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  1. Article ; Online: MRI findings in athletic groin pain: correlation of imaging with history and examination in symptomatic and asymptomatic athletes.

    Ooi, Michelle Wei Xin / Marzetti, Matthew / Rowbotham, Emma / Bertham, Dominic / Robinson, Philip

    Skeletal radiology

    2024  

    Abstract: Objective: To determine differences in prevalence and diagnostic accuracy of MRI findings between asymptomatic athletes and athletes with longstanding groin pain.: Materials and methods: One hundred twenty-three adult male athletes were approached ... ...

    Abstract Objective: To determine differences in prevalence and diagnostic accuracy of MRI findings between asymptomatic athletes and athletes with longstanding groin pain.
    Materials and methods: One hundred twenty-three adult male athletes were approached with 85 consecutive athletes recruited. Group 1 (symptomatic, n = 34) athletes referred for longstanding groin pain (insidious onset, > 3 weeks duration). Group 2 (control, n = 51) athletes referred for injuries remote from the pelvis and no groin pain in the last 12 weeks. All referrers completed a clinical examination proforma documenting absence or presence of pelvis and hip abnormality. All patients completed the Copenhagen Hip and Groin Outcome Score (HAGOS) questionnaire and underwent a 3T MRI groin and hip protocol. MRIs were scored independently by two musculoskeletal radiologists blinded to clinical details. Statistical analysis was performed to evaluate associations between MRI findings, inter-reader reliability, clinical examination and HAGOS scores.
    Results: Pubic body subchondral bone oedema, capsule/aponeurosis junction tear and soft tissue oedema were more prevalent in the symptomatic group (p = 0.0003, 0.0273 and 0.0005, respectively) and in athletes with clinical abnormality at symphysis pubis, adductor insertion, rectus abdominis, psoas and inguinal canal (p = 0.0002, 0.0459 and 0.00002, respectively). Pubic body and subchondral oedema and capsule/aponeurosis tear and oedema significantly correlated with lower (worse) HAGOS scores (p = 0.004, 0.00009, 0.0004 and 0.002, respectively). Inter-reader reliability was excellent, 0.87 (range 0.58-1). Symphyseal bone spurring, disc protrusion and labral tears were highly prevalent in both groups.
    Conclusion: Clinical assessment and MRI findings of pubic subchondral bone oedema and capsule/aponeurosis abnormality appear to be the strongest correlators with longstanding groin pain.
    Language English
    Publishing date 2024-02-02
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 527592-1
    ISSN 1432-2161 ; 0364-2348
    ISSN (online) 1432-2161
    ISSN 0364-2348
    DOI 10.1007/s00256-024-04603-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Rotator cuff assessment on imaging.

    Xin Ooi, Michelle Wei / Fenning, Leah / Dhir, Varun / Basu, Subhasis

    Journal of clinical orthopaedics and trauma

    2021  Volume 18, Page(s) 121–135

    Abstract: The rotator cuff is a group of four muscles and tendons surrounding the shoulder joint providing it strength and stability. The rotator cuff consists of the subscapularis, supraspinatus, infraspinatus and teres minor. Many shoulder complaints are caused ... ...

    Abstract The rotator cuff is a group of four muscles and tendons surrounding the shoulder joint providing it strength and stability. The rotator cuff consists of the subscapularis, supraspinatus, infraspinatus and teres minor. Many shoulder complaints are caused by rotator cuff pathology such as impingement syndrome, tendon tears and other diseases e.g. calcific tendonitis. Diagnosis starts with clinical history and physical examination, after which imaging is often used to help confirm clinical findings depending on the differential diagnosis. The aim of the article is to review the frequently used imaging modalities to assess the rotator cuff and cuff-related disease, specifically focusing on radiography, ultrasonography and magnetic resonance imaging. This article will outline the advantages and disadvantages for each modality and illustrate typical radiological findings of common rotator cuff pathologies.
    Language English
    Publishing date 2021-04-21
    Publishing country India
    Document type Journal Article
    ZDB-ID 2596956-0
    ISSN 2213-3445 ; 0976-5662
    ISSN (online) 2213-3445
    ISSN 0976-5662
    DOI 10.1016/j.jcot.2021.04.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Role of dynamic ultrasound in assessment of the snapping elbow and distal biceps tendon injury.

