Engineering topics

Stoiber, Marcus

Publications and source records attributed to Stoiber, Marcus.

2 records

DOE OSTI2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis -regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

basecRAWller v0.1

This software implements the first base caller for nanopore data that calls bases directly from raw data. The basecRAWller algorithm has two major advantages over current nanopore base calling software: (1) streaming base calling and (2) base calling from information rich raw signal. The ability to perform truly streaming base calling as signal is received from the sequencer can be very powerful as this is one of the major advantages of this technology as compared to other sequencing technologies. As such enabling as much streaming potential as possible will be incredibly important as this technology continues to become more widely applied in biosciences. All other base callers currently employ the Viterbi algorithm which requires the whole sequence to employ the complete base calling procedure and thus precludes a natural streaming base calling procedure. The other major advantage of the basecRAWller algorithm is the prediction of bases from raw signal which contains much richer information than the segmented chunks that current algorithms employ. This leads to the potential for much more accurate base calls which would make this technology much more valuable to all of the growing user base for this technology.

Brown, JamesB↗