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gEVAL - A web based browser for evaluating genome assemblies [article]

William Chow, Kim Brugger, Mario Caccamo, Ian Sealy, James Torrance, Kerstin Howe
2016 bioRxiv   pre-print
For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency
more » ... optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. While gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.
doi:10.1101/038638 fatcat:bhq5x5jwgbdovoax34vrf4soam

Genomic comparison of archaeal conjugative plasmids fromSulfolobus

Bo Greve, Susanne Jensen, Kim Brügger, Wolfram Zillig, Roger A. Garrett
2004 Archaea  
Like other secreted proteins of Sulfolobus, it is rich in 234 GREVE, JENSEN, BRÜGGER, ZILLIG AND GARRETT ARCHAEA VOLUME 1, 2004 Figure 2.  ... 
doi:10.1155/2004/151926 pmid:15810432 pmcid:PMC2685578 fatcat:epdodkvlufdnjfddapjigl46gy

A putative viral defence mechanism in archaeal cells

Reidun Lillestøl, Peter Redder, Roger A. Garrett, Kim Brügger
2006 Archaea  
Brügger and P. Redder, with K. Brügger also receiving grants from the Danish Science Research Council.  ...  surprising, given the large number of mobile elements in some archaeal genomes and the large variety of spacer sequences that could provide potential target sites for the insertion of mobile elements (Brügger  ...  shares a 14 bp inverted terminal repeat and a 3 bp direct repeat with the IS element, ISMac11, which exists in the same chromosome and encodes a transposase likely responsible for the MITE transposition (Brügger  ... 
doi:10.1155/2006/542818 pmid:16877322 pmcid:PMC2685585 fatcat:wv7aby34lvfsnlvh5sfnpodlv4

All-photoplastic microstencil with self-alignment for multiple layer shadow-mask patterning

Gyuman Kim, Beomjoon Kim, Jürgen Brugger
2003 Sensors and Actuators A-Physical  
A rapid and simple method to fabricate tiny shadow-masks and their use in multi-layer surface patterning with in situ micromechanical alignment is presented. Instead of using silicon micromachining with through-wafer etching to define the thin membrane with etched apertures, we are using photoplastic SU-8-based resist as structural material of both membrane and support rim. Two layers, 5 and 150 m thick, are structured by lithography and finally released from the surface. The free-standing SU-8
more » ... membranes have apertures ranging from 6 to 300 m. They are placed and mechanically fixed to the surface, which needs to be patterned. Deposition by evaporation of Cr, Au, Al or other material through the membrane apertures results in an accurate 1:1 replication of the aperture pattern. In view of multi-layer patterning, we used in situ micromechanical alignment pins or jigs and achieved an overlay precision of <2 m in both x-and y-directions. The reusable shadow-masks allows for a low-cost surface patterning technique without the need for photolithography related process steps. It allows unconventional surfaces to be patterned in a rapid and vacuum-clean way on arbitrary surfaces.
doi:10.1016/s0924-4247(03)00298-x fatcat:gafxcvraejfjhjg2ee7ioogwoy

Surface modification with self-assembled monolayers for nanoscale replication of photoplastic MEMS

Gyu Man Kim, Beomjoon Kim, M. Liebau, J. Huskens, D.N. Reinhoudt, J. Brugger
2002 Journal of microelectromechanical systems  
A release technique that enables to lift microfabricated structures mechanically off the surface without using wet chemistry is presented. A self-assembled monolayer of dodecyltrichlorosilane forms a very uniform 1.5-nm-thick anti-adhesion coating on the silicon dioxide surface, on full wafer scale. The structural layers are formed directly onto the organic layer. They consist here of a 100-nm-thick aluminum film and a high-aspect ratio photoplastic SU-8 structure. After the microfabrication
more » ... structure can be lifted off the surface together with the aluminum layer. This generic technique was used to make a variety of novel structures. First, aluminum electrodes that are embedded in plastic are made using lithography, etching and surface transfer techniques. Second, using a patterned monolayer as defined by microcontact printing, resulted in a spatial variation of the surface adhesion forces. This was used to directly transfer the stamped pattern into a metal structure without using additional transfer etching steps. Third, the monolayer's ability to cover surface features down to nanometer scale was exploited to replicate sharp surface molds into metal coated photoplastic tips with 30-nm radii for use in scanning probe instruments such as near-field optical techniques. The advantage compared to standard sacrificial layer techniques is the ability of replication at the nanoscale and the absence of etchants or solvents in the final process steps. [672]
doi:10.1109/jmems.2002.1007395 fatcat:b3y3gmu7kjhdzhkohjq7nca4cy

gEVAL — a web-based browser for evaluating genome assemblies

William Chow, Kim Brugger, Mario Caccamo, Ian Sealy, James Torrance, Kerstin Howe
2016 Bioinformatics  
Motivation: For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and
more » ... istency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. Although gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including from Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly. Availability and Implementation: Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.
doi:10.1093/bioinformatics/btw159 pmid:27153597 pmcid:PMC4978925 fatcat:lrolp4phx5celhyvibnwi26dsy

