Publications at KAUST

Publications at KAUST

2018
149. Kalkatawi M, Magana-Mora A, Jankovic B, Bajic VB (2018) DeepGSR: An optimized deep-learning structure for the recognition of genomic signals and regions. Bioinformatics.​ doi: 10.1093/bioinformatics/bty752​ 

148.  Kordopati V, Salhi A, Razali R, Radovanovic A, Tifratene F, Uludag M, Li Y, Bokhari A, AlSaieedi A, Bin Raies A, Van Neste C, Essack M, Bajic VB (2018) DES-Mutation: System for Exploring Links of Mutations and Diseases. Scientific Reports​. 2018; 8: 13359. doi: 10.1038/s41598-018-31439-w​​​

147. Motwalli O, Essack M, Salhi A, Hanks J, Mijakovic I, Bajic VB (2018) BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria. PLoS One. 13(8):e0202002. doi:10.1371/journal.pone.0202002​

146. Kobiyama A, Ikeo K, Reza MS, Rashid J, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S. Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay. Gene. 2018 Jul 30;665:149-154. doi: 10.1016/j.gene.2018.04.073​

145. Rashid J, Kobiyama A, Reza MS, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S. Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing. Gene. 2018 Jul 30;665:127-132. doi: 10.1016/j.gene.2018.04.071​

144. Kudo T, Kobiyama A, Rashid J, Reza MS, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Mineta K, Bajic V, Gojobori T, Watabe S. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis. Gene. 2018 Jul 30;665:174-184. doi: 10.1016/j.gene.2018.04.072​

143. Reza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S. Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay. Gene. 2018 Jul 30;665:185-191. doi: 10.1016/j.gene.2018.04.074​

142. Reza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S. Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay. Gene. 2018 Jul 30;665:192-200. doi: 10.1016/j.gene.2018.04.075

141. Khamis AM, Motwalli O, Oliva R, Jankovic BR, Medvedeva YA, Ashoor H, Essack M, Gao X, Bajic VB. A novel method for improved accuracy of transcription factor binding site prediction. Nucleic Acids Res. 2018 Jul 6;46(12):e72. doi: 10.1093/nar/gky237​

140. Olayan RS, Ashoor H, Bajic VB. (corrected proof) DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. Bioinformatics. 2018 Jun 15. doi: 10.1093/bioinformatics/bty417​. [Epub ahead of print]

139. Soufan O, Ba-Alawi W, Magana-Mora A, Essack M, Bajic VB. DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. Sci Rep. 2018 Jun 14;8(1):9110. doi: 10.1038/s41598-018-27495-x​.

138. Raies AB, Bajic VB. In silico toxicology: comprehensive benchmarking of multi-label classification methods applied to chemical toxicity data. Wiley Interdiscip Rev Comput Mol Sci. 2018 May-Jun;8(3):e1352. doi: 10.1002/wcms.1352​. Review.

137. Othoum G, Bougouffa S, Razali R, Bokhari A, Alamoudi S, Antunes A, Gao X, Hoehndorf R, Arold ST, Gojobori T, Hirt H, Mijakovic I, Bajic VB, Lafi FF, Essack M. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters. BMC Genomics. 2018 May 22;19(1):382. doi: 10.1186/s12864-018-4796-5​.

136. 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, Guler R, Bajic VB, Brombacher F, Suzuki H. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Sci Rep. 2018 Apr 30;8(1):6758. doi: 10.1038/s41598-018-24509-6​.

135. Zhang W, Tian RM, Sun J, Bougouffa S, Ding W, Cai L, Lan Y, Tong H, Li Y, Jamieson AJ, Bajic VB, Drazen JC, Bartlett D, Qian PY. Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean's Deepest Point. mSystems. 2018 Apr 10;3(3). pii: e00009-18. doi: 10.1128/mSystems.00009-18​. eCollection 2018 May-Jun.​

134. Olayan RS, Ashoor H, Bajic VB. DDR: Efficient computational method to predict drug–target interactions using graph mining and machine learning approaches. Bioinformatics, 2018 Apr 1;34(7):1164-1173. doi: 10.1093/bioinformatics/btx731​

133. Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934​. eCollection 2018 Mar.

132. An R, Lin P, Bougouffa S, Essack M, Boxrud D, Bajic VB, Vidovic S. Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts. Genome Announc. 2018 Jan 25;6(4). pii: e01550-17. doi: 10.1128/genomeA.01550-17​.

131. Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259. doi: 10.1093/nar/gkx1106​.  
       ​
2017

130. Magana-Mora A, Kalkatawi M, Bajic VB. Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA. BMC Genomics. 2017 Aug 15;18(1):620.  doi:10.1186/s12864-017-4033-7​

129. Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biol. 2017 Jul 3;14(7):963-971.  doi:10.1080/15476286.2017.1312243​

128. Jimenez-Infante F, Ngugi DK, Vinu M, Blom J, Alam I, Bajic VB, Stingl U. Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade. FEMS Microbiol Ecol. 2017 Jul 1;93(7). doi:10.1093/femsec/fix083​

 
127. Magana-Mora A, Bajic VB. OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models. Scientific Reports. 2017 Jun 20;7(1):3898. doi:10.1038/s41598-017-04281-9​

126. Nielsen J, Archer J, Essack M, Bajic VB, Gojobori T, Mijakovic I. Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Appl Microbiol Biotechnol. 2017 Jun;101(12):4837-4851. doi:10.1007/s00253-017-8310-9​

125. Ashoor H, Louis-Brennetot C, Janoueix-Lerosey I, Bajic VB, Boeva V. HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. Nucleic Acids Res. 2017 May 5;45(8):e58. doi:10.1093/nar/gkw1319​

124. Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R. Semantic prioritization of novel causative genomic variants. PLoS Comput Biol. 2017 Apr 17;13(4):e1005500.
doi:10.1371/journal.pcbi.1005500

123. Alshahrani M, Soufan O, Magana-Mora A, Bajic VB. DANNP: an efficient artificial neural network pruning tool. PeerJ Computer Science. 2017; 3:e137. doi:10.7717/peerj-cs.137​

122. Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks J, Kapfer C, Mineta K, Gojobori T, Bajic VB. FARNA: Knowledgebase of Inferred Functions of Non-coding RNA Transcripts. Nucleic Acids Res. 2017 Mar 17;45(5):2838-2848. 

121. Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM. Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium. Genome Announc. 2017 Mar 2;5(9). pii: e01707-16. ​doi:10.1128/genomeA.01707-16​

120. Kleftogiannis D, Kalnis P, Arner E, Bajic VB. Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Res. 2017 Feb 28;45(4):e25. doi:10.1093/nar/gkw1015​

119. Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM. Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea. Genome Announc. 2017 Feb 16;5(7). pii: e01638-16. doi:10.1128/genomeA.01638-16

118. Shahmuradov IA, Razali RM, Bougouffa S, Radovanovic A, Bajic VB. bTSSfinder: a novel tool for the prediction of promoters in Cyanobacteria and Escherichia coli. Bioinformatics. 2017 Feb 1;33(3):334-340.​ doi:10.1093/bioinformatics/btw629​

117. Lafi FF, AlBladi ML, Salem NM, Al-Banna L, Alam I, Bajic VB, Hirt H, Saad MM. Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan. Genome Announc. 2017 Jan 12;5(2). pii: e01437-16. doi:10.1128/genomeA.01437-16​

116. Motwalli O, Essack M, Jankovic BR, Ji B, Liu X, Ansari HR, Hoehndorf R, Gao X, Arold ST, Mineta K, Archer JA, Gojobori T, Mijakovic I, Bajic VB. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics. 2017 Jan 5;18(1):33. doi:10.1186/s12864-016-3389-4

115. Schmeier S, Alam T, Essack M, Bajic VB. TcoF-DB v2: Update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Res. 2017 Jan 4;45(D1):D145-D150.​ doi:10.1093/nar/gkw1007​


2016

114. Wang, Y., Gao, ZM., Li, JT, Bougouffa S, Tian RM, Bajic VB, Qian PY (2016) Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments. Science Bulletin 61:1176. doi:10.1007/s11434-016-1135-6​

113. Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, LaJeunesse TC, Voolstra CR (2016) Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci Rep. 2016 Dec 22;6:39734. doi:10.1038/srep39734​

112. Lafi FF, Ramirez-Prado JS, Alam I, Bajic VB, Hirt H, Saad MM (2016) Draft Genome Sequence of Plant Growth-Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia. Genome Announc 5(4):e01520-16. doi:10.1128/genomeA.01520-16​

111. Soufan O, Ba-Alawi W, Afeef M, Essack M, Kalnis P, Bajic VB (2016) DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning. J Cheminform 8:64. doi:10.1186/s13321-016-0177-8​

110. Al-Amoudi S, Razali R, Essack M, Amini MS, Bougouffa S, Archer JA, Lafi FF, Bajic VB (2016) Metagenomics as a Preliminary Screen for Antimicrobial Bioprospecting Gene 594(2):248–258. doi:10.1016/j.gene.2016.09.021​

