Journal Publications

    2017

  1. Jamil M, Kountche BA, Haider I, Guo X, Ntui VO, Jia K, Ali S, Hameed US, Nakamura H, Lyu Y, Kai J, Hirabayashi K, Tanokura M, Arold ST, Asami T, Al-Babili S (2017) Methyl Phenlactonoates are efficient strigolactone analogs with simple structure. Journal of Experimental Botany (accepted).
  2. Grötzinger SW, Karan R, Strillinger E, Bader S, Frank A, Al Rowaihi IS, Akal AL, Wackerow W, Archer JA, Rueping M, Weuster-Botz D, Groll M, Eppinger J, Arold ST (2017) Identification and experimental characterization of an extremophilic brine pool alcohol dehydrogenase from single amplified genomes. ACS Chem Biol. (accepted).
  3. Arab W, Rauf S, Al-Harbi O, Hauser CAE (2017) Novel Ultrashort Self-Assembling Peptide Bioinks for 3D Culture of Muscle Myoblast Cells. Int. J. Bioprinting (accepted).
  4. Costa RM, Rauf S, Hauser CAE (2017) Towards biologically relevant synthetic designer matrices in 3D bioprinting for tissue engineering and regenerative medicine. Current Opinion in Biomedical Engineering doi:10.1016/j.cobme.2017.05.001
  5. Chan KH, Xue B, Robinson RC, Hauser CAE (2017) Systematic Moiety Variations of Ultrashort Peptides Produce Profound Effects on Self-Assembly, Nanostructure Formation, Hydrogelation, and Phase Transition. Sci Rep. 7(1):12897. doi:10.1038/s41598-017-12694-9.
  6. Raies AB, Bajic VB (2017) In silico toxicology: comprehensive benchmarking of multi-label classification methods applied to chemical toxicity data. WIREs Comput Mol Sci. e1352 (in press). doi:10.1002/wcms.1352
  7. Alshahrani M, Soufan O, Magana-Mora A, Bajic VB (2017) DANNP: an efficient artificial neural network pruning tool. PeerJ Computer Science. 3:e137. doi:10.7717/peerj-cs.137
  8. Lftikhar S, Khan S, Bilal A, Manzoor S, Abdullah M, Emwas A, Sioud S, Gao X, Chotana G, Faisal A, Saleem R (2017) Synthesis and evaluation of modified chalcone based p53 stabilizing agents. Bioorganic & Medicinal Chemistry Letters. 27(17):4101-4106. doi:10.1016/j.bmcl.2017.07.042
  9. Wang J, Cui X, Yu G, Guo L, Gao X (2017) When sparse coding meets ranking: a joint framework for learning sparse coding and ranking scores. Neural Computing and Applications. (in press). doi:10.1007/s00521-017-3102-9
  10. Han R, Wan X, Wang Z, Hao Y, Chen Y, Gao X, Liu X, Ren F, Sun F, Zhang F (2017) AuTom: a novel automatic platform for electron tomography reconstruction. Journal of Structural Biology. 199(3):196-208. doi:10.1016/j.jsb.2017.07.008
  11. Wu S, Wang D, Liu J, Feng Y, Weng J, Li Y, Gao X, Liu J, Wang W (2017) The dynamic multisite interactions between two intrinsically disordered proteins. Angewandte Chemie. 56(26):7515-7519. doi:10.1002/anie.201701883
  12. Yang P, Zhao P, Gao X (2017) Robust online multi-task learning with correlative and personalized structures. IEEE Transactions on Knowledge and Data Engineering (TKDE). 29(11):2510-2521. doi:10.1109/TKDE.2017.2703106
  13. Rapakoulia T, Gao X, Huang Y, de Hoon M, Okada-Hatakeyama M, Suzuki H, Arner E (2017) Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. Bioinformatics. (in press). doi:10.1093/bioinformatics/btx503
  14. Dai H, Umarov R, Kuwahara H, Li Y, Song L, Gao X (2017) Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. Bioinformatics. (in press). doi:10.1093/bioinformatics/btx480
  15. Han R, Zhang F, Gao X (2017) A fast fiducial marker tracking model for fully automatic alignment in electron tomography. Bioinformatics. (in press). doi:10.1093/bioinformatics/btx653
  16. Li Y, Wang S, Umarov R, Xie B, Fan M, Li L, Gao X (2017) DEEPre: sequence-based enzyme EC number prediction by deep learning. Bioinformatics. (in press). doi:10.1093/bioinformatics/btx680
  17. Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T (2017) The emerging facets of noncancerous Warburg effect. Frontiers in Endocrinology. 8:279. doi:10.3389/fendo.2017.00279
  18. Kulmanov M, Khan MA, Hoehndorf R (2017) DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinformatics (in press). doi:10.1093/bioinformatics/btx624
  19. Lafi FF, AlBladi ML, Salem NM, Al-Banna L, Alam I, Bajic VB, Hirt H, Saad MM (2017) Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan. Genome Announc. 5(2):e01437-16. doi:10.1128/genomeA.01437-16
  20. Anazi S, Maddirevula S, Salpietro V, Asi YT, Alsahli S, Alhashem A, Shamseldin HE, Al Zahrani F, Patel N, Ibrahim N, Abdulwahab FM, Hashem M, Alhashmi N, Al Murshedi F, Al Kindy A, Alshaer A, Rumayyan A, Al Tala S, Kurdi W, Alsaman A, Alasmari A, Banu S, Sultan T, Saleh MM, Alkuraya H, Salih MA, Aldhalaan H, Ben-Omran T, Al Musafri F, Ali R, Suleiman J, Tabarki B, El-Hattab AW, Bupp C, Alfadhel M, Al Tassan N, Monies D, Arold ST, Abouelhoda M, Lashley T, Houlden H, Faqeih E, Alkuraya FS (2017) Expanding the genetic heterogeneity of intellectual disability. Hum Genet (in press). doi:10.1007/s00439-017-1843-2
  21. Magana-Mora A, Kalkatawi M, Bajic VB (2017) Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA. BMC Genomics. 18(1):620. doi:10.1186/s12864-017-4033-7
  22. Maddirevula S, Coskun S, Alhassan S, Elnour A, Alsaif HS, Ibrahim N, Abdulwahab F, Arold ST, Alkuraya FS (2017) Female infertility caused by mutations in the oocyte-specific translational repressor PATL2. American Journal of Human Genetics 101(4):603-608. doi:10.1016/j.ajhg.2017.08.009
  23. Gadd S, Huff V, Walz AL, Ooms AHAG, Armstrong AE, Gerhard DS, Smith MA, Auvil JMG, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ (2017) A Children's Oncology Group and TARGET Initiative Exploring the Genetic Landscape of Wilms Tumor. Nature Genetics. 49(10):1487-1494. doi:10.1038/ng.3940
  24. Jimenez-Infante F, Ngugi DK, Vinu M, Blom J, Alam I, Bajic VB, Stingl U (2017) Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade. FEMS Microbiol Ecol. 93(7):fix083. doi:10.1093/femsec/fix083
  25. Wang S, Li Z, Yu Y, Xu J (2017) Folding membrane proteins by deep transfer learning. Cell System 5(3):202-211.e3. doi:10.1016/j.cels.2017.09.001
  26. Magana-Mora A, Bajic VB (2017) OmniGA: Optimized Omnivariate Decision Trees for Generalizable Classification Models. Scientific Reports 7:3898. doi:10.1038/s41598-017-04281-9
  27. Hoehndorf R, Queralt-Rosinach N (2017) Data science and symbolic AI: Synergies, challenges and opportunities. Data Science doi:10.3233/DS-170004
  28. Nielsen J, Archer J, Essack M, Bajic VB, Gojobori T, Mijakovic I (2017) Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Appl Microbiol Biotechnol. 101(12):4837-4851. doi:10.1007/s00253-017-8310-9
  29. Foy JP, Bertolus C, Michallet MC, Deneuve S, Incitti R, Bendriss-Vermare N, Albaret MA, Ortiz-Cuaran S, Thomas E, Colombe A, Py C, Gadot N, Michot JP, Fayette J, Viari A, Van den Eynde B, Goudot P, Devouassoux-Shisheboran M, Puisieux A, Caux C, Zrounba P, Lantuejoul S, Saintigny P (2017) The immune microenvironment of HPV-negative oral squamous cell carcinoma from never-smokers and never-drinkers patients suggests higher clinical benefit of IDO1 and PD1/PD-L1 blockade. Ann Oncol. 28(8):1934-1941. doi:10.1093/annonc/mdx210
  30. Shao M, Ma J, Wang S (2017) DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields. Bioinformatics. 33(14):i267–i273. doi:10.1093/bioinformatics/btx267
  31. Komatsu S, Wang X, Yin X, Nanjo Y, Ohyanagi H, Sakata K (2017) Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database. J Proteomics. 163:52-66. doi:10.1016/j.jprot.2017.05.009