    Ooi, Michelle Wei Xin / Tham, Jun-Li / Al-Ani, Zeid

    Ultrasound (Leeds, England)

    2021  Volume 30, Issue 4, Page(s) 315–321

    Abstract: Introduction: Ultrasound is useful in assessing patients with snapping syndromes around the elbow joint. The dynamic nature of the examination allows for direct visualisation of the underlying causative factor.: Discussion: Ulnar nerve instability ... ...

    Abstract Introduction: Ultrasound is useful in assessing patients with snapping syndromes around the elbow joint. The dynamic nature of the examination allows for direct visualisation of the underlying causative factor.
    Discussion: Ulnar nerve instability and snapping triceps can be assessed via a medial approach with the transducer placed transversely between the medial epicondyle and the olecranon. In ulnar nerve instability, the nerve can be seen crossing over the medial epicondyle on elbow flexion. In snapping triceps syndrome, both the ulnar nerve and the distal triceps can be seen dislocating over the medial epicondyle. Dynamic assessment of the distal biceps tendon using a lateral approach minimises anisotropy artefact often seen on the anterior approach. Passive pronation and supination of the forearm will reveal little or no movement in a completely torn tendon whereas moving tendon fibres will be appreciated in partial tears. In a snapping brachialis, the medial portion of brachialis will be seen abnormally translocating anterolateral to the medial border of the trochlea during elbow flexion and snapping back into its normal position on elbow extension.
    Conclusion: Dynamic ultrasound of the elbow is valuable in diagnosing patients with snapping sensations around the joint and in evaluating the integrity of the distal biceps tendon.
    Language English
    Publishing date 2021-11-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2298926-2
    ISSN 1743-1344 ; 1742-271X
    ISSN (online) 1743-1344
    ISSN 1742-271X
    DOI 10.1177/1742271X211057204
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Role of complementary Ct chest in patients presenting with acute abdominal symptoms during covid-19 pandemic: a UK experience.

    Ooi, Michelle Wei Xin / Liong, Sue Yin / Baguley, Nathan / Sharman, Anna / Tuck, Jonathan

    Clinical imaging

    2020  Volume 69, Page(s) 289–292

    Abstract: Background: In March 2020, the UK Intercollegiate General Surgery Guidance on COVID-19 recommended that patients undergoing emergency abdominal CT should have a complementary CT chest for COVID-19 screening.: Purpose: To establish if complementary CT ...

    Abstract Background: In March 2020, the UK Intercollegiate General Surgery Guidance on COVID-19 recommended that patients undergoing emergency abdominal CT should have a complementary CT chest for COVID-19 screening.
    Purpose: To establish if complementary CT chest was performed as recommended, and if CT chest influenced surgical intervention decision. To assess detection rate of COVID-19 on CT and its correlation with RT-PCR swab results. To determine if COVID-19 changes is reliably detected within the lung bases which are usually imaged in standard abdominal CT.
    Methods: Patients with acute abdominal symptoms presenting to a single institution between 1st and 30th April 2020 who had abdominal CT and complementary CT chest were retrospectively extracted from Computerised Radiology Information System. CT COVID-19 changes were categorised according to British Society of Thoracic Radiology reporting guidance. Patient demographics (age and gender), RT-PCR swab results and management pathway (conservative or intervention) were recorded from electronic patient records. Statistical analyses were performed to evaluate any significant association between variables. p values ≤0.05 were regarded as statistically significant.
    Results: Compliancy rate in performing complementary CT chest was 92.5% (148/160). Thirty-five patients (35/148,23.6%) underwent intervention during admission. There was no significant association (p = 0.9085) between acquisition of CT chest and management pathway (conservative vs intervention). CT chest had 57% sensitivity (CI 18.41% to 90.1%) and 100% specificity (CI 92% to 100%) in COVID-19 diagnosis. Three of ten patients who had classic COVID-19 changes on CT chest did not have corresponding changes in lung bases.
    Conclusion: Compliance with performing complementary CT chest in acute abdomen patients for COVID-19 screening was high and it did not influence subsequent surgical or interventional management.
    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections/epidemiology ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; Retrospective Studies ; Role ; SARS-CoV-2 ; Thorax/diagnostic imaging ; Tomography, X-Ray Computed ; United Kingdom/epidemiology
    Keywords covid19
    Language English
    Publishing date 2020-10-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1028123-x
    ISSN 1873-4499 ; 0899-7071
    ISSN (online) 1873-4499
    ISSN 0899-7071
    DOI 10.1016/j.clinimag.2020.09.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The radiological findings in complex elbow fracture-dislocation injuries.

