By Dr Omid Faridani

Journal articles

Schnegg-Kaufmann AS; Thoms JAI; Bhuyan GS; Hampton HR; Vaughan L; Rutherford K; Kakadia PM; Lee HM; Johansson Beves EMV; Failes TW; Arndt GM; Koval J; Lindeman R; Warburton P; Rodriguez-Meira A; Mead AJ; Unnikrishnan A; Davidson S; Polizzotto MN; Hertzberg M; Papaemmanuil E; Bohlander SK; Faridani OR; Jolly CJ; Zanini F; Pimanda JE, 2023, 'Contribution of mutant HSC clones to immature and mature cells in MDS and CMML, and variations with AZA therapy', Blood, 141, pp. 1316 - 1321, http://dx.doi.org/10.1182/blood.2022018602

Baumann V; Athanasiou AT; Faridani OR; Schwerdtfeger AR; Wallner B; Steinborn R, 2023, 'Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma', Frontiers in Genetics, 13, http://dx.doi.org/10.3389/fgene.2022.1058668

Salignon J; Faridani OR; Miliotis T; Janssens GE; Chen P; Zarrouki B; Sandberg R; Davidsson P; Riedel CG, 2023, 'Age prediction from human blood plasma using proteomic and small RNA data: a comparative analysis', Aging, 15, pp. 5240 - 5265, http://dx.doi.org/10.18632/aging.204787

Baumann V; Athanasiou AT; Faridani OR; Schwerdtfeger AR; Wallner B; Steinborn R, 2023, 'Corrigendum: Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma, (Front. Genet, (2023), 13, (1058668), 10.3389/fgene.2022.1058668)', Frontiers in Genetics, 14, http://dx.doi.org/10.3389/fgene.2023.1216150

Thoms JAI; Schnegg-Kaufmann A; Bhuyan GS; Hampton HR; Vaughan L; Rutherford K; Kakadia PM; Lee HM; Johansson E; Failes TW; Arndt GM; Koval J; Davidson S; Lindeman R; Warburton P; Rodriguez-Meira A; Mead AJ; Unnikrishnan A; Hertzberg M; Polizzotto MN; Papaemmanuil E; Bohlander SK; Faridani O; Jolly CJ; Zanini F; Pimanda JE, 2022, 'Clinical Response to Azacytidine (AZA) Is Associated with Increased Contribution from Mutated Blood Progenitors: Insights from Single Cell Genotyping of Matched Stem/Progenitor and Mature Blood Cells from MDS/CMML Patients Pre- and Post-AZA Treatment', Blood, 140, pp. 9751 - 9752, http://dx.doi.org/10.1182/blood-2022-163158

Schnegg-Kaufmann A; Thoms J; Bhuyan GS; Henry H; Vaughan L; Rutherford K; Kakadia P; Johansson E; Failes T; Greg A; Koval J; Lindeman R; Warburton P; Rodriguez-Meira A; Mead A; Unnikrishnan A; Bohlander S; Pappaemmanuil E; Faridani O; Jolly C; Zanini F; Pimanda J, 2022, 'P748: SINGLE CELL GENOTYPING OF MATCHED BONE MARROW AND PERIPHERAL BLOOD CELLS IN TREATMENT NAIVE AND AZA-TREATED MDS AND CMML', HemaSphere, 6, pp. 643 - 644, http://dx.doi.org/10.1097/01.hs9.0000845876.01682.15

Von Grothusen C; Frisendahl C; Modhukur V; Lalitkumar PG; Peters M; Faridani OR; Salumets A; Boggavarapu NR; Gemzell-Danielsson K, 2022, 'Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure', Human Reproduction, 37, pp. 734 - 746, http://dx.doi.org/10.1093/humrep/deac019

Godakumara K; Ord J; Lättekivi F; Dissanayake K; Viil J; Boggavarapu NR; Faridani OR; Jääger K; Velthut-Meikas A; Jaakma Ü; Salumets A; Fazeli A, 2021, 'Trophoblast derived extracellular vesicles specifically alter the transcriptome of endometrial cells and may constitute a critical component of embryo-maternal communication', Reproductive Biology and Endocrinology, 19, http://dx.doi.org/10.1186/s12958-021-00801-5

Zheleznyakova GY; Piket E; Needhamsen M; Hagemann-Jensen M; Ekman D; Han Y; James T; Khademi M; Al Nimer F; Scicluna P; Huang J; Kockum I; Faridani OR; Olsson T; Piehl F; Jagodic M, 2021, 'Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology', Proceedings of the National Academy of Sciences of the United States of America, 118, http://dx.doi.org/10.1073/pnas.2011574118

Hagemann-Jensen M; Ziegenhain C; Chen P; Ramsköld D; Hendriks GJ; Larsson AJM; Faridani OR; Sandberg R, 2020, 'Single-cell RNA counting at allele and isoform resolution using Smart-seq3', Nature Biotechnology, 38, pp. 708 - 714, http://dx.doi.org/10.1038/s41587-020-0497-0

