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Certified Memory Usage Analysis [chapter]

David Cachera, Thomas Jensen, David Pichardie, Gerardo Schneider
<span title="">2005</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
We present a certified algorithm for resource usage analysis, applicable to languages in the style of Java byte code. The algorithm verifies that a program executes in bounded memory.  ...  of the analysis with respect to an operational semantics of the program.  ...  Introduction This paper presents a certified algorithm for resource usage analysis, aimed at verifying that a program executes in bounded memory.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11526841_8">doi:10.1007/11526841_8</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pfpfqiqsknfxpcyihgzqmyjhwy">fatcat:pfpfqiqsknfxpcyihgzqmyjhwy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090630195329/http://www-sop.inria.fr/everest/personnel/David.Pichardie/Publis/memoryusage.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bb/07/bb0761696d169d794473c6d4ff806a2d5f372272.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11526841_8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

The MOBIUS Proof Carrying Code Infrastructure [chapter]

Gilles Barthe, Pierre Crégut, Benjamin Grégoire, Thomas Jensen, David Pichardie
<span title="">2008</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
depends on confidential data resource usage: memory usage, billable actions,...  ...  information flow: public outputs should not depends on confidential data resource usage: memory usage, billable actions,...  ...  analyses are highly desirable for mobile code but require complex and powerful analyses Proof Carrying Code allows to clearly separate proof search and proof checking to make on-device checking pratical Certified  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-92188-2_1">doi:10.1007/978-3-540-92188-2_1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a4sdtprwgvc7fnmp7qflsq35ca">fatcat:a4sdtprwgvc7fnmp7qflsq35ca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830042048/http://www.rennes.supelec.fr/diwall/talks/pichardie.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/84/3e/843ec164dbf73a77e3506dd6a4b86b15b41e85ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-92188-2_1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

A single-cell genomic strategy for alternative transcript start sites identification [article]

Yanling Peng, Qitong Huang, Rui Kamada, Keiko Ozato, Yubo Zhang, Jun Zhu
<span title="2021-12-10">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals.  ...  utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis  ...  Memory ISGs related-TSSs biological process. (a) The identification of memory and non-memory ISGs and GO analysis for the identified memory and nonmemory ISGs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.12.09.472038">doi:10.1101/2021.12.09.472038</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/knsy5qgjevcftbtvkpkvuozzwu">fatcat:knsy5qgjevcftbtvkpkvuozzwu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220204224800/https://www.biorxiv.org/content/biorxiv/early/2021/12/10/2021.12.09.472038.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/98/8e989389bfca835ff69d2a0d7f15e3b07404b969.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.12.09.472038"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

MethylStar: A fast and robust pipeline for high-throughput analysis of bulk or single-cell WGBS data [article]

Yadollah Shahryary Dizaji, Rashmi R. Hazarika, Frank Johannes
<span title="2019-12-21">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We show that MethylStar outperforms existing tools/pipelines for bulk and single-cell WGBS analysis.  ...  The computational analysis of this data poses major challenges and creates unnecessary bottlenecks for biological interpretation.  ...  The size of the dot indicates the peak memory usage by each component.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2019.12.20.884536">doi:10.1101/2019.12.20.884536</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g4qkppobabgitdwrbisdljhxvm">fatcat:g4qkppobabgitdwrbisdljhxvm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201103033743/https://www.biorxiv.org/content/biorxiv/early/2020/03/12/2019.12.20.884536.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/55/23/5523bc47097f959e3118e26f6167dfd7fd0afc50.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2019.12.20.884536"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow [article]

Jochen Bathke, Gesine Lühken
<span title="2021-05-13">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Moreover resource usage is lowered to a minimum. Thereby variant calling projects should become more standardized, reducing the barrier further for smaller institutions or groups.  ...  One key player in the field is the Genome Analysis Toolkit (GATK). The GATK Best Practices are commonly referred recipe for variant calling on human sequencing data.  ...  as memory usage (see rows).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.12.443585">doi:10.1101/2021.05.12.443585</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ojs5pc5j6za5pl6txp7axkp2ea">fatcat:ojs5pc5j6za5pl6txp7axkp2ea</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718055327/https://www.biorxiv.org/content/biorxiv/early/2021/05/13/2021.05.12.443585.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/29/8e291c0e298e193eab9facfd1b044c3c4d8186fa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.12.443585"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Multimodal repertoire analysis unveils B cell biology in health and immune-mediated diseases [article]