109. Lafi FF, Ramirez-Prado JS, Alam I, Bajic VB, Hirt H, Saad MM (2016) Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance in Planta Genome Announcements 4(6):e01214-e01216. doi:10.1128/genomeA.01214-16​

108. Al-Amoudi S, Essack M, Simões MF, Bougouffa S, Soloviev I, Archer JA, Lafi FF, Bajic VB (2016) Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential. Mar. Drugs 14(9):E165. doi:10.3390/md14090165​

107. Lafi FF, Bokhari A, Alam I, Bajic VB, Hirt H, Saad MM (2016) Draft genome sequence of the plant growth-promoting Cupriavidus gilardii strain JZ4 isolated from the desert plant Tribulus terrestris. Genome Announc 4(4):e00678-16. doi:10.1128/genomeA.00678-16​

106. Ba-Alawi W, Soufan O, Essack M, Kalnis P, Bajic VB (2016) DASPfind: new efficient method to predict drug–target interactions. Journal of Cheminformatics 8:15. doi:10.1186/s13321-016-0128-4​

105. Cao H, Dong C, Bougouffa S, Li JT, Zhang W, Shao Z, Bajic V, Qian PY (2016) Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge. Sci Rep 6:22842. doi:10.1038/srep22842​

104. Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U (2016) Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea. Scientific Reports Jan 13;6:19181. doi:10.1038/srep19181​

103. Jimenez-Infante F, Ngugi D, Vinu M, Alam I, Kamau A, Blom J, Bajic VB, Stingl U (2016) Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs. Appl Environ Microbiol. 82(4):1215-1226. doi:10.1128/AEM.02852-15 pii: AEM.02852-15​.

102. Bin Raies A, Bajic VB (2016) In silico toxicology: computational methods for the prediction of chemical toxicity. WIREs Comput Mol Sci 6:147–172. doi:10.1002/wcms.1240​

101. Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev V (2016) HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res 44(D1):D116-D125. doi:10.1093/nar/gkv1249 pii: S1672-0229(15)00138-2​

100. Salhi A, Essack M, Radovanovic A, Marchand B, Bougouffa S, Antunes A, Simões M, Lafi F, Motwalli O, Bokhari A, Malas T, Al Amoudi S, Othoum G, Alam I, Mineta K, Gao X, Hoehndorf R, Archer JAC, Gojobori T, Bajic V (2016) DESM: Portal for microbial knowledge exploration systems. Nucleic Acids Res 44(D1):D624-D633. doi:10.1093/nar/gkv1147​ pii:gkv1147 PMID: 26546514


2015
99. Zhao F, Bajic VB (2015) The Value and Significance of Metagenomics of Marine Environments. Genomics, Proteomics & Bioinformatics Special Issue: Metagenomics of Marine Environments, 13(5):271-274. doi:10.1016/j.gpb.2015.10.002​

98. Othman S, Ba-alawi W, Afeef M, Essack M, Rodionov V, Kalnis P, Bajic VB (2015) Mining chemical activity status from high-throughput screening assays. PLoS One 2015 Dec 14;10(12):e0144426. doi:10.1371/journal.pone.0144426​

97.Simões AF, Antunes A, Ottoni C, Amini MS, Alam I, Alzubaidy H, Mokhtar NA, Archer JAC, Bajic VB (2015) Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea - A Metagenomic Approach. Genomics, Proteomics & Bioinformatics. Special Issue: Metagenomics of Marine Environments, 13(5):310-320. doi:10.1016/j.gpb.2015.07.002​ pii: S1672-0229(15)00138-2

96. Alzubaidy H, Essack M, Malas TB, Bokhari A, Motwalli O, Kamanu FK, Jamhor SA, Mokhtar NA, Antunes A, Simões MF, Alam I, Bougouffa S, Lafi FF, Bajic VB, Archer JA (2015) Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea. Gene 576(2):626-636. doi:10.1016/j.gene.2015.10.032​ PMID: 26475934

95. Antunes A, Alam I, Simões MF, Daniels C, Ferreira AJS, Siam R, El-Dorry H, Bajic VB (2015) First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea. Genomics, Proteomics & Bioinformatics. Special Issue: Metagenomics of Marine Environments, 13(5):304-309. doi:10.1016/j.gpb.2015.06.004​ pii: S1672-0229(15)00137-0

94. Kleftogiannis D, Kalnis P, Bajic VB (2015) Progress and challenges in bioinformatics approaches for enhancer identification. Brief Bioinform Dec. 3, Advanced Access doi:10.1093/bib/bbv101​ pii: bbv101