Ramsköld D; Luo S; Wang YC; Li R; Deng Q; Faridani OR; Daniels GA; Khrebtukova I; Loring JF; Laurent LC; Schroth GP; Sandberg R, 2020, 'Author Correction: Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells (Nature Biotechnology, (2012), 30, 8, (777-782), 10.1038/nbt.2282)', Nature Biotechnology, 38, pp. 374, http://dx.doi.org/10.1038/s41587-020-0427-1

Zheleznyakova GY; Piket E; Needhamsen M; Hagemann-Jensen M; Ekman D; Khademi M; Nimer FA; Scicluna P; Faridani O; Olsson T; Piehl F; Jagodic M, 2020, 'Profiling of small non-coding RNAs across cellular and biofluid compartments: implications for multiple sclerosis immunopathology', , http://dx.doi.org/10.1101/2020.05.15.097519

Larsson AJM; Johnsson P; Hagemann-Jensen M; Hartmanis L; Faridani OR; Reinius B; Segerstolpe Å; Rivera CM; Ren B; Sandberg R, 2019, 'Genomic encoding of transcriptional burst kinetics', Nature, 565, pp. 251 - 254, http://dx.doi.org/10.1038/s41586-018-0836-1

Hagemann-Jensen M; Abdullayev I; Sandberg R; Faridani OR, 2018, 'Small-seq for single-cell small-RNA sequencing', Nature Protocols, 13, pp. 2407 - 2424, http://dx.doi.org/10.1038/s41596-018-0049-y

Faridani OR; Abdullayev I; Hagemann-Jensen M; Schell JP; Lanner F; Sandberg R, 2016, 'Single-cell sequencing of the small-RNA transcriptome', Nature Biotechnology, 34, pp. 1264 - 1266, http://dx.doi.org/10.1038/nbt.3701

Simonson OE; Mougiakakos D; Heldring N; Bassi G; Johansson HJ; Dalén M; Jitschin R; Rodin S; Corbascio M; El Andaloussi S; Wiklander OPB; Nordin JZ; Skog J; Romain C; Koestler T; Hellgren-Johansson L; Schiller P; Joachimsson P-O; Hägglund H; Mattsson M; Lehtiö J; Faridani OR; Sandberg R; Korsgren O; Krampera M; Weiss DJ; Grinnemo K-H; Le Blanc K, 2016, 'In Vivo Effects of Mesenchymal Stromal Cells in Two Patients With Severe Acute Respiratory Distress Syndrome', Stem Cells Translational Medicine, 5, pp. 845 - 845, http://dx.doi.org/10.5966/sctm.2015-0021erratum

Simonson OE; Mougiakakos D; Heldring N; Bassi G; Johansson HJ; Dalén M; Jitschin R; Rodin S; Corbascio M; El Andaloussi S; Wiklander OPB; Nordin JZ; Skog J; Romain C; Koestler T; Hellgren-Johansson L; Schiller P; Joachimsson PO; Hägglund H; Mattiasmattsson M; Lehtiö J; Faridani OR; Sandberg R; Korsgren O; Krampera M; Weiss DJ; Grinnemo KH; Le Blanc K, 2015, 'In vivo effects of mesenchymal stromal cells in two patients with severe acute respiratory distress syndrome', Stem Cells Translational Medicine, 4, pp. 1199 - 1213, http://dx.doi.org/10.5966/sctm.2015-0021

Faridani OR; Sandberg R, 2015, 'Putting cells in their place', Nature biotechnology, 33, pp. 490 - 491, http://dx.doi.org/10.1038/nbt.3219

Callegari S; Gastaldello S; Faridani OR; Masucci MG, 2014, 'Epstein-Barr virus encoded microRNAs target SUMO-regulated cellular functions', FEBS Journal, 281, pp. 4935 - 4950, http://dx.doi.org/10.1111/febs.13040

Picelli S; Faridani OR; Björklund AK; Winberg G; Sagasser S; Sandberg R, 2014, 'Full-length RNA-seq from single cells using Smart-seq2', Nature Protocols, 9, pp. 171 - 181, http://dx.doi.org/10.1038/nprot.2014.006

Picelli S; Björklund AK; Faridani OR; Sagasser S; Winberg G; Sandberg R, 2013, 'Smart-seq2 for sensitive full-length transcriptome profiling in single cells', Nature Methods, 10, pp. 1096 - 1100, http://dx.doi.org/10.1038/nmeth.2639

Ramsköld D; Luo S; Wang YC; Li R; Deng Q; Faridani OR; Daniels GA; Khrebtukova I; Loring JF; Laurent LC; Schroth GP; Sandberg R, 2012, 'Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells', Nature Biotechnology, 30, pp. 777 - 782, http://dx.doi.org/10.1038/nbt.2282