  32. Kobayashi M, Ohyanagi H, Takanashi H, Asano S, Kudo T, Kajiya-Kanegae H, Nagano AJ, Tainaka H, Tokunaga T, Sazuka T, Iwata H, Tsutsumi N, Yano K (2017) Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Res. 24(4):397–405. doi:10.1093/dnares/dsx012
  33. Nakagawa S, Niimura Y, Gojobori T (2017) Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes. Nucleic Acids Res. 45(7):3922-3931. doi:10.1093/nar/gkx124
  34. Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM (2017) Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium. Genome Announc. 5:e01707-16. doi:10.1128/genomeA.01707-16
  35. Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB (2017) DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biol. 14(7):963-971. doi:10.1080/15476286.2017.1312243
  36. Arae T, Isai S, Sakai A, Mineta K, Hirai MY, Suzuki Y, Kanaya S, Yamaguchi J, Naito S, Chiba Y (2017) Coordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells. Plant Cell Physiol. 58(6):1090-1102. doi:10.1093/pcp/pcx059
  37. Alshahrani M, Khan MA, Maddouri O, Kinjo AR, Queralt-Rosinach N, Hoehndorf R (2017) Neuro-symbolic representation learning on biological knowledge graphs. Bioinformatics btx275. doi:10.1093/bioinformatics/btx275
  38. Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLoS Comput Biol. 13(4):e1005500. doi:10.1371/journal.pcbi.1005500
  39. Gkoutos GV, Schofield PN, Hoehndorf R (2017) The anatomy of phenotype ontologies: principles, properties and applications. Brief Bioinform bbx035. doi:10.1093/bib/bbx035
  40. Alzahrani M, Kuwahara H, Wang W, Gao X (2017) Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. Bioinformatics 33(16):2523–2531. doi:10.1093/bioinformatics/btx199
  41. Kuwahara H, Cui X, Umarov R, Grünberg R, Myers CJ, Gao X (2017) SBOLme: a Repository of SBOL Parts for Metabolic Engineering. ACS Synth Biol. 6(4):732–736. doi:10.1021/acssynbio.6b00278
  42. Wang JJY, Tsang IWH, Cui X, Lu Z, Gao X (2017) Multi-instance dictionary learning via multivariate performance measure optimization. Pattern Recognition 66:448-459. doi:10.1016/j.patcog.2016.12.023
  43. Weng J, Gu S, Gao X, Huang X, Wang W (2017) Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK(2). Phys Chem Chem Phys. 19:9366-9373. doi:10.1039/c6cp07943a
  44. Kuwahara H, Umarov R, Almasri I, Gao X (2017) ACRE: absolute concentration robustness exploration in module-based combinatorial networks. Synth Biol. 2(1): ysx001. doi:10.1093/synbio/ysx001
  45. Najibi SM, Maadooliat M, Zhou L, Huang JZ, Gao X (2017) Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions. Comput Struct Biotechnol J. 15:243-254. doi:10.1016/j.csbj.2017.01.011
  46. Kudo T, Kobayashi M, Terashima S, Katayama M, Ozaki S, Kanno M, Saito M, Yokoyama K, Ohyanagi H, Aoki K, Kubo Y, Yano K (2017) TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. Plant Cell Physiol. 58(1):e8. doi:10.1093/pcp/pcw207
  47. Kulmanov M, Hoehndorf R (2017) Evaluating the effect of annotation size on measures of semantic similarity. Journal of Biomedical Semantics 8:7. doi:10.1186/s13326-017-0119-z
  48. Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJ, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EG, Guo X, Momin AA, Negrão S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, Linden CG, van Loo EN, Jellen EN, Maughan PJ, Tester M (2017) The genome of Chenopodium quinoa. Nature 542(7641):307-312. doi:10.1038/nature21370 PMID:28178233
  49. Monies D, Maddirevula S, Kurdi W, Alanazi M, Al Khalidi H, Al-Owain M, Sulaiman RA, Faqeih E, Goljan E, Ibrahim N, Abdulwahab F, Hashem M, Abouelhoda M, Shaheen R, Arold ST, Alkuraya FS (2017) Autozygosity Reveals Recessive Mutations and Novel Mechanisms in Dominant Genes: Implications in Variant Interpretation. Genet Med. 19:1144–1150. doi:10.1038/gim.2017.22
  50. 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 (2017) In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics 18(1):33. doi:10.1186/s12864-016-3389-4 PMID: 28056772
  51. Ashoor H, Louis-Brennetot C, Janoueix-Lerosey I, Bajic VB, Boeva V (2017) HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. Nucleic Acids Res. 45(8):e58. doi:10.1093/nar/gkw1319
  52. Sulaiman RA, Patel N, Alsharif H, Arold ST, Alkuraya FS (2017) A novel mutation in SLC25A46 causes optic atrophy and progressive limb spasticity, with no cerebellar atrophy or axonal neuropathy. Clin Genet. 92(2):230-231. doi:10.1111/cge.12963
  53. Lafi FF, Alam I, Geurts R, Bisseling T, Bajic VB, Hirt H, Saad MM (2017) Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea. Genome Announc 5:e01638-16. doi:10.1128/genomeA.01638-16
  54. Shamseldin HE, Khalifa O, Binamer YM, Almutawa A, Arold ST, Zaidan H, Alkuraya FS (2017) KDF1, encoding keratinocyte differentiation factor 1, is mutated in a multigenerational family with ectodermal dysplasia. Hum Genet 136(1):99-105. doi:10.1007/s00439-016-1741-z
  55. Kleftogiannis D, Kalnis P, Arner E, Bajic VB (2017) Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Res. 45(4):e25 doi:10.1093/nar/gkw1015
  56. Schmeier S, Alam T, Essack M, Bajic VB (2017) TcoF-DB v2: Update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Res. 45(D1):D145-D150. doi:10.1093/nar/gkw1007
  57. Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks J, Kapfer C, Mineta K, Gojobori T, Bajic VB (2017) FARNA: Knowledgebase of Inferred Functions of Non-coding RNA Transcripts. Nucleic Acids Res. 45(5):2838-2848. doi:10.1093/nar/gkw973
  58. Shahmuradov IA, Razali RM, Bougouffa S, Radovanovic A, Bajic VB (2017) bTSSfinder: a novel tool for the prediction of promoters in Cyanobacteria and Escherichia coli. Bioinformatics 33(3):334-340. doi:10.1093/bioinformatics/btw629
  59. Ling Y, Alshareef S, Butt H, Lozano-Juste J, Li L, Galal AA, Moustafa A, Momin AA, Tashkandi M, Richardson DN, Fujii H, Arold S, Rodriguez PL, Duque P, Mahfouz MM (2017) Pre-mRNA splicing repression triggers abiotic stress signaling in plants. Plant J. 89(2):291-309. doi:10.1111/tpj.13383
  60. Anazi S, Maddirevula S, Faqeih E, Alsedairy H, AlZahrani F, Shamseldin HE, Patel N, Hashem M, Ibrahim N, Abdulwahab F, Ewida N, Alsaif HS, Al sharif H, Alamoudi W, KentabA, Bashiri FA, Alnaser M, AlWadei AH , Alfadhel M, Eyaid W, Hashem A, Al Asmari A, Saleh MM, AlSaman A, Alhasan KA, Alsughayir M, Al Shammari M, Mahmoud A, Al-Hassnan ZN, Al-Husain M, Khalil RO, El.Meguid NA, Masri A, Ali R, El.Fishway P, Hashish A, Sencicek AE, State M, Alazami AM, Salih MA, Altassan N, Arold ST, Abouelhoda M, Wakil SM, Monies D, Shaheen R, Alkuraya FS (2017) Clinical Genomics Expands the Morbid Genome of Intellectual Disability and Offers a High Diagnostic Yield. Mol Psychiatry. 22(4):615-624. doi:10.1038/mp.2016.113
  61. Cui X, Gao X (2017) K-nearest uphill clustering in the protein structure space. Neurocomputing 220:52–59. doi:10.1016/j.neucom.2016.04.065
  62. Lu Z, Fu Z, Xiang T, Han P, Wang L, Gao X (2017) Learning from Weak and Noisy Labels for Semantic Segmentation. IEEE Trans Pattern Anal Mach Intell. 39(3):486-500. doi:10.1109/TPAMI.2016.2552172
  63. Fujii C, Kuwahara H, Yu G, Guo L, Gao X (2017) Learning gene regulatory networks from gene expression data using weighted consensus. Neurocomputing 220:23–33. doi:10.1016/j.neucom.2016.02.087
  64. 2016