93. Ashoor H, Kleftogiannis D, Radovanovic A, Bajic VB (2015) DENdb: database of integrated human enhancers. Database 2015:bav085 doi:10.1093/database/bav085​

92. Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li Y, Cai L, Wong YH, Zhang G, Zhou G, Zhang X, Bajic VB, Al-Suwailem A, Qian PY (2015) Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. Environ Microbiol 17(10):4089-4104. doi:10.1111/1462-2920.12978​

91. Gao ZM, Wang Y, Tian RM, Lee OO, Wong YH, Batang ZB, Al-Suwailem A, Lafi FF, Bajic VB, Qian PY (2015) Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora. PeerJ 3:e890. doi:10.7717/peerj.890​

90. Kalkatawi M, Alam I, Bajic VB (2015) BEACON: automated tool for Bacterial gEnome Annotation ComparisON. BMC Genomics 16(1):1-8. doi:10.1186/s12864-015-1826-4​

89. Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, Guler R, Consortium F, Brombacher F, Suzuki H (2015) Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Nucleic Acids Res 43(14):6969-6982. doi:10.1093/nar/gkv646​

88. Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB (2015) Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Sci Rep 5:11136. doi:10.1038/srep11136​

87. Ngugi DK, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U (2015) Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. The ISME journal 9(2):396-411. 
doi:10.1038/ismej.2014.137

86. Soufan O, Kleftogiannis D, Kalnis P, Bajic VB (2015) DWFS: A Wrapper Feature Selection Tool Based on a Parallel Genetic Algorithm. PLoS One 10(2):e0117988. doi:10.1371/journal.pone.0117988​

85. Chen L, Sun J, Zhang H, Au DW, Lam PK, Zhang W, Bajic V, Qiu J, Qian P (2015) Hepatic proteomic responses in marine medaka (Oryzias melastigma) chronically exposed to antifouling compound butenolide [5-octylfuran-2(5H)-one] or 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT). Environ Sci Technol 49(3):1851-1869. doi:10.1021/es5046748​

84. Khamis AM, Essack M, Gao X, Bajic VB (2015) Distinct Profiling of Antimicrobial Peptide Families. Bioinformatics 31(6):849-856. doi:10.1093/bioinformatics/btu738​


2014

83. Chen L, Zhang H, Sun J, Wong YH, Han Z, Au DW, Bajic VB, Qian PY (2014) Proteomic changes in brain tissues of marine medaka (Oryzias melastigma) after chronic exposure to two antifouling compounds: Butenolide and 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT). Aquat Toxicol. 157:47-56. doi:10.1016/j.aquatox.2014.09.010​

82. Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z (2014) LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res 43(Database issue):D187-192. doi:10.1093/nar/gku1167​

81. Kleftogiannis D, Kalnis P, Bajic VB (2014) DEEP: A general computational framework for predicting enhancers. Nucleic Acids Res 43(1):e6. doi:10.1093/nar/gku1058​

80. Essack M, Alzubaidy HS, Bajic VB, Archer JA (2014) Chemical Compounds Toxic to Invertebrates Isolated from Marine Cyanobacteria of Potential Relevance to the Agricultural Industry. Toxins 6(11):3058-3076. doi:10.3390/toxins6113058​

79. Tian RM, Wang Y, Bougouffa S, Gao ZM, Cai L, Zhang WP, Bajic VB, Qian PY (2014) Effect of copper treatment on the bacterial community in the sponge Haliclona cymaeformis. MBio 5(6):e01980. doi:10.1128/mBio.01980-14​

78. Bougouffa S, Radovanovic A, Essack M, Bajic VB (2014) DEOP: a database on osmoprotectants and associated pathways. Database (Oxford) doi:10.1093/database/bau100​

77. Grötzinger SW, Alam I, Ba Alawi W, Bajic VB, Stingl U, Eppinger J (2014) Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). Front Microbiol 5:134. doi:10.3389/fmicb.2014.00134​

76. Tian RM, Wang Y, Bougouffa S, Gao ZM, Cai L, Bajic V, Qian PY (2014) Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge. Environ Microbiol 16(11):3548-3561. 
doi:10.1111/1462-2920.12586
75. Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R (2014) Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Frontiers in Microbiology section Aquatic Microbiology 5:487. doi:10.3389/fmicb.2014.00487​

74. Gao ZM, Wang Y, Lee OO, Tian RM, Wong YH, Bougouffa S, Batang Z, Al-Suwailem A, Lafi FF, Bajic VB, Qian PY (2014) Pyrosequencing Reveals the Microbial Communities in the Red Sea Sponge Carteriospongia foliascens and Their Impressive Shifts in Abnormal Tissues. Microb Ecol. 68(3):621-632. doi:10.1007/s00248-014-0419-0​

73. Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, Stingl U, Archer JAC, Jankovic BR, Sogin M, Bajic VB, El-Dorry H (2014) Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS One 9(6):e97338. doi:10.1371/journal.pone.0097338​

72. The FANTOM Consortium and the RIKEN PMI and CLST (DGT) (2014) A promoter-level mammalian expression atlas. Nature 507:462-470. doi:10.1038/nature13182​ (The core members of FANTOM5 phase 1 were Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Timo Lassmann, Masayoshi Itoh, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci and Yoshihide Hayashizaki)

71. Gao ZM, Wang Y, Tian RM, Wong YH, Batang ZB, Al-Suwailem AM, Bajic VB, Qian PV (2014) Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont candidatus Synechococcus spongiarum. MBio 5(2):e00079-14. doi:10.1128/mBio.00079-14​

70. Lee OO, Wang Y, Tian R, Zhang W, Shek CS, Bougouffa S, Al-Suwailem A, Batang ZB, Xu W, Wang GC, Zhang X, Lafi FF, Bajic VB, Qian PY (2014) In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system. Sci Rep 4:3587. doi:10.1038/srep03587​

69. Alam T, Medvedeva YA, Jia H, Brown JB, Lipovich L, Bajic VB (2014) Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PLoS One 9(10):e109443. 
doi:10.1371/journal.pone.0109443
68. Bin Raies A, Mansour H, Incitti R, Bajic VB (2014) DDMGD: the database of text-mined associations between genes methylated in diseases from different species. Nucleic Acids Res 43(Database issue):D879-886. doi:10.1093/nar/gku1168​

67. Jimenez-Infante F, Ngugi DK, Alam I, Rashid M, Baalawi W, Kamau AA, Bajic VB, Stingl U (2014) Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats. FEMS Microbiol Ecol 89(1):181-197. doi:10.1111/1574-6941.12348​

66. Medvedeva YA, Khamis AM, Kulakovskiy IV, Ba-Alawi W, Bhuyan MSI, Kawaji H, Lassmann T, Harbers M, Forrest ARR, Bajic VB and The FANTOM consortium (2104) Effects of cytosine methylation on transcription factor binding sites. BMC Genomics 15:119. doi:10.1186/1471-2164-15-11915:119​

65. Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB, Siam R, El-Dorry H (2014) A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. J Biol Chem 289(3):1675-1687. doi:10.1074/jbc.M113.493429​

64. Sagar S, Esau L, Moosa B, Khashab NM, Bajic VB, Kaur M (2014) Cytotoxicity and Apoptosis Induced by a Plumbagin Derivative in Estrogen Positive MCF-7 Breast Cancer Cells. Anticancer Agents Med Chem 14(1):170-180. doi:10.2174/18715206113136660369​


2013

63. Sagar S, Esau L, Holtermann K, Hikmawan T, Zhang G, Stingl U, Bajic VB, Kaur M (2013) Induction of Apoptosis in Cancer Cell Lines by the Red Sea Brine Pool Bacterial Extracts. BMC Complementary and Alternative Medicine 13:344. doi:10.1186/1472-6882-13-344​

62. Sarhan A, Bocca S, Yu L, Anderson S, Jacot T, Burch T, Nyalwidhe JO, Sullivan C, Kaur M, Bajic VB and Oehninger S (2013) Human endometrial milk fat globule-epidermal growth factor 8 (MFGE8) is up regulated by estradiol at the transcriptional level, and its secretion via microvesicles is stimulated by human chorionic gonadotropin (hCG). Cell Signal Traffic 1:1. doi:10.7243/2054-1481-1-1​

61. Alam I, Antunes A, Kamau AA, Ba alawi W, Kalkatawi M, Stingl U, Bajic VB (2013) INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles. PLoS One 8(12):e82210. doi:10.1371/journal.pone.0082210​

60. Kamanu TKK, Radovanovic A, Archer JAC, Bajic VB (2013) Exploration of miRNA families for hypotheses generation. Sci Rep 3:2940. doi:10.1038/srep02940​

59. Bin Raies A, Mansour H, Incitti R, Bajic VB (2013) Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text. PLoS One 8(10):e77848. doi:10.1371/journal.pone.0077848​

58. Ashoor H, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V (2013) HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. Bioinformatics 29(23):2979-2986. doi:10.1093/bioinformatics/btt524​

57. Kleftogiannis D, Kalnis P, Bajic VB (2013) Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures. PLoS One 8(9):e75505. doi:10.1371/journal.pone.0075505​