Mineto Ota, Masahiro Nakano, Yasuo Nagafuchi, Satomi Kobayashi, Hiroaki Hatano, Ryochi Yoshida, Yuko Akutsu, Tkahiro Itamiya, Atsushi Matsuo, Yumi Tsuchida, Hirofumi Shoda, Kazuhiko Yamamoto (+3 others)
<span title="2022-01-05">2022</span> <i title="Cold Spring Harbor Laboratory"> medRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
VDJ gene usage was skewed especially in plasmablasts and unswitched-memory B cells of systemic lupus erythematosus patients with frequent usage of VDJ genes used mainly in naive B cells and not unswitched-memory  ...  Our multimodal repertoire analysis brings new insights to B cell biology.  ...  Principal component analysis based on VDJ gene usage All B cell samples used in this study except those samples after belimumab treatment were utilized for PCA analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.01.04.22268769">doi:10.1101/2022.01.04.22268769</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xkknkrt3p5cebdpbcxr3cqz25a">fatcat:xkknkrt3p5cebdpbcxr3cqz25a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220131083022/https://www.medrxiv.org/content/medrxiv/early/2022/01/05/2022.01.04.22268769.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b7/83/b78305590f0f50c67e49a316925dd9083ba5f87c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.01.04.22268769"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> medrxiv.org </button> </a>

CD4+ T cell subsets present stable relationships in their T cell receptor repertoires [article]

Shiyu Wang, Longlong Wang, Ya Liu
<span title="2020-11-02">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Here, we examined the features of TCR beta (TCRB) repertoire of the top clones within naive, memory and regular T cell (Treg) subsets: repertoire structure, gene usage, length distribution and sequence  ...  Second, we found that the correlations between the features of memory subsets and naive were positively related to differentiation levels of memory subsets.  ...  In conclusion, NT, memory subsets and Treg have distinct gene usages, and 188 the gene usage of NT is more similar to less-differentiated memory subsets (CMT and Tscm) 189 rather than EMT. 190 The V-and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.01.364224">doi:10.1101/2020.11.01.364224</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3thdcgjdszew5p2ujdns33cety">fatcat:3thdcgjdszew5p2ujdns33cety</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201213162232/https://www.biorxiv.org/content/biorxiv/early/2020/11/02/2020.11.01.364224.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/08/b0083ae5876bf7e6ac3f285fa2e128f0507ad997.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.01.364224"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

FastQTLmapping: an ultra-fast package for mQTL-like analysis [article]

Xingjian Gao, Jiarui Li, Xinxuan Liu, Qianqian Peng, Han Jing, Sijia Wang, Fan Liu
<span title="2021-11-19">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In a large dataset consisting of 3,500 individuals, 8 million SNPs, 0.8 million CpGs and 20 covariates, fastQTLmapping completed the mQTL analysis in 7 hours with 230GB peak memory usage.  ...  Compared to the state-of-the-art MatrixEQTL, fastQTLmapping was an order of magnitude faster with much lower peak memory usage.  ...  variables with covariates, which is particularly helpful in mQTL-like analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.11.16.468610">doi:10.1101/2021.11.16.468610</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/puu2phmkgnhcjl5jmpjwzlq26a">fatcat:puu2phmkgnhcjl5jmpjwzlq26a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220206004222/https://www.biorxiv.org/content/biorxiv/early/2021/11/19/2021.11.16.468610.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/14/60/14602d66e04c35bd83422b2e36b5700579a1d2ee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.11.16.468610"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Stereotyped B-cell responses are linked to IgG constant region polymorphisms in multiple sclerosis [article]

Ida Lindeman, Justyna Polak, Shuo-Wang Qiao, Trygve Holmøy, Rune A. Høglund, Frode Vartdal, Pål Berg-Hansen, Ludvig M. Sollid, Andreas Lossius
<span title="2021-04-23">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
There was a strong dominance of the G1m1 allotype constant region polymorphisms in ASCs, but not in memory B cells.  ...  The data also suggest that the dominance of the G1m1 allotype in ASCs may occur as a result of biased differentiation of intrathecal memory B cells.  ...  In the G1m1-expressing memory B-cell population, on the other hand, we did not detect a similar bias of IGHV4 gene segments usage (Figure 5A ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.04.23.441098">doi:10.1101/2021.04.23.441098</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fh75cfk675cy3j3x7x4vglulua">fatcat:fh75cfk675cy3j3x7x4vglulua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220526142740/https://www.biorxiv.org/content/biorxiv/early/2021/04/23/2021.04.23.441098.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b9/b6/b9b6fd2aa97c5c506166cf32bfe04e457ac5a227.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.04.23.441098"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The carbon footprint of bioinformatics [article]

Jason G Grealey, Loïc Lannelongue, Woeiyuh Saw, Jonathan Marten, Guillaume Méric, Sergio Ruiz Carmona, Michael Inouye
<span title="2021-03-09">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Memory over-allocation can be a substantial contributor to an algorithm's carbon footprint.  ...  297 used [70], [71]; thus, having too much memory available for a task results in unnecessary 298 energy usage and GHG emissions.  ...  Although memory is usually a fixed parameter when 299 Memory 296 Table 2 ) 2 (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.03.08.434372">doi:10.1101/2021.03.08.434372</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tdybp6qetrdfzo5mcswehirbd4">fatcat:tdybp6qetrdfzo5mcswehirbd4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210325042527/https://www.biorxiv.org/content/biorxiv/early/2021/03/09/2021.03.08.434372.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2c/d1/2cd1e7c621b8e6e32d342bf297fc382cf06995f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.03.08.434372"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Clonally expanded virus-specific CD8 T cells acquire diverse transcriptional phenotypes during acute, chronic, and latent infections [article]