自己組織化単分子膜のマイクロマシニングへの応用
MEMS to SAMs and SAMs for MAMS

Beomjoon KIM, Gyuman KIM, Juergen BRUGGER
2002 Seisan Kenkyu  
The corresponding 'negative' pattern is attached to the SU-8 structure that has been lifted-off (not shown here) .本著者らは近年 Twente 大学の Brugger らの研究者と マイクロマシンニングで製作する新走査型近接場顕微鏡プ ローブの開発の研究に従事した.そのプロセスの時,ナノ  ...  95328 等が研究さ れている.なお IBM から Aperture が先端に作られた SPM 自己組織化単分子膜のマイクロマシニングへの応用 MEMS to SAMs and SAMs for MAMS Poly technique Federale de Lausanne (EPFL), Switzerland プローブをナノステンシルとして利用し,直接パターンし た例もある 10) .そこで,Brugger  ... 
doi:10.11188/seisankenkyu.54.198 fatcat:n5b7vmapcfbmndgnvheoeh4zka

A self-assembled monolayer-assisted surface microfabrication and release technique

B.J. Kim, M. Liebau, J. Huskens, D.N. Reinhoudt, J. Brugger
2001 Microelectronic Engineering  
This paper describes a method of thin film and MEMS processing which uses self-assembled monolayers as ultra-thin organic surface coating to enable a simple removal of microfabricated devices off the surface without wet chemical etching. A 1.5-nm thick self-assembled monolayer of dodecyltrichlorosilane reduces the adhesion between the SiO substrate surface 2 and a 100-nm thick evaporated aluminum film. A 100-mm thick layer of photoplastic SU-8, which is spun and structured by lithography and
more » ... elopment on top of the monolayer / aluminum sandwich layer, can be mechanically lifted off the surface with the aluminum layer. The organic monolayer provides enough stability for the microfabrication process including photoresist spinning and thermal steps. The aluminum film has a surface roughness of less than 1 nm rms as measured by AFM. Photolithographic microstructuring of the aluminum film prior to the photoplastic process allows for transparent embedded bottom-side metal electrodes. As first application example, molded nanoprobes for scanning near-field optical microscopy, has been demonstrated using this technique.
doi:10.1016/s0167-9317(01)00469-5 fatcat:j5tekwvienffffkrbn4drnghfe

Micromechanical testing of SU-8 cantilevers

M. HOPCROFT, T. KRAMER, G. KIM, K. TAKASHIMA, Y. HIGO, D. MOORE, J. BRUGGER
2005 Fatigue & Fracture of Engineering Materials & Structures  
Brugger. E-mail: juergen.brugger@epfl.ch cantilever is scanned over the sample surface.  ... 
doi:10.1111/j.1460-2695.2005.00873.x fatcat:5iovgcw4mbeqxmcnjtat5mwy64

Inkjet-Printed Multicolor Arrays of Highly Luminescent Nanocrystal-Based Nanocomposites

Joo Yeon Kim, Chiara Ingrosso, Vahid Fakhfouri, Marinella Striccoli, Angela Agostiano, M. Lucia Curri, Jurgen Brugger
2009 Small  
Kim and C. Ingrosso contributed equally to this work. This work was partially supported by the EC-funded Project NOVOPOLY (Contract no.  ... 
doi:10.1002/smll.200801315 pmid:19199336 fatcat:5z6ag3myj5ahhabd4flcoj4bmu

Photoplastic near-field optical probe with sub-100 nm aperture made by replication from a nanomould

G. M. Kim, B. J. Kim, E. S. Ten Have, F. Segerink, N. F. Van Hulst, J. Brugger
2003 Journal of Microscopy  
In earlier studies, direct FIB milling of sub-micrmetre scale aperture on free-standing probes were reported (Veerman et al ., 1998; Kim et al ., 2001) .  ...  ., 2001; Kim et al ., 2001) have been presented. Here, we present an improved manufacturing process for a photopolymer NSOM probe using a nanomould technique.  ... 
doi:10.1046/j.1365-2818.2003.01134.x fatcat:4epn4dkc5vf5hgdxfzttomtcl4

A higher burden of multiple sclerosis genetic risk confers an earlier onset [article]

