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A primer on deep learning in genomics.

Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A.

Nat Genet. 2018 Nov 26. doi: 10.1038/s41588-018-0295-5. [Epub ahead of print] Review.


Including 793/B type avian infectious bronchitis vaccine in 1-day-old chicken increased the protection against QX genotype.

Karimi V, Mohammadi P, Ghalyanchilangeroudi A, Ghafouri SA, Hashemzadeh M, Farahani RK, Maghsouldoo H, Isakakroudi N.

Trop Anim Health Prod. 2018 Oct 29. doi: 10.1007/s11250-018-1730-4. [Epub ahead of print]


Phase transitions as intermediate steps in the formation of molecularly engineered protein fibers.

Mohammadi P, Aranko AS, Lemetti L, Cenev Z, Zhou Q, Virtanen S, Landowski CP, Penttilä M, Fischer WJ, Wagermaier W, Linder MB.

Commun Biol. 2018 Jul 2;1:86. doi: 10.1038/s42003-018-0090-y. eCollection 2018.


Self-Coacervation of a Silk-Like Protein and Its Use As an Adhesive for Cellulosic Materials.

Mohammadi P, Beaune G, Stokke BT, Timonen JVI, Linder MB.

ACS Macro Lett. 2018 Sep 18;7(9):1120-1125. doi: 10.1021/acsmacrolett.8b00527. Epub 2018 Sep 5.


Antifungal, antibacterial, antibiofilm and colorimetric sensing of toxic metals activities of eco friendly, economical synthesized Ag/AgCl nanoparticles using Malva Sylvestris leaf extracts.

Feizi S, Taghipour E, Ghadam P, Mohammadi P.

Microb Pathog. 2018 Dec;125:33-42. doi: 10.1016/j.micpath.2018.08.054. Epub 2018 Aug 29.


Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk.

Castel SE, Cervera A, Mohammadi P, Aguet F, Reverter F, Wolman A, Guigo R, Iossifov I, Vasileva A, Lappalainen T.

Nat Genet. 2018 Sep;50(9):1327-1334. doi: 10.1038/s41588-018-0192-y. Epub 2018 Aug 20.


Amniotic Membrane Extract Eye Drop Promotes Limbal Stem Cell Proliferation and Corneal Epithelium Healing.

Shayan Asl N, Nejat F, Mohammadi P, Nekoukar A, Hesam S, Ebrahimi M, Jadidi K.

Cell J. 2019 Jan;20(4):459-468. doi: 10.22074/cellj.2019.5423. Epub 2018 Aug 1.


Coacervation of resilin fusion proteins containing terminal functionalities.

Fang W, Nonappa, Vitikainen M, Mohammadi P, Koskela S, Soikkeli M, Westerholm-Parvinen A, Landowski CP, Penttilä M, Linder MB, Laaksonen P.

Colloids Surf B Biointerfaces. 2018 Nov 1;171:590-596. doi: 10.1016/j.colsurfb.2018.07.048. Epub 2018 Jul 24.


One-carbon cycle support rescues sperm damage in experimentally induced varicocoele in rats.

Mohammadi P, Hassani-Bafrani H, Tavalaee M, Dattilo M, Nasr-Esfahani MH.

BJU Int. 2018 Sep;122(3):480-489. doi: 10.1111/bju.14385. Epub 2018 Jun 3.


High rate treatment of hospital wastewater using activated sludge process induced by high-frequency ultrasound.

Karami N, Mohammadi P, Zinatizadeh A, Falahi F, Aghamohammadi N.

Ultrason Sonochem. 2018 Sep;46:89-98. doi: 10.1016/j.ultsonch.2018.04.009. Epub 2018 Apr 19.


A single-arm open-label clinical trial of autologous epidermal cell transplantation for stable vitiligo: A 30-month follow-up.

Orouji Z, Bajouri A, Ghasemi M, Mohammadi P, Fallah N, Shahbazi A, Rezvani M, Vaezirad F, Khalajasadi Z, Alizadeh A, Taghiabadi E, Dashtbozorgi S, Aghdami R, Hosseini SE, Bahahrvand H, Shafieyan S, Aghdami N.