  65. 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
  66. Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W (2016) Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angew Chem Int Ed Engl. 55(45):13990-13994. doi:10.1002/anie.201606613
  67. Zhu L, Jiang H, Sheong FK, Cui X, Wang Y, Gao X, Huang X (2017) Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. Prog Biophys Mol Biol. 128:39-46. doi:10.1016/j.pbiomolbio.2016.09.008
  68. Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW (2016) A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal. 14(1):17. doi:10.1186/s12964-016-0140-3
  69. Gojobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, Kinoshita K, Kwon Y, Migita O, Mizutani H, Muraoka M, Nagata K, Omori S, Sugawara H, Yamada D, Yura K (2016) VaProS: a database-integration approach for protein/genome information retrieval. J Struct Funct Genomics 17(4):69–81. doi:10.1007/s10969-016-9211-3
  70. Nozawa M, Onizuka K, Fujimi M, Ikeo K, Gojobori T (2016) Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nat Commun 7:13659. doi:10.1038/ncomms13659
  71. Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, Chakraborty R, Gojobori T, Imanishi T (2016) Selection pressure on human STR loci and its relevance in repeat expansion disease. Mol Genet Genomics 291(5):1851-69. doi:10.1007/s00438-016-1219-7
  72. Nozawa M, Fujimi M, Iwamoto C, Onizuka K, Fukuda N, Ikeo K, Gojobori T (2016) Evolutionary Transitions of MicroRNA-Target Pairs. Genome Biol Evol. 8(5):1621-33. doi:10.1093/gbe/evw092
  73. 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
  74. 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
  75. Hoehndorf R, Alshahrani M, Gkoutos GV, Gosline G, Groom Q, Hamann T, Kattge J, de Oliveira SM, Schmidt M, Sierra S, Smets E, Vos RA, Weiland C (2016) The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. J Biomed Semantics 7(1):65. doi:10.1186/s13326-016-0107-8
  76. Sakata K, Saito T, Ohyanagi H, Okumura J, Ishige K, Suzuki H, Nakamura T, Komatsu S (2016) Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli. Sci Rep 6:35946. doi:10.1038/srep35946
  77. 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
  78. Hungler A, Momin A, Diederichs K, Arold ST (2016) ContaMiner and ContaBase: a web server and database for early identification of unwantedly crystallised protein contaminants. J Appl Crystallogr. 49(Pt 6):2252-2258. doi:10.1107/S1600576716014965
  79. Ishikawa M, Shimizu H, Nozawa M, Ikeo K, Gojobori T (2016) Two-step evolution of endosymbiosis between hydra and algae. Mol Phylogenet Evol 103:19-25. doi:10.1016/j.ympev.2016.07.010
  80. 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
  81. 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
  82. 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
  83. Roperch JP, Grandchamp B, Desgrandchamps F, Mongiat-Artus P, Ravery V, Ouzaid I, Roupret M, Phe V, Ciofu C, Tubach F, Cussenot O, Incitti R (2016) Promoter hypermethylation of HS3ST2, SEPTIN9 and SLIT2 combined with FGFR3 mutations as a sensitive/specific urinary assay for diagnosis and surveillance in patients with low or high-risk non-muscle-invasive bladder cancer. BMC Cancer 16:704. doi:10.1186/s12885-016-2748-5
  84. Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016) Notions of similarity for systems biology models. Brief Bioinform (in press) doi:10.1093/bib/bbw090
  85. Fisher HM, Hoehndorf R, Bazelato BS, Dadras SS, King LE Jr, Gkoutos GV, Sundberg JP, Schofield PN (2016) DermO; an ontology for the description of dermatologic disease. J Biomed Semantics 7:38. doi:10.1186/s13326-016-0085-x
  86. Slater L, Gkoutos GV, Schofield PN, Hoehndorf R (2016) Using AberOWL for fast and scalable reasoning over BioPortal ontologies. J Biomed Semantics 7(1):49. doi:10.1186/s13326-016-0090-0
  87. Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V (2016) Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining. PLoS One 11(7):e0158896. doi:10.1371/journal.pone.0158896
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  89. 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
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  337. Haywood AF, Merner ND, Hodgkinson KA, Houston J, Syrris P, Booth V, Connors S, Pantazis A, Quarta G, Elliott P, McKenna W, Young TL (2013) Recurrent missense mutations in TMEM43 (ARVD5) due to founder effects cause arrhythmogenic cardiomyopathies in the UK and Canada. Eur Heart J 34(13):1002-1011. doi:10.1093/eurheartj/ehs383
  338. 2012