    Al-Ani, Zeid / Tham, Jun-Li / Ooi, Michelle Wei Xin / Wright, Andrew / Ricks, Matthew / Watts, Adam C

    Skeletal radiology

    2021  Volume 51, Issue 5, Page(s) 891–904

    Abstract: Elbow fracture-dislocation is a complex injury which can lead to significant bony and soft tissue damage. Surgical intervention is guided towards restoring joint stability, allowing early mobilization and preventing long-term joint stiffness. The most ... ...

    Abstract Elbow fracture-dislocation is a complex injury which can lead to significant bony and soft tissue damage. Surgical intervention is guided towards restoring joint stability, allowing early mobilization and preventing long-term joint stiffness. The most common types are posterolateral, posteromedial, Monteggia type (and variants), and anterior trans-olecranon fracture-dislocations. Posterolateral fracture-dislocation is characterized by a radial head fracture (± anterolateral coronoid fracture) and typically capsuloligamentous disruption (lateral collateral ligaments injury is the most common). A posterolateral fracture-dislocation with radial head and coronoid anterolateral facet fractures is termed a terrible triad injury. In posteromedial fracture-dislocation, there is a fracture of the anteromedial facet of the coronoid, typically with proximal avulsion of the lateral collateral ligaments (± injury to the posterior bundle of the ulnar collateral ligament). Monteggia fracture-dislocation injuries demonstrate proximal ulnar fracture (with possible involvement of the olecranon and the coronoid) and radial head dislocation. These can be divided into apex anterior or apex posterior variants. The latter are commonly associated with radial head fractures and lateral ligamentous injury, and have a worse prognosis. In trans-olecranon fracture-dislocation, there is significant disruption of the greater sigmoid notch and the olecranon, with various involvement of the coronoid and the proximal ulna. The article describes the radiological findings and outlines the management principles in complex elbow fracture-dislocation injuries.
    MeSH term(s) Collateral Ligaments/injuries ; Elbow ; Elbow Joint/injuries ; Humans ; Joint Dislocations/diagnostic imaging ; Joint Dislocations/surgery ; Radius Fractures/surgery ; Ulna Fractures/diagnostic imaging ; Ulna Fractures/surgery
    Language English
    Publishing date 2021-09-04
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 527592-1
    ISSN 1432-2161 ; 0364-2348
    ISSN (online) 1432-2161
    ISSN 0364-2348
    DOI 10.1007/s00256-021-03900-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Role of complementary Ct chest in patients presenting with acute abdominal symptoms during covid-19 pandemic: a UK experience

    Ooi, Michelle Wei Xin / Liong, Sue Yin / Baguley, Nathan / Sharman, Anna / Tuck, Jonathan

    Clin Imaging

    Abstract: BACKGROUND: In March 2020, the UK Intercollegiate General Surgery Guidance on COVID-19 recommended that patients undergoing emergency abdominal CT should have a complementary CT chest for COVID-19 screening. PURPOSE: To establish if complementary CT ... ...