56. Xie B, Jankovic BR, Bajic VB, Song L, Gao X (2013) Poly(A) motif prediction using spectral latent features from human DNA sequences. Bioinformatics 29(13):i316-i325. doi:10.1093/bioinformatics/btt218​

55. Piatek MJ, Schramm MC, Burra DD, binShbreen A, Jankovic BR, Chowdhary R, Archer JAC, Bajic VB (2013) Simplified Method for Predicting a Functional Class of Proteins in Transcription Factor Complexes. PLoS One 8(7):e68857. 
doi:10.1371/journal.pone.0068857
54. Kalkatawi M, Rangkuti F, Schramm M, Jankovic BR, Kamau A, Chowdhary R, Archer JAC, Bajic VB (2013) Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics 29(11):1484. doi:10.1093/bioinformatics/btt161​

53. Esack M, Radovanovic A, Bajic VB (2013) Information exploration system for sickle cell disease and repurposing of hydroxyfasudil. PLoS One 8(6):e65190. doi:10.1371/journal.pone.0065190​

52. Chowdhary R, Zhang J, Tan SL, Osborne DE, Bajic VB, Liu JS (2013) PIMiner: a web tool for extraction of Protein Interactions from biomedical literature. Int. J. Data Mining and Bioinformatics 7(4):450-462. doi:10.1504/IJDMB.2013.054232

51. Ma L, Bajic VB, Zhang Z (2013) On the classification of long non-coding RNAs. RNA Biology 10(6):924–933. doi:10.4161/rna.24604

50. Holert J, Alam I, Larsen M, Antunes A, Bajic VB, Stingl U, Philipp B (2013) Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds. Genome Announc 1(1): e00014-12.
doi:10.1128/genomeA.00014-12

49. Sagar S, Kaur M, Radovanovic A, Bajic VB (2013) Dragon Exploration System on Marine Sponge Compounds Interactions. Journal of Cheminformatics 5(1):11. doi:10.1186/1758-2946-5-11

48. Sagar S, Esau L, Hikmawan T, Antunes A, Holtermann K, Stingl U, Bajic VB, Kaur M (2013) Cytotoxic and apoptotic evaluations of marine bacteria isolated from brine-seawater interface of the Red Sea. BMC Complementary and Alternative Medicine 13:29. doi:10.1186/1472-6882-13-29

47. Narasimhan K, Lin SL, Tong T, Baig S, Ho S, Sukumar P, Biswas A, Hahn S, Bajic VB, Choolani M (2013) Maternal serum protein profile and immune response protein subunits as markers for non-invasive prenatal diagnosis of trisomy 21, 18, and 13. Prenatal Diagnosis 33(3):223-231. doi:10.1002/pd.4047

46. Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res 41(Database issue):D195-202. 
doi:10.1093/nar/gks1089

45. Mora AM, Ashoor H, Jankovic BR, Kamau A, Awara K, Chowdhary R, Archer JA, Bajic VB (2013) Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics 29(1):117-118. 
doi:10.1093/bioinformatics/bts638
2012

44. Essack M, Macpherson CR, Schmeier S, Bajic VB (2012) Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. BMC Syst Biol 6:135. doi:10.1186/1752-0509-6-135​

43. Messih MA, Chitale M, Bajic VB, Kihara D, Gao X (2012) Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics 28(18):i444-i450. doi:10.1093/bioinformatics/bts398

42. Siam R, Mustafa GA, Sharaf H, Moustafa A, Ramadan AR, Antunes A, Bajic VB, Stingl U, Marsis NG, Coolen MJ, Sogin M, Ferreira AJ, Dorry HE (2012) Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools. PLoS One 7(8):e42872. doi:10.1371/journal.pone.0042872

41. Essack M, Bajic VB, Archer JA (2012) Conotoxins that Confer Therapeutic Possibilities. Mar Drugs 10(6):1244-1265. doi:10.3390/md10061244

40. Kamanu FK, Medvedeva YA, Schaefer U, Jankovic BR, Archer JAC, Bajic VB (2012) Mutations and binding sites of human transcription factors. Front Genet 3:100. doi:10.3389/fgene.2012.00100

39. Woo J, MacPherson CR, Liu J, Wang H, Kiba T, Hannah M, Wang XJ, Bajic VB, Chua NH (2012) The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biology 12(1):62. doi:10.1186/1471-2229-12-62

38. Chowdhary R, Tan SL, Zhang J, Karnik S, Bajic VB, Liu JS (2012) Context-specific Protein Network Miner - an online system for exploring context-specific protein interaction networks from the literature. PLoS One 7(4):e34480. doi:10.1371/journal.pone.0034480