  339. Dai L, Gao X, Guo Y, XiaoJ, Zhang Z (2012) Bioinformatics clouds for big data manipulation. Biol Direct 7:43. doi:10.1186/1745-6150-7-43
  340. Ho YS, Adroub SA, Abadi M, Al Alwan B, Alkhateeb R, Gao G, Ragab A, Ali S, van Soolingen D, Bitter W, Pain A, Abdallah AM (2012) Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954. J Bacteriol 194(22):6339-6340. doi:10.1128/JB.01462-12
  341. Ho YS, Adroub SA, Aleisa F, Mahmood H, Othoum G, Rashid F, Zaher M, Ali S, Bitter W, Pain A, Abdallah AM (2012) Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain DSM46621 J Bacteriol 194(22):6337-6338. doi:10.1128/JB.01461-12
  342. Ammirati E, Cannistraci CV, Cristell NA, Vecchio V, Palini AG, Tornvall P, Paganoni AM, Miendlarzewska EA, Sangalli LM, Monello A, Pernow J, Bjornstedt Bennermo M, Marenzi G, Hu D, Uren NG, Cianflone D, Ravasi T, Manfredi AA, Maseri A (2012) Identification and Predictive Value of Interleukin-6+ Interleukin-10+ and Interleukin-6- Interleukin-10+ Cytokine Patterns in ST-Elevation Acute Myocardial Infarction. Circ Res 111(10):1336-1348. doi:10.1161/CIRCRESAHA.111.262477
  343. 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
  344. Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, Kosuge T, Suzuki Y, Sato Y, Kawashima S, Katayama T, Wakaguri H, Inoue N, Homma K, Tada-Umezaki M, Yagi Y, Fujii Y, Habara T, Kanehisa M, Watanabe H, Ito K, Gojobori T, Sugawara H, Imanishi T, Weir W, Gardner M, Pain A, Shiels B, Hattori M, Nene V, Sugimoto C (2012) Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. MBio 3(5):e00204-12. doi:10.1128/mBio.00204-12
  345. Köser CU, Feuerriegel S, Summers DK, Archer JA, Niemann S (2012) Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance. Antimicrob Agents Chemother 56(12):6080-6087. doi:10.1128/AAC.01641-12
  346. 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
  347. Giles EC, Kamke J, Moitinho-Silva L, Taylor MW, Hentschel U, Ravasi T, Schmitt S (2012) Bacterial community profiles in low microbial abundance sponges. FEMS Microbiol Ecol. 83(1):232-241. doi:10.1111/j.1574-6941.2012.01467.x
  348. 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
  349. Fan M, Wong KC, Ryu T, Ravasi T, Gao X (2012) SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification. PLoS One 7(6):e39475. doi:10.1371/journal.pone.0039475
  350. Zelman AK, Dawe A, Gehring C, Berkowitz GA (2012) Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels. Front Plant Sci 3:95. doi:10.3389/fpls.2012.00095
  351. Essack M, Bajic VB, Archer JA (2012) Conotoxins that Confer Therapeutic Possibilities. Mar Drugs 10(6):1244-1265. doi:10.3390/md10061244
  352. 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
  353. Abdallah AM, Rashid M, Adroub SA, Arnoux M, Ali S, van Soolingen D, Bitter W, Pain A (2012) Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174. J. Bacteriol 194(12):3284-3285. doi:10.1128/JB.00485-12
  354. Abdallah AM, Rashid M, Adroub SA, Elabdalaoui H, Ali S, van Soolingen D, Bitter W, Pain A (2012) Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367. J Bacteriol 194(12):3282-3283. doi:10.1128/JB.00482-12
  355. 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
  356. 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
  357. Lawton J, Brugat T, Yam XY, Reid AJ, Boehme U, Otto TD, Pain A, Jackson A, Berriman M, Cunningham D, Preiser P, Langhorne J (2012) Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). BMC Genomics 13(1):125. doi:10.1186/1471-2164-13-125
  358. Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J (2012) Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 13(1):43. doi:10.1186/1471-2105-13-43
  359. Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Konen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A, Wastling JM (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog 8(3):e1002567. doi:10.1371/journal.ppat.1002567
  360. Wong YH, Wang H, Ravasi T, Qian PY (2012) Involvement of Wnt signaling pathways in the metamorphosis of the bryozoan Bugula neritina. PLoS One 7(3):e33323. doi:10.1371/journal.pone.0033323
  361. 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
  362. 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
  363. Zhi L, Ahmed A, Bing-Yi J and Xin G (2012) WaVPeak: picking NMR peaks through wavelet transform and volume-based ltering. Bioinformatics 28(7):914-920. doi:10.1093/bioinformatics/bts078
  364. 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
  365. 2011

  366. Olivieri S, Conti A, Iannaccone S, Cannistraci CV, Campanella A, Barbariga M, Codazzi F, Pelizzoni I, Magnani G, Pesca M, Franciotta D, Cappa SF, Alessio M (2011) Ceruloplasmin oxidation, a feature of Parkinson’s disease CSF, inhibits ferroxidase activity and promotes cellular iron retention. J Neurosci 31(50):18568-18577. doi:10.1523/JNEUROSCI.3768-11.2011
  367. 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.
  368. Ramaprasad A, Pain A, Ravasi T (2011) Defining the protein interaction network of human malaria parasite Plasmodium falciparum. Genomics 99(2):69-75. doi:10.1016/j.ygeno.2011.11.006 PMID:22178265.
  369. 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
  370. Feuerriegel S, Köser CU, Baù D, Rüsch-Gerdes S, Summers DK, Archer JA, Marti-Renom MA, Niemann S (2011) Impact of fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824. Antimicrob Agents Chemother 55(12):5718-5722. doi:10.1128/AAC.05500-11
  371. 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
  372. Jankovic B, Seoighe C, Alqurashi M, Gehring C (2011) Is there evidence of optimisation for carbon efficiency in plant proteomes? Plant Biol 13(6):831-834. doi:10.1111/j.1438-8677.2011.00494.x
  373. Bokil NJ, Totsika M, Carey AJ, Stacey KJ, Hancock V, Saunders BM, Ravasi T, Ulett GC, Schembri MA, Sweet MJ (2011) Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages. Immunobiology 216(11):1164-1171. doi:10.1016/j.imbio.2011.05.011
  374. Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ (2011) A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinformatics 27(19):2621-2624. doi:10.1093/bioinformatics/btr453
  375. Pfander C, Anar B, Schwach F, Otto TD, Brochet M, Volkmann K, Quail MA, Pain A, Rosen B, Skarnes W, Rayner JC, Billker O (2011) A scalable pipeline for highly effective genetic modification of a malaria parasite. Nat Methods 8(12):1078-1082. doi:10.1038/nmeth.1742
  376. 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
  377. Projahn M, Köser CU, Homolka S, Summers DK, Archer JA, Niemann S (2011) Polymorphisms in isoniazid and prothionamide resistance genes of the Mycobacterium tuberculosis complex. Antimicrob Agents Chemother 55(9):4408-4411. doi:10.1128/AAC.00555-11
  378. 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
  379. 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
  380. 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. doi:10.1128/JB.05461-11
  381. 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
  382. 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
  383. Romeo G, Materia L, Modica MN, Pittala V, Salerno L, Siracusa MA, Manetti M, Botta M, Minneman KP (2011) Novel 4-Phenylpiperidine-2,6-dione Derivatives. Ligands for alpha1-adrenoceptor subtypes. Eur J Medicina Chem 46:2676-2690. doi:10.1016/j.ejmech.2011.03.054
  384. 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
  385. 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
  386. Köser CU, Niemann S, Summers DK, Archer JA (2011) Overview of errors in the reference sequence and annotation of Mycobacterium tuberculosis H37Rv, and variation amongst its isolates. Infect Genet Evol 12(4):807-810. doi:10.1016/j.meegid.2011.06.011
  387. 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
  388. Gomes-Santos CS, Braks J, Prudencio M, Carret C, Gomes AR, Pain A, Feltwell T, Khan S, Waters A, Janse C, Mair GR, Mota MM (2011) Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio. PLoS Pathog 7(5):e1002046. doi:10.1371/journal.ppat.1002046
  389. Köser CU, Summers DK, Archer JA (2011) Thr270Ile in embC (Rv3793) is not a marker for ethambutol resistance in the Mycobacterium tuberculosis complex. Antimicrob Agents Chemother 55(4):1825. doi:10.1128/AAC.01607-10
  390. Ryu T, Mavromatis CH, Bayer T, Voolstra CR, Ravasi T (2011) Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. BMC Syst Biol 5(1):58. doi:10.1186/1752-0509-5-58
  391. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, Qian PY (2011) Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J 5(4):650-664. doi:10.1038/ismej.2010.165
  392. 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
  393. Qian PY, Wang Y, Lee OO, Lau SC, Yang J, Lafi FF, Al-Suwailem A, Wong TY (2011) Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J 5(3):507-518. doi:10.1038/ismej.2010.112
  394. Köser CU, Summers DK, Archer JA (2011) Comment on: Isoniazid and rifampicin resistance-associated mutations in Mycobacterium tuberculosis isolates from Yangon, Myanmar: implications for rapid molecular testing. J Antimicrob Chemother 66(3):686-687. doi:10.1093/jac/dkq492
  395. Ogun SA, Tewari R, Otto TD, Howell SA, Knuepfer E, Cunningham DA, Xu Z, Pain A, Holder AA (2011) Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein. PLoS Pathog 7(2):e1001288. doi:10.1371/journal.ppat.1001288
  396. 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
  397. Zhang H, Wong YH, Wang H, Chen Z, Arellano SM, Ravasi T, Qian PY (2011) Quantitative Proteomics Identify Molecular Targets That Are Crucial in Larval Settlement and Metamorphosis of Bugula neritina. J Proteome Res 10(1):349-360. doi:10.1021/pr100817v
  398. 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
  399. 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
  400. 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
  401. Kowald A, Schmeier S (2011) Text Mining for Systems Modelling. Methods Mol Biol 696:305-318. doi:10.1007/978-1-60761-987-1_19
  402. 2010