    Abstract BACKGROUND: In March 2020, the UK Intercollegiate General Surgery Guidance on COVID-19 recommended that patients undergoing emergency abdominal CT should have a complementary CT chest for COVID-19 screening. PURPOSE: To establish if complementary CT chest was performed as recommended, and if CT chest influenced surgical intervention decision. To assess detection rate of COVID-19 on CT and its correlation with RT-PCR swab results. To determine if COVID-19 changes is reliably detected within the lung bases which are usually imaged in standard abdominal CT. METHODS: Patients with acute abdominal symptoms presenting to a single institution between 1st and 30th April 2020 who had abdominal CT and complementary CT chest were retrospectively extracted from Computerised Radiology Information System. CT COVID-19 changes were categorised according to British Society of Thoracic Radiology reporting guidance. Patient demographics (age and gender), RT-PCR swab results and management pathway (conservative or intervention) were recorded from electronic patient records. Statistical analyses were performed to evaluate any significant association between variables. p values ≤0.05 were regarded as statistically significant. RESULTS: Compliancy rate in performing complementary CT chest was 92.5% (148/160). Thirty-five patients (35/148,23.6%) underwent intervention during admission. There was no significant association (p = 0.9085) between acquisition of CT chest and management pathway (conservative vs intervention). CT chest had 57% sensitivity (CI 18.41% to 90.1%) and 100% specificity (CI 92% to 100%) in COVID-19 diagnosis. Three of ten patients who had classic COVID-19 changes on CT chest did not have corresponding changes in lung bases. CONCLUSION: Compliance with performing complementary CT chest in acute abdomen patients for COVID-19 screening was high and it did not influence subsequent surgical or interventional management.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #816358
    Database COVID19

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  7. Article: Resonance metallic ureteric stent in a case of ketamine bladder induced bilateral ureteric obstruction with one year follow up.

    Yong, Guo Liang / Kong, Chia Yew / Ooi, Michelle Wei Xin / Lee, Eng Geap

    International journal of surgery case reports

    2015  Volume 8C, Page(s) 49–51

    Abstract: Introduction: Upper urinary tract occlusion is well recognized in patients with chronic ketamine abuse. The mechanism is generally unknown, but the ulcerative cystitis contracture may be responsible for obstruction. We present the first reported use of ... ...

    Abstract Introduction: Upper urinary tract occlusion is well recognized in patients with chronic ketamine abuse. The mechanism is generally unknown, but the ulcerative cystitis contracture may be responsible for obstruction. We present the first reported use of the Resonance metallic ureteric stent in the management ureteric obstruction caused by ketamine-induced uropathy.
    Presentation of case: A 31-year-old lady with one-year history of recreational ketamine abuse presented with symptoms related to drug-induced ulcerative cystitis over twelve-months. She presented with acute renal failure with bilateral pyonephrosis and sepsis, and was initially treated with bilateral nephrostomy insertions and antegrade stenting. The J stents recovered the renal function, but the patient suffered from recurrent urinary tract infections (UTI's) with the prosthesis in-situ. The patient successfully underwent bilateral insertion of 12cm 6.0 French Cook Resonance metallic ureteric stents. One year following the placement of the metallic stents, the patient maintained optimal renal function with no episode of UTI.
    Discussion: Ketamine induced uropathy is a well documented complication of chronic drug-induced ulcerative cystitis. The mechanical strength and inert property of metallic ureteric stents make it an ideal device to manage this problematic benign cause of ureteric obstruction.
    Conclusion: This is the first reported case of therapeutic bilateral metallic ureteric stents in the management of patients with ketamine induced uropathy with one year follow up.
    Language English
    Publishing date 2015-01-12
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2210-2612
    ISSN 2210-2612
    DOI 10.1016/j.ijscr.2015.01.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales

    Kalisvar Marimuthu / Indumathi Venkatachalam / Vanessa Koh / Stephan Harbarth / Eli Perencevich / Benjamin Pei Zhi Cherng / Raymond Kok Choon Fong / Surinder Kaur Pada / Say Tat Ooi / Nares Smitasin / Koh Cheng Thoon / Paul Anantharajah Tambyah / Li Yang Hsu / Tse Hsien Koh / Partha Pratim De / Thean Yen Tan / Douglas Chan / Rama Narayana Deepak / Nancy Wen Sim Tee /
    Andrea Kwa / Yiying Cai / Yik-Ying Teo / Natascha May Thevasagayam / Sai Rama Sridatta Prakki / Weizhen Xu / Wei Xin Khong / David Henderson / Nicole Stoesser / David W. Eyre / Derrick Crook / Michelle Ang / Raymond Tzer Pin Lin / Angela Chow / Alex R. Cook / Jeanette Teo / Oon Tek Ng / Carbapenemase-Producing Enterobacteriaceae in Singapore (CaPES) Study Group

