9):1789-1799. doi: 10.1038/npp.2017.53. Epub 2017 Mar 15.


Pre- Versus Posttransplant Treatment of Hepatitis C Virus With Direct-Acting Antivirals in Liver Transplant Recipients: More Issues to be Solved.

Abdelqader A, Kabacam G, Woreta TA, Hamilton JP, Luu H, Al Khalloufi K, Saberi B, Philosophe B, Cameron AM, Gurakar A.

Exp Clin Transplant. 2017 Feb;15(Suppl 1):1-5.


Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays.

Langlois PA, Snelling J, Hamilton JP, Bragard C, Koebnik R, Verdier V, Triplett LR, Blom J, Tisserat NA, Leach JE.

Phytopathology. 2017 May;107(5):519-527. doi: 10.1094/PHYTO-08-16-0286-R. Epub 2017 Mar 28.


Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation.

Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, Reynoso M, Pauluzzi G, Funkhouser S, Cui Y, Bailey-Serres J, Jiang J, Buell CR, Jiang N.

G3 (Bethesda). 2017 Jan 5;7(1):203-219. doi: 10.1534/g3.116.036020.


Cognitive and neural consequences of memory suppression in major depressive disorder.

Sacchet MD, Levy BJ, Hamilton JP, Maksimovskiy A, Hertel PT, Joormann J, Anderson MC, Wagner AD, Gotlib IH.

Cogn Affect Behav Neurosci. 2017 Feb;17(1):77-93. doi: 10.3758/s13415-016-0464-x.


Applying a free-water correction to diffusion imaging data uncovers stress-related neural pathology in depression.

Bergamino M, Pasternak O, Farmer M, Shenton ME, Hamilton JP.

Neuroimage Clin. 2015 Nov 30;10:336-42. doi: 10.1016/j.nicl.2015.11.020. eCollection 2016.


Effects of salience-network-node neurofeedback training on affective biases in major depressive disorder.

Hamilton JP, Glover GH, Bagarinao E, Chang C, Mackey S, Sacchet MD, Gotlib IH.

Psychiatry Res Neuroimaging. 2016 Mar 30;249:91-6. doi: 10.1016/j.pscychresns.2016.01.016. Epub 2016 Jan 19.


Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.

Stapleton JA, Kim J, Hamilton JP, Wu M, Irber LC, Maddamsetti R, Briney B, Newton L, Burton DR, Brown CT, Chan C, Buell CR, Whitehead TA.

PLoS One. 2016 Jan 20;11(1):e0147229. doi: 10.1371/journal.pone.0147229. eCollection 2016.


Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum.

Hardigan MA, Crisovan E, Hamilton JP, Kim J, Laimbeer P, Leisner CP, Manrique-Carpintero NC, Newton L, Pham GM, Vaillancourt B, Yang X, Zeng Z, Douches DS, Jiang J, Veilleux RE, Buell CR.

Plant Cell. 2016 Feb;28(2):388-405. doi: 10.1105/tpc.15.00538. Epub 2016 Jan 15.


Systemic PEGylated TRAIL treatment ameliorates liver cirrhosis in rats by eliminating activated hepatic stellate cells.

Oh Y, Park O, Swierczewska M, Hamilton JP, Park JS, Kim TH, Lim SM, Eom H, Jo DG, Lee CE, Kechrid R, Mastorakos P, Zhang C, Hahn SK, Jeon OC, Byun Y, Kim K, Hanes J, Lee KC, Pomper MG, Gao B, Lee S.

Hepatology. 2016 Jul;64(1):209-23. doi: 10.1002/hep.28432. Epub 2016 Mar 3.


Activation of liver X receptor/retinoid X receptor pathway ameliorates liver disease in Atp7B(-/-) (Wilson disease) mice.

Hamilton JP, Koganti L, Muchenditsi A, Pendyala VS, Huso D, Hankin J, Murphy RC, Huster D, Merle U, Mangels C, Yang N, Potter JJ, Mezey E, Lutsenko S.

Hepatology. 2016 Jun;63(6):1828-41. doi: 10.1002/hep.28406. Epub 2016 Feb 22.


Deregulation of energy metabolism promotes antifibrotic effects in human hepatic stellate cells and prevents liver fibrosis in a mouse model.

Karthikeyan S, Potter JJ, Geschwind JF, Sur S, Hamilton JP, Vogelstein B, Kinzler KW, Mezey E, Ganapathy-Kanniappan S.

Biochem Biophys Res Commun. 2016 Jan 15;469(3):463-9. doi: 10.1016/j.bbrc.2015.10.101. Epub 2015 Oct 23.


A neural substrate for behavioral inhibition in the risk for major depressive disorder.

Frost Bellgowan J, Molfese P, Marx M, Thomason M, Glen D, Santiago J, Gotlib IH, Drevets WC, Hamilton JP.