  403. 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.x
  404. Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T (2010) Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res 20(12):1672-1678. doi:10.1101/gr.111765.110
  405. Köser CU, Summers DK, Archer JA (2010) Role of the dihydrofolate reductase DfrA (Rv2763c) in trimethoprim-sulfamethoxazole (co-trimoxazole) resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 54(11):4951-4952. doi:10.1128/AAC.00876-10
  406. Feuerriegel S, Köser CU, Trube L, Archer J, Rusch Gerdes S, Richter E, Niemann S (2010) Thr202Ala in thyA Is a Marker for the Latin American Mediterranean Lineage of the Mycobacterium tuberculosis complex rather than para-aminosalicylic acid resistance. Antimicrob Agents Chemother 54(11):4794-4798. doi:10.1128/AAC.00738-10
  407. 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
  408. Tewari R, Straschil U, Bateman A, Bohme U, Cherevach I, Gong P, Pain A, Billker O (2010) The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission. Cell Host Microbes 8(4):377-387. doi:10.1016/j.chom.2010.09.006
  409. Sagar S, Kaur M, Minneman KP (2010) Antiviral lead compounds from marine sponges. Mar Drugs 8(10):2619-2638. doi:10.3390/md8102619
  410. Puglisi E, Cahill MJ, Lessard PA, Capri E, Sinskey AJ, Archer JA, Boccazzi P (2010) Transcriptional response of Rhodococcus aetherivorans I24 to polychlorinated biphenyl-contaminated sediments. Microb Ecol. 60(3):505-515. doi:10.1007/s00248-010-9650-5
  411. Köser CU, Veerapen-Pierce RN, Summers DK, Archer JA (2010) Role of mutations in dihydrofolate reductase DfrA (Rv2763c) and thymidylate synthase ThyA (Rv2764c) in Mycobacterium tuberculosis drug resistance. Antimicrob Agents Chemother 54(10):4522-4523. doi:10.1128/AAC.00422-10
  412. Pain A, Hertz-Fowler C (2010) Plant killers on the spot. Nature Reviews Microbiology 8(9):615. doi:10.1038/nrmicro2433
  413. Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC (2010) Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics 6(9):e1001099. doi:10.1371/journal.pgen.1001099
  414. Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M (2010) Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics 26(18):i531-539. doi:10.1093/bioinformatics/btq376
  415. Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D, Loewe L, Fawcett R, Kumar S, Thomson M, Trivedi U, Otto TD, Pain A, Blaxter M, Cravo P (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics 11(1):499. doi:10.1186/1471-2164-11-499
  416. 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. doi:10.1016/j.ejmech.2010.06.021
  417. 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
  418. Salem M, Xiao C, Womack J, Rexroad CE III, Yao J (2010) A microRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss). Mar Biotechnol (NY) 12(4):410-429. doi:10.1007/s10126-009-9232-z
  419. Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernandez JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T (2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics 1(1):8. doi:10.1186/2041-1480-1-8
  420. Zhang H, Zhao C, Li X, Zhu Y, Gan CS, Wang Y, Ravasi T, Qian PY, Wong SC, Sze SK (2010) Study of monocyte membrane proteome perturbation during lipopolysaccharide-induced tolerance using iTRAQ-based quantitative proteomic approach. Proteomics 10(15):2780-2789. doi:10.1002/pmic.201000066
  421. 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
  422. Tripurani SK, Xiao C, Salem M, Yao J (2010) Cloning and analysis of fetal ovary microRNAs in cattle. Anim Reprod Sci 120(1-4):16-22. doi:10.1016/j.anireprosci.2010.03.001
  423. Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11(7):R77. doi:10.1186/gb-2010-11-7-r77
  424. Garavaglia BS, Thomas L, Gottig N, Zimaro T, Garofalo CG, Gehring C, Ottado J (2010) Shedding light on the role of photosynthesis in pathogen colonization and host defense. Commun Integr Biol 3(4):383-384. doi:10.4161/cib.3.4.12029 PMCID: PMC2928325
  425. Cahill MJ, Koser CU, Ross NE, Archer JA (2010) Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies. PLoS One 5(7):e11518. doi:10.1371/journal.pone.0011518
  426. Shrestha R, Arnaud E, Mauleon R, Senger M, Davenport GF, Hancock D, Morrison N, Bruskiewich R, McLaren G (2010) Multifunctional crop trait ontology for breeders data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants doi:doi:10.1093/aobpla/plq008
  427. Wong YH, Arellano SM, Zhang H, Ravasi T, Qian PY (2010) Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina. Proteome Sci 8:25. doi:10.1186/1477-5956-8-25
  428. 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
  429. Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Beroud C, Dobson G, Lehvaslaiho H, Taschner PE, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR (2010) Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med 2(4):24. doi:10.1186/gm145
  430. 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.
  431. Garavaglia BS, Thomas L, Zimaro T, Gottig N, Daurelio LD, Ndimba B, Orellano EG, Ottado J, Gehring C (2010) A plant natriuretic peptide-like molecule of the pathogen Xanthomonas axonopodis pv. citri causes rapid changes in the proteome of its citrus host. BMC Plant Biol 10:51. doi:10.1186/1471-2229-10-51
  432. 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
  433. Salem M, Kenney PB, Rexroad CE III, Yao J (2010) Proteomic signature of muscle atrophy in rainbow trout. J Proteomics 73(4):778-789. doi:10.1016/j.jprot.2009.10.014
  434. 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
  435. 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
  436. 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
  437. Jung J, Ryu T, Hwang Y, Lee E, Lee D (2010) Prediction of extracellular matrix proteins based on distinctive sequence and domain characteristics. J Comput Biol 17(1):97-105. doi:10.1089/cmb.2008.0236
  438. 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
  439. Meier S, Ruzvidzo O, Morse M, Donaldson L, Kwezi L, Gehring C (2010) The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. PLoS One 5(1):e8904. doi:10.1371/journal.pone.0008904
  440. Kim YI, Ryu T, Lee J, Heo YS, Ahnn J, Lee SJ, Yoo O (2010) A genetic screen for modifiers of Drosophila caspase Dcp-1 reveals caspase involvement in autophagy and novel caspase-related genes. BMC Cell Biol 11:9. doi:10.1186/1471-2121-11-9
  441. 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
  442. Garavaglia BS, Thomas L, Gottig N, Dunger G, Garofalo CG, Daurelio LD, Ndimba B, Orellano EG, Gehring C, Ottado J (2010) A eukaryotic-acquired gene by a biotrophic phytopathogen allows prolonged survival on the host by counteracting the shut-down of plant photosynthesis. PLoS One 5(1):e8950. doi:10.1371/journal.pone.0008950
  443. 2009