37. Chowdhary R, Tan SL, Pavesi G, Jin J, Dong D, Mathur SK, Burkart A, Narang V, Glurich I, Raby BA, Weiss ST, Wong L, Liu JS, Bajic VB (2012) A database of annotated promoters of genes associated with common respiratory and related diseases. Am J Respir Cell Mol Biol 47(1):112-119. doi:10.1165/rcmb.2011-0419OC

36. Seshadri Sundararajan V, Gabere MN, Pretorius A, Adam S, Christoffels A, Lehvaslaiho M, Archer JAC, Bajic VB (2012) DAMPD: A manually curated antimicrobial peptide database. Nucleic Acids Res 40(Database issue):D1108-1112. doi:10.1093/nar/gkr1063

35. Kalkatawi M, Rangkuti F, Schramm M, Jankovic BR, Kamau A, Chowdhary R, Archer JAC, Bajic VB (2012) Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics 28(1):127-129. doi:10.1093/bioinformatics/btr602

2011

34. Dawe AS, Radovanovic A, Kaur M, Sagar S, Seshadri SV, Schaefer U, Kamau AA, Christoffels A, Bajic VB (2011) DESTAF: A database of text-mined associations for reproductive toxins potentially affecting human fertility. Reprod Toxicol 33(1):99-105. doi:10.1016/j.reprotox.2011.12.007 PMID:22198179.

33. Pretorius A, Kaur M, Wamalwa M, February MF, Essack M, Bajic VB, Rees DJG (2011) Functional Analysis and Characterization of the Human RBBP6 Promoters Based on a Combination of Molecular Biology and in Silico Approaches Provide Additional Evidence for RBBP6 Role in Apoptosis. The GSTF Journal on Bioinformatics and Biotechnology 1(1). doi:10.5176/ 2251-3159_1.1.2

32. Schmeier S, Schaefer U, Essack M, Bajic VB (2011) Network analysis of microRNAs and their regulation in human ovarian cancer. BMC Syst Biol 5(1):183. doi:10.1186/1752-0509-5-183

31. Essack M, Bajic VB, Archer JAC (2011) Recently Confirmed Apoptosis-Inducing Lead Compounds Isolated from Marine Sponge of Potential Relevance in Cancer Treatment. Mar Drugs 9(9):1580-1606. doi:10.3390/md9091580

30. Kaur M, Macpherson CR, Schmeier S, Narasimhan K, Choolani M, Bajic VB (2011) In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. BMC Syst Biol 5(1):144. doi:10.1186/1752-0509-5-144

29. Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A (2011) HCVpro: Hepatitis C virus protein interaction database. Infect Genet Evol 11(8):1971-1977. doi:10.1016/j.meegid.2011.09.001

28. Antunes A, Alam I, El Dorry H, Siam R, Robertson A, Bajic VB, Stingl U (2011) Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake. J Bacteriol 193(17):4551-4552. 

27. Antunes A, Alam I, Bajic VB, Stingl U (2011) Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake. J Bacteriol 193(17):4553-4554. doi:10.1128/JB.05462-11

26. Antunes A, Alam I, Bajic VB, Stingl U (2011) Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea. J Bacteriol 193(17):4555-4556. doi:10.1128/JB.05459-11

25. Chen ZF, Matsumura K, Wang H, Arellano SM, Yan X, Alam I, Archer JA, Bajic VB, Qian PY (2011) Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach. PLoS One 6(7):e22913. doi:10.1371/journal.pone.0022913

24. Schmeier S, Jankovic B, Bajic VB (2011) Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PLoS One 6(7):e21887. 
doi:10.1371/journal.pone.0021887

23. Kwofie SK, Radovanovic A, Sundararajan VS, Maqungo M, Christoffels A, Bajic VB (2011) Dragon Exploratory System on Hepatitis C Virus (DESHCV). Infect Genet Evol 11(4):734-739. doi:10.1016/j.meegid.2010.12.006

22. D’Amato ME, Bajic VB, Davison S (2011) Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system. Forensic Sci Int Genet 5(2):122-125. doi:10.1016/j.fsigen.2010.08.015

21. Schmeier S, Schaefer U, MacPherson CR, Bajic VB (2011) dPORE-miRNA: polymorphic regulation of microRNA genes. PLoS One 6(2):e16657. doi:10.1371/journal.pone.0016657

20. Schaefer U, Schmeier S, Bajic VB (2011) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res 39(1):D106-110. doi:10.1093/nar/gkq945