Arefian E; Kiani J; Soleimani M; Shariati SAM; Aghaee-Bakhtiari SH; Atashi A; Gheisari Y; Ahmadbeigi N; Banaei-Moghaddam AM; Naderi M; Namvarasl N; Good L; Faridani OR, 2011, 'Analysis of microRNA signatures using size-coded ligation-mediated PCR', Nucleic Acids Research, 39, pp. e80 - e80, http://dx.doi.org/10.1093/nar/gkr214

Gastaldello S; Hildebrand S; Faridani O; Callegari S; Palmkvist M; Di Guglielmo C; Masucci MG, 2010, 'A deneddylase encoded by Epstein-Barr virus promotes viral DNA replication by regulating the activity of cullin-RING ligases', Nature Cell Biology, 12, pp. 351 - 361, http://dx.doi.org/10.1038/ncb2035

Faridani OR; Mcinerney GM; Gradin K; Good L, 2008, 'Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions', Nucleic Acids Research, 36, pp. e99, http://dx.doi.org/10.1093/nar/gkn445

Nikravesh A; Dryselius R; Faridani OR; Goh S; Sadeghizadeh M; Behmanesh M; Ganyu A; Klok EJ; Zain R; Good L, 2007, 'Antisense PNA accumulates in Escherichia coli and mediates a long post-antibiotic effect', Molecular Therapy, 15, pp. 1537 - 1542, http://dx.doi.org/10.1038/sj.mt.6300209

Faridani OR; Nikravesh A; Pandey DP; Gerdes K; Good L, 2006, 'Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli', Nucleic Acids Research, 34, pp. 5915 - 5922, http://dx.doi.org/10.1093/nar/gkl750

Conference Abstracts

Von Grothusen C; Frisendahl C; Vijayachitra M; Parameswaran Grace L; Peters M; Faridani O; Andres S; Rao Boggavarapu N; Gemzell-Danielsson K, 2022, 'P-420 Dysregulated microRNAs in uterine fluid from women with recurrent implantation failure are linked to endometrial receptivity and implantation', in Human Reproduction, Oxford University Press (OUP), Vol. 37, http://dx.doi.org/10.1093/humrep/deac107.397

Zheleznyakova G; Piket E; Needhamsen M; Hagemann-Jensen M; Ekman D; Khademi M; Al Nimer F; Scicluna P; Faridani O; Olsson T; Piehl F; Jagodic M, 2020, 'Profiling of small non-coding rnas across cellular and biofluid compartments in patients with multiple sclerosis', in MULTIPLE SCLEROSIS JOURNAL, SAGE PUBLICATIONS LTD, ELECTR NETWORK, Vol. 26, pp. 183 - 184, presented at 8th Joint ACTRIMS-ECTRIMS Meeting (MSVirtual), ELECTR NETWORK, 11 September 2020 - 13 September 2020, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000596547100364&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Zheleznyakova G; Piket E; Needhamsen M; Hagemann-Jensen M; Faridani O; Marabita F; Khademi M; Piehl F; Olsson T; Jagodic M, 2019, 'Genome-wide small-noncoding RNA analysis in patients with multiple sclerosis', in MULTIPLE SCLEROSIS JOURNAL, SAGE PUBLICATIONS LTD, SWEDEN, Stockholm, Vol. 25, pp. 726 - 726, presented at 35th Congress of the European-Committee-for-Treatment-and-Research-in-Multiple-Sclerosis (ECTRIMS) / 24th Annual Conference of Rehabilitation in MS, SWEDEN, Stockholm, 11 September 2019 - 13 September 2019, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000485303103126&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Preprints

Frisendahl C; Gemzell-Danielsson K; Nair K; Koch F; Menezes J; Sheiki M; Dahlgren K; Alnahal W; Lindgren K; Bohlin T; Olofsson J; Töhönen V; Vafaee F; Lalitkumar PG; Boggavarapu NR; Faridani OR, 2025, Blastocoel fluid RNA predicts pregnancy outcome in assisted reproduction, http://dx.doi.org/10.1101/2025.03.09.641486

Tarbier M; Mackowiak SD; Sekar V; Bonath F; Yapar E; Fromm B; Faridani OR; Biryukova I; Friedländer MR, 2024, Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells, http://dx.doi.org/10.1101/2024.03.24.586475

Schnegg-Kaufmann A; Thoms J; Bhuyan GS; Hampton H; Vaughan L; Rutherford K; Kakadia P; Johansson E; Failes T; Arndt G; Koval J; Lindeman R; Warburton P; Rodriguez-Meira A; Mead A; Unnikrishnan A; Bohlander S; Papaemmanuil E; Faridani O; Jolly C; Zanini F; Pimanda J, 2022, Single cell genotyping of matched bone marrow and peripheral blood cells in treatment naive and AZA-treated MDS and CMML, http://dx.doi.org/10.1101/2022.01.20.476890

Hagemann-Jensen M; Ziegenhain C; Chen P; Ramsköld D; Hendriks G-J; Larsson AJM; Faridani O; Sandberg R, 2019, Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3, http://dx.doi.org/10.1101/817924

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