  444. Dawe AS, Bodhicharla RK, Graham NS, May ST, Reader T, Loader B, Gregory A, Swicord M, Bit-Babik G, de Pomerai DI (2009) Low-intensity microwave irradiation does not substantially alter gene expression in late larval and adult Caenorhabditis elegans. Bioelectromagnetics 30(8):602-612. doi:10.1002/bem.20515
  445. Ryu T, Lee S, Hur CG, Lee D (2009) CONVIRT: a web-based tool for transcriptional regulatory site identification using a conserved virtual chromosome. BMB Rep 42(12):823-828. PMID:20044955
  446. 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
  447. 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 Genet 5(12):e1000754. doi:10.1371/journal.pgen.1000754
  448. Sanchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE III (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10:559. doi:10.1186/1471-2164-10-559
  449. Niemann S, Koser CU, Gagneux S, Plinke C, Homolka S, Bignell H, Carter RJ, Cheetham RK, Cox A, Gormley NA, Kokko-Gonzales P, Murray LJ, Rigatti R, Smith VP, Arends FP, Cox HS, Smith G, Archer JA (2009) Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One 4(10):e7407. doi:10.1371/journal.pone.0007407
  450. Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS (2009) An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. J Neurosci 29(40):12467-12476. doi:10.1523/JNEUROSCI.3180-09.2009
  451. RamachandraRao SP, Zhu Y, Ravasi T, McGowan TA, Toh I, Dunn SR, Okada S, Shaw MA, Sharma K (2009) Pirfenidone is renoprotective in diabetic kidney disease. J Am Soc Nephrol 20(8):1765-1775. doi:10.1681/ASN.2008090931
  452. 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
  453. 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

Book Chapters

    2016

  1. Hoehndorf R, Gkoutos GV, Schofield PN (2016) Datamining with Ontologies. Data Mining Techniques for the Life Sciences Volume 1415 of the series Methods in Molecular Biology pp 385-397, Springer. doi:10.1007/978-1-4939-3572-7_19
  2. Hoehndorf R, Mencel L, Gkoutos GV, Schofield PN (2016) Large-Scale Reasoning over Functions in Biomedical Ontologies. In: Formal Ontology in Information Systems, Frontiers in Artificial Intelligence and Applications 283:299-312 doi:10.3233/978-1-61499-660-6-299
  3. Kobayashi M, Ohyanagi H, Yano K (2016) Databases for Solanaceae and Cucurbitaceae Research. Functional Genomics and Biotechnology in Solanaceae and Cucurbitaceae Crops. Ezura, H. et al. (Editors) Chapter 3 (pp.31-42), Springer. doi:10.1007/978-3-662-48535-4
  4. 2015

  5. Kobayashi M, Ohyanagi H, Yano K (2015) Expression Analysis and Genome Annotations with RNA Sequencing. Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches. Sablok, G. et al. (Editors) Chapter 1 (pp.1-12), Springer. doi:10.1007/978-3-319-17157-9
  6. Kobayashi M, Ohyanagi H, Yano K (2015) Omics Analysis and Databases for Plant Science. Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods, Second Edition. Bagchi D., Swaroop A., Bagchi M. (Editors) Chapter 13 (pp.150-159), John Wiley & Sons, Ltd. doi:10.1002/9781118930458
  7. Khamis AM, Bajic VB, Harbers M (2015) Transcriptome profiling strategies. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing Chapter 4 (accepted)
  8. Antunes A (2015) Extreme Red Sea: Life in the Deep-Sea Anoxic Brine Lakes. in Red Sea VI Proceedings. Edited by A. Agius, E. Khalil & E. Scerri. Leiden, The Netherlands: E.J. Brill, 2015 (in press).
  9. 2014

  10. Kato, S.; Matsumoto, A.; Yoshimura, K.; Katsuki, T.; Iwamoto, K.; Kawahara, T.; Mukai, Y.; Tsuda, Y.; Ishio, S.; Nakamura, K.; Moriwaki, K.; Shiroishi, T.; Gojobori, T.; Yoshimaru, H. Origins of Japanese flowering cherry (Prunus subgenus Cerasus) cultivars revealed using nuclear SSR markers, in Tree Genetics & Genomes 2014, pp 1-13. doi:10.1007/s11295-014-0697-1
  11. 2013

  12. Chowdhary R, Jankovic JR, Stankowski RV, Archer JAC, Zhang X, Gao X, Bajic VB (2013) Automated mining of disease-specific protein interaction networks based on biomedical literature. Biological Data Mining and Its Applications in Healthcare Edited by Xiaoli Li, See-Kiong Ng and Jason TL Wang, Science, Engineering and Biology Informatics, Vol. 8, Chapter 14, Page 393-415, World Scientific, 2013. eISBN:978-981-4551-02-1
  13. Koyanagi KO, Imanishi T, Gojobori T (2013) Bidirectional Gene Pairs in the Human Genome. Encyclopedia of Life Science (ELS) John Wiley & Wons, Ltd. 2013, pp 1-9. doi:10.1002/9780470015902.a0020776.pub2
  14. 2012

  15. Ashoor H, Mora AM, Awara K, Jankovic BR, Chowdhary R, Archer JAC, Bajic VB (2012) Recognition of Translation Initiation Sites in Arabidopsis thaliana. Chapter 5 in Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances Eds. Paola Lecca, Dan Tulpan, Kanagasabai Rajaraman, IGI Global, 2012, 105-116. doi:10.4018/978-1-61350-435-2.ch005
  16. Jankovic BR, Archer JAC, Chowdhary R, Schaefer U, Bajic VB (2012) Promoter structures conserved between Homo sapiens, Mus musculus and Drosophila melanogaster. Chapter 4 in Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances Eds. Paola Lecca, Dan Tulpan, Kanagasabai Rajaraman, IGI Global, 2012, 92-104. doi:10.4018/978-1-61350-435-2.ch004
  17. Sagar S, Gehring C, Minneman KP (2012) Methods to Isolate and Identify New Plant Signaling Peptides. Chapter 12 in Plant Signaling Peptides Eds. Helen Irving and Christoph Gehring, Springer, 2012, pp.217-239. doi:10.1007/978-3-642-27603-3_12
  18. 2011

  19. Zhang Z, Bajic VB, Yu J, Cheung KH, Townsend JP (2011) Data Integration in Bioinformatics: Current Efforts and Challenges in Bioinformatics - Trends and Methodologies, Mahmood A. Mahdavi (Ed.), InTech ISBN:978-953-307-282-1
  20. 2010

  21. Dwivedi S, Upadhyaya H, Subudhi P, Gehring C, Bajic V, Ortiz R (2010) Enhancing abiotic stress tolerance in cereals through breeding and transgenic interventions in Plant Breeding Reviews (John Wiley & Sons, Inc.). 33:31-114. ISBN:978-0-470-52585-2
  22. Tegnéer J, Björkegren J, Ravasi T, Bajic VB (2010) Transcription Regulatory Networks Analysis Using CAGE Cap-Analysis of Gene Expression (CAGE): The Science of Decoding Genes Transcription, Ed. P Carninci, Pan Stanford Publishing Pte Ltd 153-168. eISBN: 9789814241359
  23. Gottig N, Garavaglia BS, Garofalo CG, Zimaro T, Sgro G, Ficarra FA, Dunger G, Daurelio LD, Thomas L, Gehring C, Orellano EG, Ottado J (2010) Mechanisms of infection used by Xanthomonas axonopodis pv. citri in citrus canker disease Current Research Technology and Education Topics in Applied Microbiology and Microbial Biotechnology, Ed A. Mendez-Vilas 1-10. ISBN-13: 978-84-614-6194-3

Approved Patents

    2015

  1. Bajic V, Kaur M. Molecular biomarker set for early detection of ovarian cancer Filed: March 8, 2012 Issued: June 16, 2015 Assignee: King Abdullah University of Science and Technology Patent number: 9057107