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 11

    Abstract: Carbapenemase-producing Enterobacterales cause healthcare-associated infections but modes of transmission are not well understood. Here, the authors find evidence of transmission without direct patient contact, indicating presence of undetected ... ...

    Abstract Carbapenemase-producing Enterobacterales cause healthcare-associated infections but modes of transmission are not well understood. Here, the authors find evidence of transmission without direct patient contact, indicating presence of undetected environmental reservoirs, whilst half of the transmission events are likely due to plasmid-mediated transmission.
    Keywords Science ; Q
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales.

    Marimuthu, Kalisvar / Venkatachalam, Indumathi / Koh, Vanessa / Harbarth, Stephan / Perencevich, Eli / Cherng, Benjamin Pei Zhi / Fong, Raymond Kok Choon / Pada, Surinder Kaur / Ooi, Say Tat / Smitasin, Nares / Thoon, Koh Cheng / Tambyah, Paul Anantharajah / Hsu, Li Yang / Koh, Tse Hsien / De, Partha Pratim / Tan, Thean Yen / Chan, Douglas / Deepak, Rama Narayana / Tee, Nancy Wen Sim /
    Kwa, Andrea / Cai, Yiying / Teo, Yik-Ying / Thevasagayam, Natascha May / Prakki, Sai Rama Sridatta / Xu, Weizhen / Khong, Wei Xin / Henderson, David / Stoesser, Nicole / Eyre, David W / Crook, Derrick / Ang, Michelle / Lin, Raymond Tzer Pin / Chow, Angela / Cook, Alex R / Teo, Jeanette / Ng, Oon Tek

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 3052

    Abstract: Carbapenemase-producing Enterobacterales (CPE) infection control practices are based on the paradigm that detected carriers in the hospital transmit to other patients who stay in the same ward. The role of plasmid-mediated transmission at population ... ...

    Abstract Carbapenemase-producing Enterobacterales (CPE) infection control practices are based on the paradigm that detected carriers in the hospital transmit to other patients who stay in the same ward. The role of plasmid-mediated transmission at population level remains largely unknown. In this retrospective cohort study over 4.7 years involving all multi-disciplinary public hospitals in Singapore, we analysed 779 patients who acquired CPE (1215 CPE isolates) detected by clinical or surveillance cultures. 42.0% met putative clonal transmission criteria, 44.8% met putative plasmid-mediated transmission criteria and 13.2% were unlinked. Only putative clonal transmissions associated with direct ward contact decreased in the second half of the study. Both putative clonal and plasmid-mediated transmission associated with indirect (no temporal overlap in patients' admission period) ward and hospital contact did not decrease during the study period. Indirect ward and hospital contact were identified as independent risk factors associated with clonal transmission. In conclusion, undetected CPE reservoirs continue to evade hospital infection prevention measures. New measures are needed to address plasmid-mediated transmission, which accounted for 50% of CPE dissemination.
    MeSH term(s) Bacterial Proteins ; Enterobacteriaceae Infections/microbiology ; Enterobacteriaceae Infections/transmission ; Gammaproteobacteria/genetics ; Humans ; Retrospective Studies ; Whole Genome Sequencing ; beta-Lactamases/genetics
    Chemical Substances Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6) ; carbapenemase (EC 3.5.2.6)
    Language English
    Publishing date 2022-06-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-30637-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

