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Fulltext Growth of Hepatocellular Carcinoma into the Right Atrium with Associated Pulmonary Tumour Emboli

Amran, A.R., Ranganathan, S.

International Medical Journal Malaysia, 2006;5(1):1-5.
MyJurnal

Hepatocellular carcinoma (HCC) presenting with right atrial metastases and pulmonary tumour embolism is rare . Intracavitary cardiac metastasis is uncommon and metastasis to the right atrium is even less common. The majority of such cases are believed to be due to advanced HCC such as Stage III or IV, in which the progression rate is high, and in infiltrative HCC it tends to be associated with vascular invasion. The diagnosis of pulmonary intravascular tumour emboli is difficult to establish both clinically and with conventional radiographic studies. We report a case hepatocellular carcinoma associated with tumour thrombus in the inferior vena cava (IVC), right atrium and pulmonary tumour embolism detected with multidetector helical computerized tomography (MDHCT).
Fulltext Moving into the digital era: a novel experience with the first full-field digital mammography system in Malaysia

Ranganathan S, Faridah Y, Ng KH

Singapore Med J, 2007 Sep;48(9):804-7.
PMID: 17728959

Breast cancer is the commonest cancer in women and represents a significant problem from the clinical and public health perspectives. The aim of this paper is to report our experience of transitioning from screen-film mammography (SFM) to computed radiography mammography (CRM), and finally to full-field digital mammography (FFDM), and to evaluate the performance of these three different types of mammographic systems.
Fulltext Haemorrhaging lesion in the breast: is there a role for embolisation?

Taib N, Yip Ch, Ranganathan S, Moosa F, Mun K

Biomed Imaging Interv J, 2006 Jul;2(3):e30.
PMID: 21614243 MyJurnal DOI: 10.2349/biij.2.3.e30

Angiosarcoma of the breast is an extremely rare condition. This case illustrates the use of embolisation as a modality of treatment for primary breast angiosarcoma. No other case has been reported on the use of embolisation for this disorder.
MRI and CT findings of cryptococcal vaginitis

Ranganathan S, Moosa F, Kamarulzaman A, Looi LM

Br J Radiol, 2005 Apr;78(928):353-4.
PMID: 15774599

Cryptococcus neoformans is a yeast like fungus, which is commonly found in bird droppings, especially pigeons. Most cases of cryptococcal infections occur in immunocompromised patients or in those who are on long term immunosuppressant therapies. Cryptococcal infection usually presents as a meningoencephalitis or a pulmonary infection. Skin, bone and genital infections are very rare. We report the second case of vaginal cryptococcossis to be reported in English literature and the first to be imaged with CT and MRI.
Fulltext Bioinformatics research in the Asia Pacific: a 2007 update

Ranganathan S, Gribskov M, Tan TW

BMC Bioinformatics, 2008;9 Suppl 1(Suppl 1):S1.
PMID: 18315840 DOI: 10.1186/1471-2105-9-S1-S1

We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.
Fulltext APBioNet-transforming bioinformatics in the Asia-Pacific region

Khan AM, Tan TW, Schönbach C, Ranganathan S

PLoS Comput Biol, 2013 Oct;9(10):e1003317.
PMID: 24204244 DOI: 10.1371/journal.pcbi.1003317
Fulltext Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

Ranganathan S, Schönbach C, Nakai K, Tan TW

BMC Genomics, 2010;11 Suppl 4:S1.
PMID: 21143792 DOI: 10.1186/1471-2164-11-S4-S1

The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InCoB), Sept. 26-28, 2010 in Tokyo, Japan. Initially, APBioNet created InCoB as forum to foster bioinformatics in the Asia Pacific region. Given the growing importance of interdisciplinary research, InCoB2010 included topics targeting scientists in the fields of genomic medicine, immunology and chemoinformatics, supporting translational research. Peer-reviewed manuscripts that were accepted for publication in this supplement, represent key areas of research interests that have emerged in our region. We also highlight some of the current challenges bioinformatics is facing in the Asia Pacific region and conclude our report with the announcement of APBioNet's 100 BioDatabases (BioDB100) initiative. BioDB100 will comply with the database criteria set out earlier in our proposal for Minimum Information about a Bioinformatics and Investigation (MIABi), setting the standards for biocuration and bioinformatics research, on which we will report at the next InCoB, Nov. 27 - Dec. 2, 2011 at Kuala Lumpur, Malaysia.
Fulltext Extending Asia Pacific bioinformatics into new realms in the "-omics" era

Ranganathan S, Eisenhaber F, Tong JC, Tan TW

BMC Genomics, 2009;10 Suppl 3:S1.
PMID: 19958472 DOI: 10.1186/1471-2164-10-S3-S1

The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.
Editorial: 21st International Conference on Bioinformatics (InCoB 2022)-accelerating innovation to meet biological challenges: the role of bioinformatics

Khan AM, Singh H, Ranganathan S, Gojobori T, Gao X

Front Genet, 2024;15:1365223.
PMID: 38333618 DOI: 10.3389/fgene.2024.1365223
Fulltext Emerging strengths in Asia Pacific bioinformatics

Ranganathan S, Hsu WL, Yang UC, Tan TW

BMC Bioinformatics, 2008 Dec 12;9 Suppl 12(Suppl 12):S1.
PMID: 19091008 DOI: 10.1186/1471-2105-9-S12-S1

The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.
Fulltext InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia

Schönbach C, Tan TW, Kelso J, Rost B, Nathan S, Ranganathan S

BMC Genomics, 2011 Nov 30;12 Suppl 3:S1.
PMID: 22369160 DOI: 10.1186/1471-2164-12-S3-S1

In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.
Fulltext Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference

Ranganathan S, Schönbach C, Kelso J, Rost B, Nathan S, Tan TW

BMC Bioinformatics, 2011;12 Suppl 13:S1.
PMID: 22372736 DOI: 10.1186/1471-2105-12-S13-S1

The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB's goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.
Quantitative assessment of breast density from digitized mammograms into Tabar's patterns

Jamal N, Ng KH, Looi LM, McLean D, Zulfiqar A, Tan SP, et al.