J Dermatol Sci. 2018 Jan;89(1):52-59. doi: 10.1016/j.jdermsci.2017.10.007. Epub 2017 Oct 18.


Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.

Mohammadi P, Castel SE, Brown AA, Lappalainen T.

Genome Res. 2017 Nov;27(11):1872-1884. doi: 10.1101/gr.216747.116. Epub 2017 Oct 11.


Aligning cellulose nanofibril dispersions for tougher fibers.

Mohammadi P, Toivonen MS, Ikkala O, Wagermaier W, Linder MB.

Sci Rep. 2017 Sep 19;7(1):11860. doi: 10.1038/s41598-017-12107-x.


Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations.

Kim-Hellmuth S, Bechheim M, Pütz B, Mohammadi P, Nédélec Y, Giangreco N, Becker J, Kaiser V, Fricker N, Beier E, Boor P, Castel SE, Nöthen MM, Barreiro LB, Pickrell JK, Müller-Myhsok B, Lappalainen T, Schumacher J, Hornung V.

Nat Commun. 2017 Aug 16;8(1):266. doi: 10.1038/s41467-017-00366-1.


Comparison of aglycon and glycosidic saponin extracts of Cyclamen coum tuber against Candida spp.

Sajjadi ST, Saboora A, Mohammadi P.

Curr Med Mycol. 2016 Jun;2(2):40-44. doi: 10.18869/acadpub.cmm.2.2.7.


Hair Follicle Generation by Injections of Adult Human Follicular Epithelial and Dermal Papilla Cells into Nude Mice.

Nilforoushzadeh M, Rahimi Jameh E, Jaffary F, Abolhasani E, Keshtmand G, Zarkob H, Mohammadi P, Aghdami N.

Cell J. 2017 Jul-Sep;19(2):259-268. doi: 10.22074/cellj.2016.3916. Epub 2017 Feb 22.


Complexes of Magnetic Nanoparticles with Cellulose Nanocrystals as Regenerable, Highly Efficient, and Selective Platform for Protein Separation.

Guo J, Filpponen I, Johansson LS, Mohammadi P, Latikka M, Linder MB, Ras RH, Rojas OJ.

Biomacromolecules. 2017 Mar 13;18(3):898-905. doi: 10.1021/acs.biomac.6b01778. Epub 2017 Feb 27.


Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy.

Mohammadi P, Beerenwinkel N, Benenson Y.

Cell Syst. 2017 Feb 22;4(2):207-218.e14. doi: 10.1016/j.cels.2017.01.003. Epub 2017 Feb 8.


IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP.

Jønsson KL, Laustsen A, Krapp C, Skipper KA, Thavachelvam K, Hotter D, Egedal JH, Kjolby M, Mohammadi P, Prabakaran T, Sørensen LK, Sun C, Jensen SB, Holm CK, Lebbink RJ, Johannsen M, Nyegaard M, Mikkelsen JG, Kirchhoff F, Paludan SR, Jakobsen MR.

Nat Commun. 2017 Feb 10;8:14391. doi: 10.1038/ncomms14391.


Corrigendum: Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W.

Sci Rep. 2017 Jan 24;7:41112. doi: 10.1038/srep41112. No abstract available.


Construction and characterization of monoclonal antibodies against the extracellular domain of B-lymphocyte antigen CD20 using DNA immunization method.

Khademi F, Mostafaie A, Parvaneh S, Gholami Rad F, Mohammadi P, Bahrami G.

Int Immunopharmacol. 2017 Feb;43:23-32. doi: 10.1016/j.intimp.2016.11.035. Epub 2016 Dec 7.


Preparation, Physicochemical Characterization and Anti-fungal Evaluation of Nystatin-Loaded PLGA-Glucosamine Nanoparticles.

Mohammadi G, Shakeri A, Fattahi A, Mohammadi P, Mikaeili A, Aliabadi A, Adibkia K.

Pharm Res. 2017 Feb;34(2):301-309. doi: 10.1007/s11095-016-2062-6. Epub 2016 Dec 7.


Screening Characteristics of Ultrasonography in Detection of Ankle Fractures.

Shojaee M, Hakimzadeh F, Mohammadi P, Sabzghabaei A, Manouchehrifar M, Arhami Dolatabadi A.