Full Patent Applications

    2014

  1. Essack M, Bajic V. PCT National Phase, Canada, Entitled: Combinatorial Drugs for Treatment of Alzheimer''''s Disease and other Neurodegenerative Disorders, application date: 11/20/2014.
  2. Essack M, Bajic V. PCT National Phase No. 2013264943, Australia, Entitled: Combinatorial Drugs for Treatment of Alzheimer''''s Disease and other Neurodegenerative Disorders, application date: 11/21/2014.
  3. Essack M, Bajic V. PCT National Phase No. EP13759309.1, Europe (EPO), Entitled: Combinatorial Drugs for Treatment of Alzheimer''''s Disease and other Neurodegenerative Disorders, application date: 12/14/2014.
  4. Essack M, Bajic V. PCT National Phase No. 14/402,385, USA, Entitled: Combinatorial Drugs for Treatment of Alzheimer''''s Disease and other Neurodegenerative Disorders, application date: 11/20/2014.
  5. Mansour H, Incitti R, Bajic V. Non-Provisional No. 14/153,651, USA, Composite DNA Methylation-based Biomarker set for Non-invasive Screening, Diagnosis and Prognosis of Ovarian Cancer, application date: 1/13/2014.
  6. Mansour H, Incitti R, Bajic V. PCT National Phase, South Africa, Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Breast Cancer, application date: 12/12/2014.
  7. Mansour H, Incitti R, Bajic V. PCT National Phase, Canada, Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Breast Cancer, application date: 12/9/2014.
  8. Mansour H, Incitti R, Bajic V. PCT National Phase No. 14/408,238, USA, Entitled: Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Breast Cancer, application date: 12/15/2014.
  9. Mansour H, Incitti R, Bajic V. PCT National Phase, South Africa, Entitled: Composite Biomarker for Non-Invasive Screening, Diagnosis and Prognosis of Prostate Cancer, application date: 12/12/2014.
  10. Mansour H, Incitti R, Bajic V. PCT National Phase, Canada, Entitled: Composite Biomarker for Non-Invasive Screening, Diagnosis and Prognosis of Prostate Cancer, application date: 12/9/2014.
  11. Mansour H, Incitti R, Bajic V. PCT National Phase No. 14/408,238, USA, Entitled: Composite Biomarker for Non-Invasive Screening, Diagnosis and Prognosis of Prostate Cancer, application date: 12/15/2014.
  12. Mansour H, Incitti R, Bajic V. PCT National Phase No. 12813096, Europe (EPO), Entitled: Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Colorectal Cancer, application date: 5/16/2014.
  13. Mansour H, Incitti R, Bajic V. PCT National Phase No. 14/352,661, USA, Entitled: Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Colorectal Cancer, application date: 4/17/201.
  14. Mansour H, Incitti R, Bajic V. PCT National Phase No. 2014/02873, South Africa, Entitled: Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Colorectal Cancer, application date: 4/22/201.
  15. Mansour H, Incitti R, Bajic V. PCT National Phase, Canada, Entitled: Composite Biomarker For Non-Invasive Screening, Diagnosis And Prognosis Of Colorectal Cancer, application date: 4/17/2014.
  16. Essack M, Radovanovic A, Bajic V. PCT National Phase No. 14/345,206, USA, Entitled: Treatment of sickle cell disease, application date: 6/23/2014.
  17. 2013

  18. Essack M, Bajic V. PCT Patent Application No.: PCT/US2013/042164; Entitled: Combinatorial Drugs for Treatment of Alzheimer`s Disease and other Neurodegenerative Disorders, Filing Date: May 22, 2013.
  19. Kaur M, Essau L, Sagar S. PCT Patent Application No.: PCT/US2013/031087 PCT/IB2013/000906; U.S. Non-Provisional Application No.: 13/802,430; Entitled: A potential anti-cancer lead molecule, Date Filed: March 13, 2013.
  20. Mansour H, Incitti R, Bajic V. PCT Patent Application No.: PCT/US13/45149, PCT/IB2013/002012; Entitled: COMPOSITE BIOMARKERS FOR NON-INVASIVE SCREENING, DIAGNOSIS AND PROGNOSIS OF BREAST CANCER, Date Filed: June 11, 2013.
  21. Mansour H, Incitti R, Bajic V. PCT Patent Application No.: PCT/US2013/045150,PCT/IB2013/001887; Entitled: COMPOSITE BIOMARKERS FOR NON-INVASIVE SCREENING, DIAGNOSIS AND PROGNOSIS OF PROSTATE CANCER, Date Filed: June 11, 2013.
  22. Kosel J, Ravasi R, Contrera M, U.S. Non-Provisional Application No. 13/919,552; Entitled: Magnetostrictive nanowires for biological cell manipulation, Date Filed: June 17, 2013.
  23. 2012

  24. Magbubah E, Radovanovic A, Bajic V. PCT Patent Application No.: PCT/IB2012/002887; Entitled: Repositioning of Hydroxyfasudil to treat sickle cell disease (SCD), Date Filed: September 13, 2012.
  25. Mansour H, Incitti R, Bajic V. PCT Patent Application No.: PCT/US12/60388; Entitled: COMPOSITE BIOMARKERS FOR NON-INVASIVE SCREENING, DIAGNOSIS AND PROGNOSIS OF COLORECTAL CANCER, Date Filed: October 15, 2012.
  26. Essack M, Radovanovic A, Bajic V. PCT Patent Application No.: PCT/US12/55042; Entitled: TREATMENT OF SICKLE CELL DISEASE, Date Filed: September 13, 2012.
  27. Bajic V, Kaur M. U.S. Non-Provisional Application No.: 13/415,004; Entitled: MOLECULAR BIOMARKER SET FOR EARLY DETECTION OF OVARIAN CANCER, Date Filed: March 8, 2012.

Provisional Patent Applications

    2016

  1. Wail Ba Alawi, Othman Soufan, Panos Kalnis, Vladimir Bajic A method to predict and rank new edges in a network Unites States Provisional Patent Application No. 62/287,471, Filed January 27, 2016, Applicant: KAUST
  2. 2013

  3. Kamanu T, Bajic V, US Provisional Patent Application No: 61/817,665; Entitled: Species-independent microRNA and microRNA gene discovery: Discovery of hidden signals on DNA/RNA sequences using symmetry and geometry properties of hairpin-like structures, as implemented in the Dragon microRNA Discovery System (DMDS), Filing Date: April 30, 2013.
  4. Kaur M, Esau L, US Provisional Patent Application No: 61/758,527; Entitled: A Novel Protocol for Adherent Cells Flow Cytometry, Filing Date: January 30, 2013.
  5. Mansour H, Incitti R, Bajic V, US Provisional Patent Application No: 61/752,156; Entitled: METHYLATION BIOMARKERS FOR OVARIAN CANCER, Filing Date: January 14, 2013.
  6. 2012

  7. Kaur M, Stingl U, Tyas H, Bajic V, Sagar S, Esau L, US Provisional Patent Application No: 61/747,351; Entitled: Cytotoxic and Apoptotic Evaluations of Marine Bacteria Isolated from Brine-Seawater Interface of the Red Sea, Filing Date: December 30, 2012.
  8. Kamau A, US Provisional Patent Application No: 61/712,478; Entitled: Discretization Algorithm, Filing Date: October 11, 2012.
  9. Kosel J, Ravasi R, Contrera M, U.S. Provisional Application No. 61/660,929; Entitled: Magnetostrictive nanowires for biological cell manipulation, Date Filed: June 18, 2012.
  10. Incitti R, Mansour H, Bajic V, US Provisional Patent Application No: 61/659,236; Entitled: METHYLATION BIOMARKERS FOR PROSTATE CANCER, Filing Date: June 13, 2012.
  11. Sagar S, Esau L and Kaur M. US Provisional Patent Application No: 61/640,255; Entitled: ANTI-CANCER LEAD MOLECULE, Filing Date: April 30, 2012.
  12. Incitti R, Mansour H, Bajic V, US Provisional Patent Application No: 61/659,239; Entitled: METHYLATION BIOMARKERS FOR BREAST CANCER, Filing Date: June 13, 2012.
  13. Essack M, Bajic V. U.S. Provisional Application No.: 61/649,964; Entitled: COMBINATORIAL DRUGS FOR TREATMENT OF ALZHEIMER\''''\''''S DISEASE AND OTHER NEURODEGENERATIVE DISORDERS, Filing Date: May 22, 2012.
  14. 2011

  15. Mansour H, Incitti R, Bajic V. U.S. Provisional Application No.: 61/548,202; Entitled: COMPOSITE BIOMARKERS FOR NON-INVASIVE SCREENING, DIAGNOSIS AND PROGNOSIS OF COLORECTAL CANCER, Filing Date: October 17, 2011.
  16. Essack M, Radovanovic A, Bajic V. U.S. Provisional Application No.: 61/534,449; Entitled: TREATMENT OF SICKLE CELL DISEASE, Filing Date: September 14, 2011.
  17. Bajic V. Kaur M. U.S. Provisional Patent Application No.: 61/450,212; Entitled: MOLECULAR BIOMARKER SET FOR EARLY DETECTION OF OVARIAN CANCER. Filing Date: 08.March 2011.