Elina Misicka, Mary Davis, Woori Kim, Steven W. Brugger, Jeremy Beales, Stephanie Loomis, Paola G. Bronson, Farren B. S. Briggs
2020 bioRxiv   pre-print
Multiple sclerosis is a neurodegenerative, autoimmune disease characterized by inrreversible neurological disability. The age at onset of multiple sclerosis is an objective and influential predictor of the evolution of multiple sclerosis independent of disease duration. Little is known about the mechanisms contributing to variation in onset age of multiple sclerosis, thoughHLA-DRB1*15:01, the predominant risk variant, confers an earlier onset. Here we present an age at onset genome-wide
more » ... ion analysis for 9.2 million variants, including gene-based and pathway enrichment analyses, for 3,495 cases who were non-Latinx white with onset ≥18 years. We investigated whether a higher burden of multiple sclerosis risk variants conferred an earlier age at onset for combinations ofHLA-DRB1*15:01alleles and quintiles of a genetic risk score for 200 risk variants that reside outside the major histocompatibility complex. The study population had a mean age at onset of 32 years, 29% was male, and 46% wereHLA-DRB1*15:01carriers.HLA-DRB1*15:01carriers were on average one year younger at onset than non-carriers (p<0.001); a similar effect was observed for a 10-risk-allele increase in the genetic risk score (p<1×10-8). Those in the highest genetic risk score quintile (n=717) were on average 2.5 years younger at onset than those in the lowest quintile (n=698; p=1.2×10-7). For those with the greatest genetic risk burden (highest genetic risk score quintile with twoHLA-DRB1*15:01alleles) were on average five years younger at onset (p=0.002) than those with the lowest genetic risk burden (lowest genetic risk score quintile with noHLA-DRB1*15:01alleles). There was an apparent inverse relationship between the genetic multiple sclerosis risk burden and age at onset of multiple sclerosis (p<5x10-8). We did not observe any individual variants reaching genome-wide significance in the genome-wide association analysis of age at onset. The most significantly associated independent genic loci (p<5x10-6) were located withinHLA-DQB1, COL21A1, LINC01484, UBR3,andCSMD1. At the gene-level, the most significant associations (p<5x10-5) were forSSB, TRAFD1, HECTD2, MMP8, NAA25andUBR3. There was an enrichment of genes involved in adaptive and innate immunity, specifically genes in the complement pathway, and genes involved in synapses and collagen biosynthesis. In summary, we demonstrated a significant gradient between elevated genetic risk burden and an earlier onset of multiple sclerosis.
doi:10.1101/2020.12.18.423477 fatcat:hlm7hexeuvfvzjt4ua32y272vm

Size-dependent free solution DNA electrophoresis in structured microfluidic systems

Thanh Tu Duong, Gyuman Kim, Robert Ros, Martin Streek, Friederike Schmid, Jürgen Brugger, Dario Anselmetti, Alexandra Ros
2003 Microelectronic Engineering  
A new concept based on microstructuring techniques is presented to achieve size-dependent electrophoretic migration of DNA in free solution. Topographically structured microfluidic channels with periodical cavities in the range of the radius of gyration of the tested DNA molecules (, 3 mm) are produced by moulding of polydimethylsiloxane on a master wafer fabricated by contact lithography of SU-8 photoresist. The electrophoretic migration of single DNA molecules stained with the intercalator
more » ... O was investigated by real-time fluorescence video microscopy. It could be demonstrated for large DNA molecules that l-DNA (48 kbp) always migrated significantly faster than T2-DNA (164 kbp) in the two tested microchannel layouts. Integration into a microdevice for DNA separation in free solution is now in progress. 
doi:10.1016/s0167-9317(03)00153-9 fatcat:5rzhfj6p6jh7vl66v5cv6goama

Fabrication of HepG2 Cell Laden Collagen Microspheres using Inkjet Printing
잉크젯 프린팅을 이용한 HepG2 세포 담지 콜라겐 마이크로스피어 제작

Jin Ho Choi, Young Ho Kim, Loic Jacot-Descombes, Jurgen Brugger, Gyu Man Kim
2014 Journal of the Korean Society for Precision Engineering  
In this study, drop-on-demand system using piezo-elecrtric inkjet printers was employed for preparation of collagen microspheres, and its application was made to the HepG2 cell-laden microsphere preparation. The collagen microspheres were injected into beaker filled with mineral oil and incubated in a water bath at 37℃ for 45 minutes to induce gelation of the collagen microsphere. The size of collagen microsphere was 100µm in diameter and 80µm in height showing spherical shape. HepG2 cells were
more » ... encapsulated in the collagen microsphere. The cellladen microspheres were inspected by the microscopic images. The encapsulation of cells may be beneficial for applications ranging from tissue engineering to cell-based diagnostic assays.
doi:10.7736/kspe.2014.31.8.743 fatcat:gdtlb4iebnd4bdm5mfaw67gdxi

Activation benchmark study at a 2.5 GeV electron accelerator

Markus Brugger, Abderrahim Errahhaoui, Minho Kim, Hee-Seock Lee, Stefan Roesler, Heinz Vincke
2014 Progress in Nuclear Science and Technology  
Samples of copper, aluminium and stainless steel with well-characterized elemental compositions were irradiated in the stray radiation field created by a 2.5 GeV electron beam hitting a copper dump. After the irradiation the induced activity in the samples was analysed with gamma-ray spectrometry. The beam intensity monitoring with a current transformer was verified in an additional study by irradiating gold-foils stacked in between copper blocks and by analysing the production of 196 Au for
more » ... ch detailed experimental cross section data exist. All results were finally compared to the predictions obtained with the FLUKA Monte-Carlo code. Excellent agreement between measurement and simulation within a few percent was obtained for the gold-foils irradiation confirming the accuracy of the beam monitoring. The benchmark of the FLUKA results with the data of the material samples showed good agreement, for many nuclides within 30%.
doi:10.15669/pnst.4.363 fatcat:lzsoikrykfccpcy3j5xghpyxdu
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