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Gamma Glutamyltransferase Reduction Is Associated With Favorable Outcomes in Pediatric Primary Sclerosing Cholangitis.

Deneau MR, Mack C, Abdou R, Amin M, Amir A, Auth M, Bazerbachi F, Marie Broderick A, Chan A, DiGuglielmo M, El-Matary W, El-Youssef M, Ferrari F, Furuya KN, Gottrand F, Gupta N, Homan M, Jensen MK, Kamath BM, Mo Kim K, Kolho KL, Konidari A, Koot B, Iorio R, Martinez M, Mohan P, Palle S, Papadopoulou A, Ricciuto A, Saubermann L, Sathya P, Shteyer E, Smolka V, Tanaka A, Valentino PL, Varier R, Venkat V, Vitola B, Vos MB, Woynarowski M, Yap J, Miloh T.

Hepatol Commun. 2018 Sep 25;2(11):1369-1378. doi: 10.1002/hep4.1251. eCollection 2018 Nov.


Homeostasis of protein and mRNA concentrations in growing cells.

Lin J, Amir A.

Nat Commun. 2018 Oct 29;9(1):4496. doi: 10.1038/s41467-018-06714-z.



Amir A, Paré JF, Smith Y, Paré D.

J Comp Neurol. 2018 Oct 12. doi: 10.1002/cne.24557. [Epub ahead of print]


Ultra-short Celiac Disease Is a Distinct and Milder Phenotype of the Disease in Children.

Doyev R, Cohen S, Ben-Tov A, Weintraub Y, Amir A, Galai T, Moran-Lev H, Yerushalmy-Feler A.

Dig Dis Sci. 2018 Oct 11. doi: 10.1007/s10620-018-5323-x. [Epub ahead of print]


Parasitic infections, malnutrition and anemia among preschool children living in rural areas of Peshawar, Pakistan.

Din ZU, Pervez L, Amir A, Abbas M, Khan I, Iqbal Z, Iqbal M.

Nutr Hosp. 2018 Oct 5;35(5):1145-1152. doi: 10.20960/nh.1685.


Genistein Loaded Nanofibers Protect Spinal Cord Tissue Following Experimental Injury in Rats.

Ismail M, Ibrahim S, El-Amir A, El-Rafei AM, Allam NK, Abdellatif A.

Biomedicines. 2018 Oct 4;6(4). pii: E96. doi: 10.3390/biomedicines6040096.


Comparison of oral collection methods for studies of microbiota.

Vogtmann E, Chen J, Kibriya MG, Amir A, Shi J, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Barmon B, Knight R, Chia N, Ahsan H, Abnet CC, Sinha R.

Cancer Epidemiol Biomarkers Prev. 2018 Sep 27. pii: cebp.0312.2018. doi: 10.1158/1055-9965.EPI-18-0312. [Epub ahead of print]


Considerations for using Natalizumab treatment in patients with a history of choroidal melanoma.

Kaye AE, Hawkes ED, Gout II, El-Amir AN, Neffendorf JE.

Mult Scler Relat Disord. 2018 Sep 12;26:74-76. doi: 10.1016/j.msard.2018.09.012. [Epub ahead of print]


Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).

Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R.

Microbiologyopen. 2018 Aug 31:e00716. doi: 10.1002/mbo3.716. [Epub ahead of print]


Plasmodium knowlesi malaria: current research perspectives.

Amir A, Cheong FW, de Silva JR, Liew JWK, Lau YL.

Infect Drug Resist. 2018 Aug 10;11:1145-1155. doi: 10.2147/IDR.S148664. eCollection 2018. Review.


EDoP Distance Between Sets of Incomplete Permutations: Application to Bacteria Classification Based on Gene Order.

Zhou X, Amir A, Guerra C, Landau G, Rossignac J.

J Comput Biol. 2018 Nov;25(11):1193-1202. doi: 10.1089/cmb.2018.0063. Epub 2018 Aug 16.


Lead Concentration in Long-Tailed Macaque (Macaca fascicularis) Hair in Kuala Selangor, Malaysia.

Hassim NA, Hambali K, Idris NSU, Amir A, Ismail A, Zulkifli SZ, Sow AY.

Trop Life Sci Res. 2018 Jul;29(2):175-186. doi: 10.21315/tlsr2018.29.2.12. Epub 2018 Jul 6.


Energy-speed-accuracy relation in complex networks for biological discrimination.

Wong F, Amir A, Gunawardena J.

Phys Rev E. 2018 Jul;98(1-1):012420. doi: 10.1103/PhysRevE.98.012420.


Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.

Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S.

ISME J. 2018 Jul 11. doi: 10.1038/s41396-018-0175-0. [Epub ahead of print]


Adverse eating behavior and its association with obesity in Indian adolescents: Evidence from a nonmetropolitan city in India.

Faizi N, Shah MS, Ahmad A, Ansari MA, Amir A, Khalique N.

J Family Med Prim Care. 2018 Jan-Feb;7(1):198-204. doi: 10.4103/jfmpc.jfmpc_139_17.


High and low body mass index may predict severe disease course in children with inflammatory bowel disease.