Emerg (Tehran). 2016 Nov;4(4):188-191.


Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W.

Sci Rep. 2016 Oct 26;6:36111. doi: 10.1038/srep36111. Erratum in: Sci Rep. 2017 Jan 24;7:41112.


Human Hair Reconstruction: Close, But Yet So Far.

Mohammadi P, Youssef KK, Abbasalizadeh S, Baharvand H, Aghdami N.

Stem Cells Dev. 2016 Dec 1;25(23):1767-1779. Epub 2016 Nov 8. Review.


Rare variant phasing and haplotypic expression from RNA sequencing with phASER.

Castel SE, Mohammadi P, Chung WK, Shen Y, Lappalainen T.

Nat Commun. 2016 Sep 8;7:12817. doi: 10.1038/ncomms12817.


A Pilot Study of CK19, CK20 and GCC mRNA in the Peripheral Blood as a Colorectal Cancer Biomarker Panel.

Mohammadi P, Saidijam M, Kaki A, Etemadi K, Shabab N, Yadegarazari R.

Int J Mol Cell Med. 2016 Winter;5(1):30-6.


A cholera outbreak in Alborz Province, Iran: a matched case-control study.

Moradi G, Rasouli MA, Mohammadi P, Elahi E, Barati H.

Epidemiol Health. 2016 May 14;38:e2016018. doi: 10.4178/epih.e2016018. eCollection 2016.


Epidemiologic and Drug Resistance Pattern of Vibrio cholerae O1 Biotype El Tor, Serotype Ogawa, in the 2011 Cholera Outbreak, in Alborz Province, Iran.

Barati H, Moradi G, Rasouli MA, Mohammadi P.

Jundishapur J Microbiol. 2015 Nov 14;8(11):e23477. doi: 10.5812/jjm.23477. eCollection 2015 Nov.


The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome.

Bartha I, Rausell A, McLaren PJ, Mohammadi P, Tardaguila M, Chaturvedi N, Fellay J, Telenti A.

PLoS Comput Biol. 2015 Dec 7;11(12):e1004647. doi: 10.1371/journal.pcbi.1004647. eCollection 2015 Dec.


Comparative Analysis of Denaturing Gradient Gel Electrophoresis and Temporal Temperature Gradient Gel Electrophoresis Profiles as a Tool for the Differentiation of Candida Species.

Mohammadi P, Hamidkhani A, Asgarani E.

Jundishapur J Microbiol. 2015 Oct 12;8(10):e22249. doi: 10.5812/jjm.22249. eCollection 2015 Oct.


Detection and Genetic Characterization of Metallo-β-Lactamase IMP-1 and VIM-2 in Pseudomonas aeruginosa Strains From Different Hospitals in Kermanshah, Iran.

Abiri R, Mohammadi P, Shavani N, Rezaei M.

Jundishapur J Microbiol. 2015 Sep 22;8(9):e22582. doi: 10.5812/jjm.22582. eCollection 2015 Sep.


Tools and best practices for data processing in allelic expression analysis.

Castel SE, Levy-Moonshine A, Mohammadi P, Banks E, Lappalainen T.

Genome Biol. 2015 Sep 17;16:195. doi: 10.1186/s13059-015-0762-6.


Facile fabrication of egg white macroporous sponges for tissue regeneration.

Jalili-Firoozinezhad S, Rajabi-Zeleti S, Mohammadi P, Gaudiello E, Bonakdar S, Solati-Hashjin M, Marsano A, Aghdami N, Scherberich A, Baharvand H, Martin I.

Adv Healthc Mater. 2015 Oct 28;4(15):2281-90. doi: 10.1002/adhm.201500482. Epub 2015 Sep 16.


BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.

Golumbeanu M, Mohammadi P, Beerenwinkel N.

Bioinformatics. 2016 Apr 1;32(7):976-83. doi: 10.1093/bioinformatics/btv520. Epub 2015 Sep 5.


HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages.

Vongrad V, Imig J, Mohammadi P, Kishore S, Jaskiewicz L, Hall J, Günthard HF, Beerenwinkel N, Metzner KJ.

PLoS One. 2015 Jul 30;10(7):e0132127. doi: 10.1371/journal.pone.0132127. eCollection 2015.


