Preprints
MinION Sequencing of colorectal cancer tumour microbiomes–a comparison with amplicon-based and RNA-Sequencing. Taylor WS, Pearson J, Miller A, Schmeier S, Frizelle FA, Purcell RV. bioRxiv. 2019, 10.1101/662270
Papers
Molecular subtyping improves prognostication of Stage 2 colorectal cancer. Purcell RV, Schmeier S, Lau YC, Pearson JF, Frizelle FA. BMC Cancer, 2019, 19, 1155
DeePEL: Deep learning architecture to recognize p-lncRNA and e-lncRNA promoters. Alam T, Islam M, Schmeier S, Househ M, Al-Thani DA. In proceedings: IEEE International Conference on Bioinformatics and Biomedicine, 2019, B516, accepted.
Effect of lncRNA-125 on mouse and human macrophage polarization and during Mtb infection. Pillay S, Tamgue O, Gcanga L, Jacobs R, Roy S, Schmeier S, Davids M, Suzuki H, Guler R, Brombacher F. European Journal of Immunology, 2019, 49, S3:256-257. (In proceedings: International Congress of Immunology ICI)
IL-4/IL-13-inducible lincRNA-MIR99AHG regulates macrophage polarization and acts as a promoter of Mtb growth. Gcanga L, Tamgue O, Ozturk M, Pillay S, Jacobs R, Schmeier S, Suzuki H, Brombacher F, Guler R. European Journal of Immunology, 2019, 49, S3:257-257. (In proceedings: International Congress of Immunology ICI)
Metagenomics and transcriptomics data from human colorectal cancer Visnovska T, Biggs P, Schmeier, Frizelle FA, Purcell RV. Sci. Data. 2019, 6:116
Differential targeting of c-MAF, Bach-1 and Elmo-1 by microRNA-143 and microRNA-365 promotes the intracellular growth of Mycobacterium tuberculosis in alternatively IL-4/IL-13 activated macrophages. Tamgue O, Gcanga L, Ozturk M, Whitehead L, Pillay S, Jacobs R, Roy S, Schmeier S, Davids M, Medvedeva YA, Dheda K, Suzuki H, Brombacher F, Guler R. Front. Immunol. 2019, 10:421.
Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. BMC Genomics, 2019, 20:71
Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes. Zhou H, Visnovska T, Gong H, Schmeier S, Hickford J, Ganley ARD. Molecular Phylogenetics and Evolution, 2018, 10.1016/j.ympev.2018.12.031.
Bioconda: sustainable and comprehensive software distribution for the life sciences. Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, The Bioconda Team (incl. Schmeier S), Köster J. Nature Methods, 2018, 15:475–476
Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Bajic VB, Guler R, Brombacher F, Suzuki H. Scientific Reports, 2018, 8:6758
An evaluation of function of multicopy non-coding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM. Molecular Biology and Evolution, 2018, msy046
Genome-wide profiling of transcribed enhancers during macrophage activation. Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. Epigenetics & Chromatin, 2017, 10:50
Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Purcell RV, Visnovska M, Biggs PJ, Schmeier S, Frizelle FA. Scientific Reports, 2017, 7(1):11590
Consensus molecular classification of colorectal cancer and association with the colonic microbiota. Purcell RV, Visnovska M, Biggs PJ, Schmeier S, Frizelle FA. Diseases of the Colon & Rectum, 2017, 60(6):E90-E91 (In proceedings: Annual Meeting of the American Society of Colon and Rectal Surgeons)
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Uludag M, Bajic VB. RNA Biology, 2017, 14(7):963-971
An atlas of human long non-coding RNAs with accurate 5' ends. Hon CC, Ramilowski JR, Harshbarger J, Bertin N, Rackham OJL, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs MA, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tan D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJL, Arner E, Hayashizaki Y, Carninci P, Forrest ARR. Nature, 2017, 543:199–204
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. Schmeier S, Alam T, Essack M, Bajic VB. Nucleic Acids Research, 2017, 45(D1): D145-D150
IRNdb: the database of immunologically relevant non-coding RNAs. Denisenko E, Ho D, Tamgue O, Ozturk M, Suzuki H, Brombacher F, Guler R, Schmeier S. Database, 2016, baw138
Batf2/Irf1 induces inflammatory responses in classically activated macrophages, LPS and mycobacterial infection. Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, de Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H. European Journal of Immunology, 2016, 46:7-7. (In proceedings: International Congress of Immunology ICI)
Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJL, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Bajic VB, Guler R, Brombacher F, Suzuki H. Nucleic Acids Research, 2015, 43(14):6969-82
Batf2/Irf1 Induces Inflammatory Responses in Classically Activated Macrophages, Lipopolysaccharides, and Mycobacterial Infection. Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, de Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H. The Journal of Immunology, 2015, 194(12):6035-6044
IL-4Rα-activated alternative macrophages are not decisive for Mycobacterium tuberculosis pathology and bacterial burden in mice. Guler R, Parihar SP, Savvi S, Logan E, Schwegmann A, Roy S, Nieuwenhuizen N, Ozturk M, Schmeier S, Suzuki H, and Brombacher F. PLoS ONE, 2015, 19;10(3):e0121070
A promoter-level mammalian expression atlas. Forrest ARR, Kawaji H, Rehli M, Baillie KJ, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, ..., Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y (The FANTOM consortium). Nature, 2014, 507:462–470
Identification of Estrogen Responsive Genes using Esophageal Squamous Cell Carcinoma (ESCC) as a Model. Essack M, MacPherson CR, Schmeier S, Bajic VB. BMC Systems Biology, 2012, 6:135
Network analysis of microRNAs and their regulation in human ovarian cancer. Schmeier S, Schaefer U, Essack M, Bajic VB. BMC Systems Biology, 2011, 5:183
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. Kaur M, MacPherson CR, Schmeier S, Narasimhan K, Choolani N, Bajic VB. BMC Systems Biology, 2011, 5:144
Simplified Method to Predict Mutual Interactions of Human Transcription Factors Based on Their Primary Structure. Schmeier S, Jankovic B, Bajic VB. PLoS ONE, 2011, 6(7):e21887
dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes. Schmeier S, Schaefer U, MacPherson CR, Bajic VB. PLoS ONE, 2011, 6(2):e16657
DDPC: Dragon Database of Genes Associated With Prostate Cancer. Maqungo MN, Kaur M, Radovanovic A, Schaefer U, Schmeier S, Christoffels A, Bajic VB. Nucleic Acids Research, 2010, 39(Database issue):D980-5
An atlas of combinatorial transcriptional regulation in mouse and man. Ravasi T, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kamburov A, Kanamori-Katayama M, Bertin N, Carninci P, ..., Lenhard B, Teichmann SA, Hume DA, Ideker T. Cell, 2010, 140(5):744-52
Dragon Database of Genes Implicated in Esophageal Cancer. Essack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, Christoffels A, Kaur M, Bajic VB. BMC Cancer, 2009, 9:219
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. Schmeier S, MacPherson CR, Essack M, Kaur M, Schaefer U, Suzuki H, Hayashizaki Y, Bajic VB. BMC Genomics, 2009, 10:595
Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information. Bajic VB, Schmeier S, MacPherson CR. CAP-ANALYSIS GENE EXPRESSION (CAGE) The Science of Decoding Genes Transcription, edited by Piero Carninci, Pan Stanford Publishing Pte Ltd, 2009
Prioritizing genes of potential relevance to diseases affected by sex hormones: An example of Myasthenia Gravis. Kaur M, Schmeier S, MacPherson CR, Hofmann O, Hide WA, Taylor S, Willcox N, Bajic VB. BMC Genomics, 2008, 9(1):481
Database for exploration of functional context of genes implicated in ovarian cancer. Kaur M, Radovanovic A, Essack M, Schaefer U, Maqungo M, Kibler T, Schmeier S, Christoffels A, Narasimhan K, Choolani M, Bajic VB. Nucleic Acids Research, 2008, 37(Database issue):D820-3
MACAT - MicroArray Chromosome Analysis Tool. Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S. Bioinformatics, 2005, 21(9):2112-2113
Finding Kinetic Parameters Using Text Mining. Hakenberg J, Schmeier S, Kowald A, Klipp E, Leser U. OMICS: A Journal of Integrative Biology, 2004, 8(2):131-152
Text Mining for Systems Biology Using Statistical Learning Methods. Schmeier S, Hakenberg J, Kowald, A, Klipp E, Leser U. Proc. of the 3. Workshop des Arbeitskreises Knowledge Discovery (AKKD), 2003, Karlsruhe, Germany
Contact
Dr. Sebastian Schmeier
Research Group Leader
Senior Lecturer in Bioinformatics/GenomicsMassey University
Auckland, New Zealand
+64 9 414 0800 (ext: 43538)
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