Yerushalmy-Feler A, Ben-Tov A, Weintraub Y, Amir A, Galai T, Moran-Lev H, Cohen S.

Scand J Gastroenterol. 2018 Jun;53(6):708-713. doi: 10.1080/00365521.2018.1464595. Epub 2018 Apr 24.


KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R.

mSystems. 2018 Mar 13;3(3). pii: e00218-17. doi: 10.1128/mSystems.00218-17. eCollection 2018 May-Jun.


Mitigate risk for Malaysia's mangroves.

Amir AA.

Science. 2018 Mar 23;359(6382):1342-1343. doi: 10.1126/science.aas9139. No abstract available.


Learning from Noise: How Observing Stochasticity May Aid Microbiology.

Amir A, Balaban NQ.

Trends Microbiol. 2018 Apr;26(4):376-385. doi: 10.1016/j.tim.2018.02.003. Epub 2018 Mar 9. Review.


Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects.

Ho PY, Lin J, Amir A.

Annu Rev Biophys. 2018 May 20;47:251-271. doi: 10.1146/annurev-biophys-070317-032955. Epub 2018 Mar 8.


Reduced red blood cell deformability in Plasmodium knowlesi malaria.

Barber BE, Russell B, Grigg MJ, Zhang R, William T, Amir A, Lau YL, Chatfield MD, Dondorp AM, Anstey NM, Yeo TW.

Blood Adv. 2018 Feb 27;2(4):433-443. doi: 10.1182/bloodadvances.2017013730.


MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis.

Hussain S, Wivagg CN, Szwedziak P, Wong F, Schaefer K, Izoré T, Renner LD, Holmes MJ, Sun Y, Bisson-Filho AW, Walker S, Amir A, Löwe J, Garner EC.

Elife. 2018 Feb 22;7. pii: e32471. doi: 10.7554/eLife.32471.


Phyto-oestrogens affect fertilisation and embryo development in vitro in sheep.

Amir AA, Kelly JM, Kleemann DO, Durmic Z, Blache D, Martin GB.

Reprod Fertil Dev. 2018 Feb 16. doi: 10.1071/RD16481. [Epub ahead of print]


Vigilance-Associated Gamma Oscillations Coordinate the Ensemble Activity of Basolateral Amygdala Neurons.

Amir A, Headley DB, Lee SC, Haufler D, Paré D.

Neuron. 2018 Feb 7;97(3):656-669.e7. doi: 10.1016/j.neuron.2017.12.035.


Gluten-free diet may improve obstructive sleep apnea-related symptoms in children with celiac disease.

Yerushalmy-Feler A, Tauman R, Derowe A, Averbuch E, Ben-Tov A, Weintraub Y, Weiner D, Amir A, Moran-Lev H, Cohen S.

BMC Pediatr. 2018 Feb 7;18(1):35. doi: 10.1186/s12887-018-1039-5.


Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction.

Zhou Y, Xu ZZ, He Y, Yang Y, Liu L, Lin Q, Nie Y, Li M, Zhi F, Liu S, Amir A, González A, Tripathi A, Chen M, Wu GD, Knight R, Zhou H, Chen Y.

mSystems. 2018 Jan 30;3(1). pii: e00188-17. doi: 10.1128/mSystems.00188-17. eCollection 2018 Jan-Feb.


De Novo Allergy and Immune-Mediated Disorders Following Solid-Organ Transplantation-Prevalence, Natural History, and Risk Factors.

Marcus N, Amir AZ, Grunebaum E, Dipchand A, Hebert D, Ng VL, Walters T, Avitzur Y.

J Pediatr. 2018 May;196:154-160.e2. doi: 10.1016/j.jpeds.2017.11.026. Epub 2018 Feb 1.


Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.

Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, Shental N.

Microbiome. 2018 Jan 26;6(1):17. doi: 10.1186/s40168-017-0396-x.


Diagnostic tools in childhood malaria.

Amir A, Cheong FW, De Silva JR, Lau YL.

Parasit Vectors. 2018 Jan 23;11(1):53. doi: 10.1186/s13071-018-2617-y. Review.


Structural and quantum mechanical computations to elucidate the altered binding mechanism of metal and drug with pyrazinamidase from Mycobacterium tuberculosis due to mutagenicity.

Rasool N, Iftikhar S, Amir A, Hussain W.

J Mol Graph Model. 2018 Mar;80:126-131. doi: 10.1016/j.jmgm.2017.12.011. Epub 2017 Dec 24.


Archaeal cells share common size control with bacteria despite noisier growth and division.

Eun YJ, Ho PY, Kim M, LaRussa S, Robert L, Renner LD, Schmid A, Garner E, Amir A.

Nat Microbiol. 2018 Feb;3(2):148-154. doi: 10.1038/s41564-017-0082-6. Epub 2017 Dec 18.


Kidney stone composition in the Kingdom of Saudi Arabia

Amir A, Matlaga BR, Ziemba JB, Sheikh S.

Clin Nephrol. 2018 May;89(5):345-348. doi: 10.5414/CN109313.


A Story of Migration of a Surgically Implanted Aortic Sutureless Valve.