19. Maqungo M, Kaur M, Kwofie SK, Radovanovic A, Schaefer U, Schmeier S, Oppon E, Christoffels A, Bajic VB (2011) DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Res 39(1):D980-985. doi:10.1093/nar/gkq849

18. Sha DH, Bajic VB (2011) An optimized recursive learning algorithm for three-layer feedforward neural networks for MIMO nonlinear system identification. Intelligent Automation and Soft Computing 17(2):133-147. doi:10.1080/10798587.2011.10643137


2010

17. Park MR, Yun KY, Mohanty B, Herath V, Xu F, Wijaya E, Bajic VB, Yun SJ, De Los Reyes BG (2010) Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. Plant Cell Environ 33(12):2209-2230. doi:10.1111/j.1365-3040.2010.02221

16. Schaefer U, Kodzius R, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB (2010) High sensitivity TSS prediction: estimates of locations where TSS cannot occur. PLoS One 5(11):e13934. doi:10.1371/journal.pone.0013934

15. Sagar S, Kaur M, Minneman KP, Bajic VB (2010) Anti-cancer activities of diospyrin, its derivatives and analogues. Eur J Med Chem 45(9):3519-3530. 

14. Tiffin N, Meintjes A, Ramesar R, Bajic VB, Rayner B (2010) Computational analysis of candidate disease genes and variants for salt-sensitive hypertension in indigenous Southern Africans. PLoS One 5(9):e12989. doi:10.1371/journal.pone.0012989

13. Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, Bajic VB, Qian PY (2010) Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Proteomics 10(16):2972-2981. 
doi:10.1002/pmic.201000056

12. Chowdhary R, Bajic VB, Dong D, Wong L, Liu JS (2010) Genome-wide analysis of regions similar to promoters of histone genes. BMC Syst Biol 4(Suppl 1):S4. doi:10.1186/1752-0509-4-S1-S4

11. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, Macpherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegner J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140(5):744-752. doi:10.1016/j.cell.2010.01.044 Erratum in: Cell. 2010 Apr 16;141(2):369.

10. Bastian R, Dawe A, Meier S, Ludidi N, Bajic VB, Gehring C (2010) Gibberellic acid and cGMP-dependent transcriptional regulation in Arabidopsis thaliana. Plant Signal Behav 5(3):224-232. doi:10.4161/psb.5.3.10718

9. Arieff Z, Kaur M, Gameeldien H, Merwe LV, Bajic VB (2010) 5-HTTLPR polymorphism: analysis in South African autistic individuals. Hum Biol 82(3):291-300. doi:10.3378/027.082.0303

8. Zhang X, Bocca S, Franchi A, Anderson S, Kaur M, Bajic VB, Oehninger S (2010) Do GnRH analogues directly affect human endometrial epithelial cell gene expression? Mol Hum Reprod 16(5):347-360. doi:10.1093/molehr/gaq012

7. Kothandaraman N, Bajic VB, Brendan PN, Huak CY, Keow PB, Razvi K, Salto-Tellez M, Choolani M (2010) E2F5 status significantly improves malignancy diagnosis of epithelial ovarian cancer. BMC Cancer 10:64. doi:10.1186/1471-2407-10-64

6. Yun KY, Park MR, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic VB, Bruskiewich R, de Los Reyes BG (2010) Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biol 10:16. doi:10.1186/1471-2229-10-16

5. Heckmann JM, Uwimpuhwe H, Ballo R, Kaur M, Bajic VB, Prince S (2010) A functional SNP in the regulatory region of the decay-accelerating factor gene associates with extraocular muscle pareses in myasthenia gravis. Genes Immun 11:1-10. doi:10.1038/gene.2009.61

2009

4. Schmeier S, Macpherson CR, Essack M, Kaur M, Schaefer U, Suzuki H, Hayashizaki Y, Bajic VB (2009) Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics 10:595. doi:10.1186/1471-2164-10-595

3. Hagg S, Skogsberg J, Lundstrom J, Noori P, Nilsson R, Zhong H, Maleki S, Shang MM, Brinne B, Bradshaw M, Bajic VB, Samnegard A, Silveira A, Kaplan LM, Gigante B, Leander K, de Faire U, Rosfors S, Lockowandt U, Liska J, Konrad P, Takolander R, Franco-Cereceda A, Schadt EE, Ivert T, Hamsten A, Tegner J, Bjorkegren J (2009) Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study. PLoS Genet5(12):e1000754. doi:10.1371/journal.pgen.1000754​

2. Essack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, Christoffels A, Kaur M, Bajic VB (2009) DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer 9: 219. doi:10.1186/1471-2407-9-219

1. Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41:553-562. doi:10.1038/ng.375​
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