Selected Conference Papers

    2017

  1. Xu Z, Ke Y, Gao X (2017) A fast algorithm for matrix eigen-decomposition. The 33rd Conference on Uncertainty in Artificial Intelligence (UAI2017), Sydney, Australia, August 2017.
  2. Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R (2017) Phenotype-driven discovery of digenic variants in personal genome sequences. Proceedings of VarI-COSI: Identification and annotation of genetic variants in the context of structure, function, and disease, 2017.
  3. 2016

  4. Slater L, Gkoutos GV, Schofield PN, Hoehndorf R (2016) To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO). Proceedings of International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016).
  5. Kulmanov M, HoehndorfR (2016). Evaluating the effect of annotation size on measures of semantic similarity. Proceedings of Bio-Ontologies SIG http://leechuck.de/sim-eval.pdf
  6. 2015

  7. Abdel-Haleem AM, Abuelela AF, Solovyev V, Jamshidi N, Lewis NE (2015) Model-driven analysis of gene expression data : Application to metabolic re-programming during T-cell activation. Proceedings of the 16th International Conference on Bioinformatics & Computational Biology (BIOCOMP'15) pp. 91-95.
  8. Sun S, Wang X, Gao X, Ren L, Sun X, Bu D, Ning K (2015) Preprocess and condensation of Raman spectrum for single-cell phenotype analysis. The 26th International Conference on Genome Informatics (GIW2015) Tokyo, Japan, September 2015.
  9. Cui X, Kuwahara H, Li S, Gao X (2015) Compare local pocket and global protein structure models by small structure patterns. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2015 (ACM-BCB2015) Atlanta, U.S., September 2015.
  10. Wang J, Gao X (2015) Partially labeled data tuple can optimize multivariate performance measures. ACM International Conference on Information and Kowledge Management (CIKM2015) Melbourne, Australia, October 2015.
  11. Slater L, Gkoutos GV, Schofield PN, Hoehndorf R (2015) Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies. Proceedings of the International Conference on Biomedical Ontologies (ICBO) 2015 (pp. 72-76).
  12. Lu Z, Gao X, Wang L, Huang S, Wen J. Social image parsing by cross-modal data refinement. The International Joint Conference on Artificial Intelligence (IJCAI-15), Buenos Aires, Argentina, July 2015.
  13. Cui X, Naveed H, Gao X. Finding optimal interaction interface alignments between biological complexes. The 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2015), Dublin, Ireland, July 2015.
  14. Alabdulmohsin I, Gao X, Zhang X. Efficient active learning of halfspaces via query synthesis. The Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI-15), Austin, US, January 2015. (pp. 2483-2489).
  15. Lu Z, Gao X, Wang L, Wen J, Huang S. Noise-robust semi-supervised learning by large-scale sparse coding. The Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI-15), Austin, US, January 2015. (pp. 2828-2834).
  16. 2014

  17. Islam A, Gao X, Fedoroff N. Quick mining of isomorphic exact large patterns from large graphs. IEEE International Conference on Data Mining Workshop (ICDMW). 2014. (pp. 517-524).
  18. Islam A. Pose-Independent Identity-based Facial Image Retrieval using Contextual Similarity. Workshop on Human Identification for Surveillance. Asian Conference on Computer Vision (ACCV 2014).
  19. Wang J, Gao X. Minimum information loss based multi-kernel for Flagellar protein recognition in Trypanosoma brucei. ICDM 2014 Workshop on Biological Data Mining and Its Applications in Healthcare (BioDM2014). Shenzhen, China, December 2014. (pp. 133-141).
  20. Wang, X., Kuwahara, H., & Gao, X. (2014). Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. The 25th International Conference on Genome Informatics (GIW / ISCB-Asia 2014). Tokyo, Japan, December 2014.
  21. Alabdulmohsin, I., Gao, X., & Zhang, X. (2014). Support vector machines with indefinite kernels. In Proceedings of the Sixth Asian Conference on Machine Learning. (pp. 32-47).
  22. Alabdulmohsin, I. M., Gao, X., & Zhang, X. (2014, November). Adding Robustness to Support Vector Machines Against Adversarial Reverse Engineering. In Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management (pp. 231-240). ACM. doi:10.1145/2661829.2662047
  23. Al-Shedivat, M., Wang, J. J. Y., Alzahrani, M., Huang, J. Z., & Gao, X. (2014, June). Supervised transfer sparse coding. In Twenty-eighth AAAI conference on artificial intelligence. (pp. 1665-1672).
  24. Wang, J. J. Y., Alzahrani, M., & Gao, X. Large margin image set representation and classification. (IJCNN), 2014 International Joint Conference on Neural Networks. IEEE. (pp. 1797-1803).
  25. Wang, J. J. Y., & Gao, X. (2014, July). Semi-supervised sparse coding. (IJCNN), 2014 International Joint Conference on Neural Networks. IEEE. (pp. 1630-1637).
  26. 2013

  27. Kuwahara H, Fan M, Wang S, Gao X. A framework for scalable parameter estimation of gene circuit models using structural information. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2013), Berlin, Germany, July 2013.
  28. Xie B, Jankovic B, Bajic V, Song L, Gao X. Poly(A) motif prediction using spectral latent features from human DNA sequences. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2013), Berlin, Germany, July 2013.
  29. 2012

  30. Wang, J. Y., Almasri, I., & Gao, X. Adaptive graph regularized nonnegative matrix factorization via feature selection. In 21st International Conference on Pattern Recognition (ICPR). IEEE. (pp. 963-966). (2012, November).
  31. Wang, J., & Almasri, I. Modeling multiple visual words assignment for bag-of-features based medical image retrieval. In Proceedings of the IASTED International Conference on Computer Graphics and Imaging. CGIM (pp. 217-224).
  32. 2011

  33. Marchand B, Bajic VB, Kaushik D. Highly Scalable Ab Initio Genomic Motif Identification. SuperComputing 2011, in Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis) Art.No. 56, Seattle, WA, USA. Nov. 12-18, 2011, ACM New York, NY, USA doi:10.1145/2063384.2063459
  34. Bellegdi, S. A., Mohandes, S., Soufan, O. M., & Arafat, S. Computational Intelligence for Cardiac Arrhythmia Classification. In Proceedings of the 11th UK Workshop on Computational Intelligence, University of Manchester, Manchester. 7th-9th September 2011. (pp. 93-97).
  35. Soufan, O., & Arafat, S. Arrhythmia Detection using Mutual Information-Based Integration Method. WConSC 2011 conference. arXiv preprint. arXiv:1502.01733. http://arxiv.org/abs/1502.01733
  36. 2009

  37. Avila-Garcia, M. S., Trefethen, A. E., Joshi, N., Gleeson, F., & Ba-alawi, W. Sharing and reusing cancer image segmentation algorithms using scientific workflows: Pros and cons. In e-Science, 2009. Fifth IEEE International Conference on e-Science''09 (2009, December). (pp. 94-101).