Publications

Computational Biology // Massey University

Preprints


Transcribed enhancers in the macrophage immune response to Mycobacterium tuberculosis infection Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. bioRxiv, 2018


Bioconda: A sustainable and comprehensive software distribution for the life sciences. Grüning B, Dale R, Sjödin A, Rowe J, Chapman BA, Tomkins-Tinch CH, Valieris R, The Bioconda Team, Köster J. bioRxiv, 2017

Papers


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





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


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








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




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


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

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Scientific Reports, 2018, 8:6758

An evaluation of function of multicopy non-coding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Molecular Biology and Evolution, 2018, msy046

Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics & Chromatin, 2017, 10:50

Tweets // latest