J Am Acad Child Adolesc Psychiatry. 2015 Oct;54(10):841-8. doi: 10.1016/j.jaac.2015.08.001. Epub 2015 Aug 20.


Meta-analysis of Functional Neuroimaging of Major Depressive Disorder in Youth.

Miller CH, Hamilton JP, Sacchet MD, Gotlib IH.

JAMA Psychiatry. 2015 Oct;72(10):1045-53. doi: 10.1001/jamapsychiatry.2015.1376.


Hepatopulmonary syndrome is a frequent cause of dyspnea in the short telomere disorders.

Gorgy AI, Jonassaint NL, Stanley SE, Koteish A, DeZern AE, Walter JE, Sopha SC, Hamilton JP, Hoover-Fong J, Chen AR, Anders RA, Kamel IR, Armanios M.

Chest. 2015 Oct;148(4):1019-1026. doi: 10.1378/chest.15-0825.


Nature experience reduces rumination and subgenual prefrontal cortex activation.

Bratman GN, Hamilton JP, Hahn KS, Daily GC, Gross JJ.

Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8567-72. doi: 10.1073/pnas.1510459112. Epub 2015 Jun 29.


Depressive Rumination, the Default-Mode Network, and the Dark Matter of Clinical Neuroscience.

Hamilton JP, Farmer M, Fogelman P, Gotlib IH.

Biol Psychiatry. 2015 Aug 15;78(4):224-30. doi: 10.1016/j.biopsych.2015.02.020. Epub 2015 Feb 24. Review.


Genome-guided investigation of plant natural product biosynthesis.

Kellner F, Kim J, Clavijo BJ, Hamilton JP, Childs KL, Vaillancourt B, Cepela J, Habermann M, Steuernagel B, Clissold L, McLay K, Buell CR, O'Connor SE.

Plant J. 2015 May;82(4):680-92. doi: 10.1111/tpj.12827. Epub 2015 Apr 11.


Amygdala reactivity as mental health risk endophenotype: a tale of many trajectories.

Hamilton JP.

Am J Psychiatry. 2015 Mar 1;172(3):214-5. doi: 10.1176/appi.ajp.2014.14121491. No abstract available.


Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma.

Peng H, Ishida M, Li L, Saito A, Kamiya A, Hamilton JP, Fu R, Olaru AV, An F, Popescu I, Iacob R, Dima S, Alexandrescu ST, Grigorie R, Nastase A, Berindan-Neagoe I, Tomuleasa C, Graur F, Zaharia F, Torbenson MS, Mezey E, Lu M, Selaru FM.

Oncotarget. 2015 Mar 20;6(8):5666-77.


Influence of menarche on the relation between diurnal cortisol production and ventral striatum activity during reward anticipation.

LeMoult J, Colich NL, Sherdell L, Hamilton JP, Gotlib IH.

Soc Cogn Affect Neurosci. 2015 Sep;10(9):1244-50. doi: 10.1093/scan/nsv016. Epub 2015 Feb 11.



Sacchet MD, Prasad G, Foland-Ross LC, Joshi SH, Hamilton JP, Thompson PM, Gotlib IH.

Proc IEEE Int Symp Biomed Imaging. 2014 Apr 29;11:592-595.


Differential methylation of the promoter and first exon of the RASSF1A gene in hepatocarcinogenesis.

Jain S, Xie L, Boldbaatar B, Lin SY, Hamilton JP, Meltzer SJ, Chen SH, Hu CT, Block TM, Song W, Su YH.

Hepatol Res. 2015 Nov;45(11):1110-23. doi: 10.1111/hepr.12449. Epub 2014 Dec 9.


Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia.

Wiersma AT, Gaines TA, Preston C, Hamilton JP, Giacomini D, Robin Buell C, Leach JE, Westra P.

Planta. 2015 Feb;241(2):463-74. doi: 10.1007/s00425-014-2197-9. Epub 2014 Nov 5.


Structural abnormality of the corticospinal tract in major depressive disorder.

Sacchet MD, Prasad G, Foland-Ross LC, Joshi SH, Hamilton JP, Thompson PM, Gotlib IH.

Biol Mood Anxiety Disord. 2014 Sep 10;4:8. doi: 10.1186/2045-5380-4-8. eCollection 2014.


A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna.

Bedewitz MA, Góngora-Castillo E, Uebler JB, Gonzales-Vigil E, Wiegert-Rininger KE, Childs KL, Hamilton JP, Vaillancourt B, Yeo YS, Chappell J, DellaPenna D, Jones AD, Buell CR, Barry CS.

Plant Cell. 2014 Sep;26(9):3745-62. doi: 10.1105/tpc.114.130534. Epub 2014 Sep 16.

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