TiMEx: a waiting time model for mutually exclusive cancer alterations.

Constantinescu S, Szczurek E, Mohammadi P, Rahnenführer J, Beerenwinkel N.

Bioinformatics. 2016 Apr 1;32(7):968-75. doi: 10.1093/bioinformatics/btv400. Epub 2015 Jul 9.


Correction: 24 Hours in the Life of HIV-1 in a T Cell Line.

Mohammadi P, Desfarges S, Bartha I, Joos B, Zangger N, Muñoz M, Günthard HF, Beerenwinkel N, Telenti A, Ciuffi A.

PLoS Pathog. 2015 Jun 15;11(6):e1005006. doi: 10.1371/journal.ppat.1005006. eCollection 2015 Jun.


Treatment of Hypertrophic Scar in Human with Autologous Transplantation of Cultured Keratinocytes and Fibroblasts along with Fibrin Glue.

Taghiabadi E, Mohammadi P, Aghdami N, Falah N, Orouji Z, Nazari A, Shafieyan S.

Cell J. 2015 Spring;17(1):49-58. Epub 2015 Apr 8.


Isolation and molecular identification of deteriorating fungi from Cyrus the Great tomb stones.

Mohammadi P, Maghboli-Balasjin N.

Iran J Microbiol. 2014 Oct;6(5):361-70.


System study of MPO promoter high-frequency polymorphic variants on transcription factor network.

Najafi M, Mohammadi P.

Gene. 2015 Apr 15;560(2):143-8. doi: 10.1016/j.gene.2015.01.055. Epub 2015 Jan 29.


Bioinformatics and HIV latency.

Ciuffi A, Mohammadi P, Golumbeanu M, di Iulio J, Telenti A.

Curr HIV/AIDS Rep. 2015 Mar;12(1):97-106. doi: 10.1007/s11904-014-0240-x. Review.


Effect of vitamin D3 supplementation on TNF-α serum level and disease activity index in Iranian IBD patients.

Dadaei T, Safapoor MH, Asadzadeh Aghdaei H, Balaii H, Pourhoseingholi MA, Naderi N, Zojaji H, Azimzadeh P, Mohammadi P, Zali MR.

Gastroenterol Hepatol Bed Bench. 2015 Winter;8(1):49-55.


Dynamic models of viral replication and latency.

Mohammadi P, Ciuffi A, Beerenwinkel N.

Curr Opin HIV AIDS. 2015 Mar;10(2):90-5. doi: 10.1097/COH.0000000000000136. Review.


A comparative proteomic analysis of responses to high temperature stress in hypocotyl of Canola (Brassica napus L.).

Ismaili A, Salavati A, Mohammadi PP.

Protein Pept Lett. 2014;22(3):285-99.


A study on literature obsolescence and core journals' cost-benefit in citations of the 'Scientific Medical Journal of Ahwaz'.

Zare-Farashbandi F, Mohammadi PP.

J Educ Health Promot. 2014 Aug 28;3:93. doi: 10.4103/2277-9531.139672. eCollection 2014.


Synergistic Effects of Bismuth Thiols and Various Antibiotics Against Pseudomonas aeruginosa Biofilm.

Varposhti M, Abdi Ali A, Mohammadi P.

Jundishapur J Microbiol. 2014 Mar;7(3):e9142. doi: 10.5812/jjm.9142. Epub 2014 Mar 1.


Assessment of Biofilm Formation and Resistance to Imipenem and Ciprofloxacin among Clinical Isolates of Acinetobacter baumannii in Tehran.

Abdi-Ali A, Hendiani S, Mohammadi P, Gharavi S.

Jundishapur J Microbiol. 2014 Jan;7(1):e8606. doi: 10.5812/jjm.8606. Epub 2014 Jan 1.


Prevalence of hepatitis D virus in hepatitis B virus infected patients referred to Taleghani hospital, Tehran, Iran.

Tahaei SM, Mohebbi SR, Azimzadeh P, Behelgardi A, Sanati A, Mohammadi P, Khanyaghma M, Hosseini Razavi A, Sharifian A, Zali MR.

Gastroenterol Hepatol Bed Bench. 2014 Summer;7(3):144-50.

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