Publications

Computational Biology // Massey University

Papers


Genome-wide profiling of transcribed enhancers during macrophage activation. Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. Epigenetics & Chromatin, 2017, accepted.
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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, doi: 10.1038/s41598-017-11237-6 //
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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, 10.1080/15476286.2017.1312243. //

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, doi: 10.1093/nar/gkw1007 //

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, doi: 10.1093/database/baw138 //
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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, doi: 10.1093/nar/gkv646 //

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, doi:10.4049/jimmunol.1402521 //

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, doi:10.1186/1752-0509-5-183 //

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, doi:10.1186/1752-0509-5-144 //

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, doi:10.1371/journal.pone.0021887 //

dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes. Schmeier S, Schaefer U, MacPherson CR, Bajic VB. PLoS ONE, 2011, 6(2):e16657, doi:10.1371/journal.pone.0016657 //


TcoF-DB: Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins. Schaefer U, Schmeier S, Bajic VB. Nucleic Acids Research, Database Issue 2011; doi:10.1093/nar/gkq945; 2010 Oct 21. //

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, Database Issue 2011; 2010; doi: 10.1093/nar/gkq849 //

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 Mar 5;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 //

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. The FANTOM consortium. Nature Genetics, 2009, 41(5):553-62 //

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/Genomics

Massey University, INMS
Auckland, New Zealand
+64 9 414 0800 (ext: 43538)

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Publications // latest

Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics & Chromatin, 2017, accepted.

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Scientific Reports, 2017, doi: 10.1038/s41598-017-11237-6

Consensus molecular classification of colorectal cancer and association with the colonic microbiota. Diseases of the Colon & Rectum, 2017, 60(6):E90-E91 (In proceedings: Annual Meeting of the American Society of Colon and Rectal Surgeons)

Workshops // upcoming

[ Nov 2017 ] Software Carpentry Workshop, Massey University Auckland

Tweets // latest