Raphael Kuhn, Ioana Sandu, Andreas Agrafiotis, Kai-Lin Hong, Daniel Neumeier, Doron Merkler, Annette Oxenius, Sai T. Reddy, Alexander Yermanos
<span title="2021-06-30">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We observed clear infection-specific populations corresponding to memory, effector, exhausted, and inflationary phenotypes.  ...  We further uncovered a mouse-specific and polyclonal T cell response, despite all T cells sharing specificity to a single viral epitope, which was accompanied by stereotypic TCR germline gene usage in  ...  Germline gene usage of GP33-specific CD8+ T cell receptors. A. Circos plots depicting the relationship between TRB and TRA V gene usage. Color corresponds to TRA gene usage.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.06.29.450285">doi:10.1101/2021.06.29.450285</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/55rhkhx37vc3hh7gyt435jyzyi">fatcat:55rhkhx37vc3hh7gyt435jyzyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718032848/https://www.biorxiv.org/content/biorxiv/early/2021/06/30/2021.06.29.450285.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6f/83/6f83261d320355f0314b6c9409e733e3ed116d91.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.06.29.450285"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Single cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine [article]

Suhas Sureshchandra, Sloan A. Lewis, Brianna Doratt, Allen Jankeel, Izabela Ibraim, Ilhem Messaoudi
<span title="2021-07-15">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
TCR gene usage, however, was variable, reflecting the diversity of repertoires and MHC polymorphism in the human population.  ...  Finally, gene usage analysis revealed preferential usage of heavy chain gene family IGHV3 -IGHV3-7, IGHV4-59 with convalescence and IGHV3-33, IGHV3-43, IGHV3-49 with vaccination (Figure 2F ).  ...  For example, flow analysis revealed a reduction in naïve but expansion of memory B cells in both groups.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.07.14.452381">doi:10.1101/2021.07.14.452381</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5uio3yhmynb6dppe7oce7ihffi">fatcat:5uio3yhmynb6dppe7oce7ihffi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220202171221/https://www.biorxiv.org/content/biorxiv/early/2021/07/15/2021.07.14.452381.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/34/d7/34d7fef77af26257e1cd0bfd2fae49e640f868c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.07.14.452381"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation [article]

Yang Liu, Wojciech Rosikiewicz, Ziwei Pan, Nathaniel Jillette, Aziz Taghbalout, Jonathan Foox, Christopher Mason, Martin Carroll, Albert Cheng, Sheng Li
<span title="2021-05-06">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Acknowledgements S.L. is supported by a startup fund from The Jackson Laboratory for Genomic Medicine, Leukemia Research Foundation New Investigator Grant, The Jackson Laboratory was not certified by peer  ...  The same analysis of run time and memory usage for other benchmarking datasets also was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.  ...  Furthermore, Nanopolish required the lowest peak memory usage (~19 GB) while Megalodon required the highest peak memory usage (22 times).  ... 
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Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes [article]

Wenjian Bi, Wei Zhou, Rounak Day, Bhramar Mukherjee, Joshua N Sampson, Seunggeun Lee
<span title="2020-10-10">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
However, due to the lack of analysis tools, methods designed for binary and quantitative traits have often been used inappropriately to analyze categorical phenotypes, which produces inflated type I error  ...  The computation time and memory usage of all 5 methods are presented in Figure S2 and Table S1.  ...  For quantitative trait analysis, Jiang et al. have demonstrated that using sparse GRM can reduce computational time and memory usage, while scenario, a total of 1 0 ଽ 5 ൈ 1 0 ି ଼ (Figures  ... 
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Face processing of social cognition in patients with first episode psychosis: Its deficits and association with the right subcallosal anterior cingulate cortex [article]

Zui Narita, Hironori Kuga, Peeraya Piancharoen, Andreia Faria, Marina Mihaljevic, Luisa Longo, Semra Etyemez, Ho Namkung, Jennifer Coughlin, Gerald Nestadt, Frederik Nucifora, Thomas Sedlak (+7 others)
<span title="2021-03-12">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Nevertheless, its brain substrates and circuitries remain elusive, lacking precise analysis between multimodal brain characteristics and behavioral sub-dimensions within social cognition.  ...  The volume of this region was also correlated with memory response time in FEP patients.  ...  been adjusted in the initial steps of brain imaging data processing; 2) we only have cannabis usage records from self-report, where the dose and frequency of cannabis (which was not certified by peer  ... 
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