Amir A, Moore A, Carvalho G, Codère-Marayuma T, Schricker T, Villeneuve V, Hatzakorzian R.

J Cardiothorac Vasc Anesth. 2018 Feb;32(1):464-466. doi: 10.1053/j.jvca.2017.06.038. Epub 2017 Jun 21. No abstract available.


Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes.

Jiang L, Amir A, Morton JT, Heller R, Arias-Castro E, Knight R.

mSystems. 2017 Nov 21;2(6). pii: e00092-17. doi: 10.1128/mSystems.00092-17. eCollection 2017 Nov-Dec.


Details Matter: Noise and Model Structure Set the Relationship between Cell Size and Cell Cycle Timing.

Barber F, Ho PY, Murray AW, Amir A.

Front Cell Dev Biol. 2017 Nov 3;5:92. doi: 10.3389/fcell.2017.00092. eCollection 2017.


Diagnostic accuracy of serum miR-122 and miR-199a in women with endometriosis.

Maged AM, Deeb WS, El Amir A, Zaki SS, El Sawah H, Al Mohamady M, Metwally AA, Katta MA.

Int J Gynaecol Obstet. 2018 Apr;141(1):14-19. doi: 10.1002/ijgo.12392. Epub 2017 Dec 16.


Evaluating the impact of domestication and captivity on the horse gut microbiome.

Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L.

Sci Rep. 2017 Nov 14;7(1):15497. doi: 10.1038/s41598-017-15375-9.


A Parallel Adder Coordinates Mycobacterial Cell-Cycle Progression and Cell-Size Homeostasis in the Context of Asymmetric Growth and Organization.

Logsdon MM, Ho PY, Papavinasasundaram K, Richardson K, Cokol M, Sassetti CM, Amir A, Aldridge BB.

Curr Biol. 2017 Nov 6;27(21):3367-3374.e7. doi: 10.1016/j.cub.2017.09.046. Epub 2017 Oct 26.


A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.


Derivation and validation of a universal vital assessment (UVA) score: a tool for predicting mortality in adult hospitalised patients in sub-Saharan Africa.

Moore CC, Hazard R, Saulters KJ, Ainsworth J, Adakun SA, Amir A, Andrews B, Auma M, Baker T, Banura P, Crump JA, Grobusch MP, Huson MAM, Jacob ST, Jarrett OD, Kellett J, Lakhi S, Majwala A, Opio M, Rubach MP, Rylance J, Michael Scheld W, Schieffelin J, Ssekitoleko R, Wheeler I, Barnes LE.

BMJ Glob Health. 2017 Jul 28;2(2):e000344. doi: 10.1136/bmjgh-2017-000344. eCollection 2017.


Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites.

Reddivari L, Veeramachaneni DNR, Walters WA, Lozupone C, Palmer J, Hewage MKK, Bhatnagar R, Amir A, Kennett MJ, Knight R, Vanamala JKP.

mSystems. 2017 Oct 10;2(5). pii: e00093-17. doi: 10.1128/mSystems.00093-17. eCollection 2017 Sep-Oct.


Oral health: Treating refugees.

Hussain SM, Sheikh H, Amir A, Hassan AA.

Br Dent J. 2017 Oct 13;223(7):463. doi: 10.1038/sj.bdj.2017.843. No abstract available.


The sponge microbiome project.

Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T.

Gigascience. 2017 Oct 1;6(10):1-7. doi: 10.1093/gigascience/gix077.


The Effects of Stochasticity at the Single-Cell Level and Cell Size Control on the Population Growth.

Lin J, Amir A.

Cell Syst. 2017 Oct 25;5(4):358-367.e4. doi: 10.1016/j.cels.2017.08.015. Epub 2017 Oct 4.


Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium.

Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S; Microbiome Quality Control Project Consortium, Abnet CC, Knight R, White O, Huttenhower C.

Nat Biotechnol. 2017 Nov;35(11):1077-1086. doi: 10.1038/nbt.3981. Epub 2017 Oct 2.


Differential Recruitment of Competing Valence-Related Amygdala Networks during Anxiety.

Lee SC, Amir A, Haufler D, Pare D.

Neuron. 2017 Sep 27;96(1):81-88.e5. doi: 10.1016/j.neuron.2017.09.002.


Concurrent administration effect of antibiotic and anti-inflammatory drugs on the immunotoxicity of bacterial endotoxins.

El Amir AM, Tanious DG, Mansour HA.

Int Immunopharmacol. 2017 Nov;52:176-184. doi: 10.1016/j.intimp.2017.09.006. Epub 2017 Sep 18.


Fluid resuscitation of patients with severe infection in Uganda: less is more.

Amir A, Saulters KJ, Muhindo R, Moore CC.

J Crit Care. 2017 Dec;42:348-349. doi: 10.1016/j.jcrc.2017.08.041. Epub 2017 Sep 5. No abstract available.


End-stage renal disease in patients with sickle cell disease.

Alkhunaizi AM, Al-Khatti AA, Al-Mueilo SH, Amir A, Yousif B.

Saudi J Kidney Dis Transpl. 2017 Jul-Aug;28(4):751-757.

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