Phys Med Biol, 2006 Nov 21;51(22):5843-57.
PMID: 17068368

We describe a semi-automated technique for the quantitative assessment of breast density from digitized mammograms in comparison with patterns suggested by Tabar. It was developed using the MATLAB-based graphical user interface applications. It is based on an interactive thresholding method, after a short automated method that shows the fibroglandular tissue area, breast area and breast density each time new thresholds are placed on the image. The breast density is taken as a percentage of the fibroglandular tissue to the breast tissue areas. It was tested in four different ways, namely by examining: (i) correlation of the quantitative assessment results with subjective classification, (ii) classification performance using the quantitative assessment technique, (iii) interobserver agreement and (iv) intraobserver agreement. The results of the quantitative assessment correlated well (r2 = 0.92) with the subjective Tabar patterns classified by the radiologist (correctly classified 83% of digitized mammograms). The average kappa coefficient for the agreement between the readers was 0.63. This indicated moderate agreement between the three observers in classifying breast density using the quantitative assessment technique. The kappa coefficient of 0.75 for intraobserver agreement reflected good agreement between two sets of readings. The technique may be useful as a supplement to the radiologist's assessment in classifying mammograms into Tabar's pattern associated with breast cancer risk.
Fulltext A bioinformatics potpourri

Schönbach C, Li J, Ma L, Horton P, Sjaugi MF, Ranganathan S

BMC Genomics, 2018 01 19;19(Suppl 1):920.
PMID: 29363432 DOI: 10.1186/s12864-017-4326-x

The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.
Fulltext Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing

Hotta K, Ranganathan S, Liu R, Wu F, Machiyama H, Gao R, et al.

PLoS Comput Biol, 2014 Apr;10(4):e1003532.
PMID: 24722239 DOI: 10.1371/journal.pcbi.1003532

Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD) of p130Cas (or BCAR1) has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2-9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing β-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing.
Fulltext Gut microbiota composition during infancy and subsequent behavioural outcomes

Loughman A, Ponsonby AL, O'Hely M, Symeonides C, Collier F, Tang MLK, et al.

EBioMedicine, 2020 Feb;52:102640.
PMID: 32062351 DOI: 10.1016/j.ebiom.2020.102640

BACKGROUND: Despite intense interest in the relationship between gut microbiota and brain development, longitudinal data from human studies are lacking. This study aimed to investigate the relationship between the composition of gut microbiota during infancy and subsequent behavioural outcomes.
METHODS: A subcohort of 201 children with behavioural outcome measures was identified within a longitudinal, Australian birth-cohort study. The faecal microbiota were analysed at 1, 6, and 12 months of age. Behavioural outcomes were measured at 2 years of age.
FINDINGS: In an unselected birth cohort, we found a clear association between decreased normalised abundance of Prevotella in faecal samples collected at 12 months of age and increased behavioural problems at 2 years, in particular Internalizing Problem scores. This association appeared independent of multiple potentially confounding variables, including maternal mental health. Recent exposure to antibiotics was the best predictor of decreased Prevotella.
INTERPRETATION: Our findings demonstrate a strong association between the composition of the gut microbiota in infancy and subsequent behavioural outcomes; and support the importance of responsible use of antibiotics during early life.
FUNDING: This study was funded by the National Health and Medical Research Council of Australia (1082307, 1147980, 1129813), The Murdoch Children's Research Institute, Barwon Health, Deakin University, Perpetual Trustees, and The Shepherd Foundation. The funders had no involvement in the data collection, analysis or interpretation, trial design, recruitment or any other aspect pertinent to the study.
Fulltext What information and the extent of information research participants need in informed consent forms: a multi-country survey

Karbwang J, Koonrungsesomboon N, Torres CE, Jimenez EB, Kaur G, Mathur R, et al.

BMC Med Ethics, 2018 09 15;19(1):79.
PMID: 30219106 DOI: 10.1186/s12910-018-0318-x

BACKGROUND: The use of lengthy, detailed, and complex informed consent forms (ICFs) is of paramount concern in biomedical research as it may not truly promote the rights and interests of research participants. The extent of information in ICFs has been the subject of debates for decades; however, no clear guidance is given. Thus, the objective of this study was to determine the perspectives of research participants about the type and extent of information they need when they are invited to participate in biomedical research.
METHODS: This multi-center, cross-sectional, descriptive survey was conducted at 54 study sites in seven Asia-Pacific countries. A modified Likert-scale questionnaire was used to determine the importance of each element in the ICF among research participants of a biomedical study, with an anchored rating scale from 1 (not important) to 5 (very important).
RESULTS: Of the 2484 questionnaires distributed, 2113 (85.1%) were returned. The majority of respondents considered most elements required in the ICF to be 'moderately important' to 'very important' for their decision making (mean score, ranging from 3.58 to 4.47). Major foreseeable risk, direct benefit, and common adverse effects of the intervention were considered to be of most concerned elements in the ICF (mean score = 4.47, 4.47, and 4.45, respectively).
CONCLUSIONS: Research participants would like to be informed of the ICF elements required by ethical guidelines and regulations; however, the importance of each element varied, e.g., risk and benefit associated with research participants were considered to be more important than the general nature or technical details of research. Using a participant-oriented approach by providing more details of the participant-interested elements while avoiding unnecessarily lengthy details of other less important elements would enhance the quality of the ICF.

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