    Gerstein, Mark B / Lu, Zhi John / Van Nostrand, Eric L / Cheng, Chao / Arshinoff, Bradley I / Liu, Tao / Yip, Kevin Y / Robilotto, Rebecca / Rechtsteiner, Andreas / Ikegami, Kohta / Alves, Pedro / Chateigner, Aurelien / Perry, Marc / Morris, Mitzi / Auerbach, Raymond K / Feng, Xin / Leng, Jing / Vielle, Anne / Niu, Wei /
    Rhrissorrakrai, Kahn / Agarwal, Ashish / Alexander, Roger P / Barber, Galt / Brdlik, Cathleen M / Brennan, Jennifer / Brouillet, Jeremy Jean / Carr, Adrian / Cheung, Ming-Sin / Clawson, Hiram / Contrino, Sergio / Dannenberg, Luke O / Dernburg, Abby F / Desai, Arshad / Dick, Lindsay / Dosé, Andréa C / Du, Jiang / Egelhofer, Thea / Ercan, Sevinc / Euskirchen, Ghia / Ewing, Brent / Feingold, Elise A / Gassmann, Reto / Good, Peter J / Green, Phil / Gullier, Francois / Gutwein, Michelle / Guyer, Mark S / Habegger, Lukas / Han, Ting / Henikoff, Jorja G / Henz, Stefan R / Hinrichs, Angie / Holster, Heather / Hyman, Tony / Iniguez, A Leo / Janette, Judith / Jensen, Morten / Kato, Masaomi / Kent, W James / Kephart, Ellen / Khivansara, Vishal / Khurana, Ekta / Kim, John K / Kolasinska-Zwierz, Paulina / Lai, Eric C / Latorre, Isabel / Leahey, Amber / Lewis, Suzanna / Lloyd, Paul / Lochovsky, Lucas / Lowdon, Rebecca F / Lubling, Yaniv / Lyne, Rachel / MacCoss, Michael / Mackowiak, Sebastian D / Mangone, Marco / McKay, Sheldon / Mecenas, Desirea / Merrihew, Gennifer / Miller, David M / Muroyama, Andrew / Murray, John I / Ooi, Siew-Loon / Pham, Hoang / Phippen, Taryn / Preston, Elicia A / Rajewsky, Nikolaus / Rätsch, Gunnar / Rosenbaum, Heidi / Rozowsky, Joel / Rutherford, Kim / Ruzanov, Peter / Sarov, Mihail / Sasidharan, Rajkumar / Sboner, Andrea / Scheid, Paul / Segal, Eran / Shin, Hyunjin / Shou, Chong / Slack, Frank J / Slightam, Cindie / Smith, Richard / Spencer, William C / Stinson, E O / Taing, Scott / Takasaki, Teruaki / Vafeados, Dionne / Voronina, Ksenia / Wang, Guilin / Washington, Nicole L / Whittle, Christina M / Wu, Beijing / Yan, Koon-Kiu / Zeller, Georg / Zha, Zheng / Zhong, Mei / Zhou, Xingliang / Ahringer, Julie / Strome, Susan / Gunsalus, Kristin C / Micklem, Gos / Liu, X Shirley / Reinke, Valerie / Kim, Stuart K / Hillier, LaDeana W / Henikoff, Steven / Piano, Fabio / Snyder, Michael / Stein, Lincoln / Lieb, Jason D / Waterston, Robert H

    Science (New York, N.Y.)

    2010  Volume 330, Issue 6012, Page(s) 1775–1787

    Abstract: We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification ... ...

    Abstract We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
    MeSH term(s) Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/growth & development ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin/ultrastructure ; Chromosomes/genetics ; Chromosomes/metabolism ; Chromosomes/ultrastructure ; Computational Biology/methods ; Conserved Sequence ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Regulatory Networks ; Genes, Helminth ; Genome, Helminth ; Genomics/methods ; Histones/metabolism ; Models, Genetic ; Molecular Sequence Annotation ; RNA, Helminth/genetics ; RNA, Helminth/metabolism ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Caenorhabditis elegans Proteins ; Chromatin ; Histones ; RNA, Helminth ; RNA, Untranslated ; Transcription Factors
    Language English
    Publishing date 2010-12-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1196914
    Database MEDical Literature Analysis and Retrieval System OnLINE

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