PYOMPA version 0.3: Technical Note

Shrikumar, Avanti; Lawrence, Rian; Casciotti, Karen L.

doi:10.1002/essoar.10507053.2

Cited by 8 publications

(10 citation statements)

References 7 publications

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“…(2019) and the python package pyompa, described in Shrikumar et al. (2022). The water masses considered are upper and lower members for Pacific Subpolar Upper Water (PSUW) and Eastern North Pacific Central Water (ENPCW), and water masses of equatorial region, namely 13˚C Water (13CW) and Northern Equatorial Pacific Intermediate Water (NEPIW).…”

Section: Methodsmentioning

confidence: 99%

Characterizing Subsurface Oxygen Variability in the California Current System (CCS) and Its Links to Water Mass Distribution

Schultz,

Dunne,

Liu

et al. 2024

JGR Oceans

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The california current system (CCS) supports a wide array of ecosystem services with hypoxia historically occurring in near‐bottom waters. Limited open ocean data coverage hinders the mechanistic understanding of CCS oxygen variability. By comparing three different models with varying horizontal resolutions, we found that dissolved oxygen (DO) anomalies in the CCS are propagated from shallower coastal areas to the deeper open ocean, where they are advected at a density and velocity consistent with basin‐scale circulation. Since DO decreases have been linked to water mass redistribution in the CCS, we conduct a water mass analysis on two of the models and on biogeochemical Argo floats that sampled multiple seasonal cycles. We found that high variability in biogeochemical variables (DO and nutrients) seen in regions of low variability of temperature and salinity could be linked to water mass mixing, as some of the water masses considered had higher gradients in biogeochemical variables compared to physical variables. Additional DO observations are needed, therefore, to further understand circulation changes in the CCS. We suggest that increased DO sampling north of 35˚N and near the shelf break would benefit model initialization and skill assessment, as well as allow for better assessment of the role of equatorial waters in driving DO in the northern CCS.

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Section: Methodsmentioning

confidence: 99%

Characterizing Subsurface Oxygen Variability in the California Current System (CCS) and Its Links to Water Mass Distribution

Schultz,

Dunne,

Liu

et al. 2024

JGR Oceans

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“…We computed importance scores for the counts output using the DeepSHAP 25 implementation of DeepLIFT algorithm 26 . We next ran the TF-MoDISco algorithm 27 to perform de novo motif discovery in each cell type. We mapped the discovered motifs to position weight matrices (PWMs) from HOCOMOCO 28 using TomTom 29 (Extended Data Fig.…”

Section: Methodsmentioning

confidence: 99%

Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging

Yeo

Zhou

Zhong

et al. 2021

Preprint

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Aging is accompanied by a deterioration in the regenerative and repair potential of stem cell regions in the brain. However, the mechanisms underlying this decline are largely unknown. Here we profile the chromatin landscape of five different cell types freshly isolated from the subventricular zone neurogenic niche of young and old mice. We find that chromatin states exhibit distinct changes with aging in different cell types. Notably, the chromatin of quiescent neural stem cells (NSCs) becomes more repressed with age whereas that of proliferative, activated NSCs becomes more open. Surprisingly, these opposing age-related chromatin changes involve cell adhesion and migration pathways. We experimentally validate that quiescent and activated NSCs exhibit opposite migratory deficits during aging. Quiescent NSCs become more migratory during aging, whereas activated NSCs and progeny become less migratory and less able to mobilize out of the niche in vivo during aging. The cellular mechanism by which aging impairs the migration of activated NSCs and progeny involves increased occurrence of force-producing focal adhesions. Inhibiting the cytoskeletal-regulating kinase ROCK in old activated NSCs and progenitors eliminates cell adhesive forces and boosts migration speed, reverting these cells to a more youthful migratory state. Our work has important implications for restoring the migratory potential of NSCs during aging and brain injury.

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“…To identify classes of informative motifs, we used TF-MoDISco [50,51] to cluster common DNA subsequences contributing to either profile or quantity. The majority of DNA sequence motifs important for predicting the quantity of transcription initiation resembled the known consensus motifs of strong transcriptional activators (Fig.…”

Section: Distinct Dna Sequence Architecture Controls Initiation Quant...mentioning

confidence: 99%

“…DeepSHAP profile and quantity scores were computed on the set of high confidence PRO-cap peaks described above. The lite implementation [50] (version 2.2.0) of TF-MoDISco [51] was used to cluster high importance subsequences (seqlets) into summary motifs (seqlets per metacluster = 100, 000), which were then matched against the JASPAR database [89] (2022, non-redundant vertebrate) using the TOMTOM algorithm [90]. We identified 116,351 quantity seqlets (115,602 positive, 749 negative) and profile seqlets 132,121 (115,989 positive, 16,132 negative), which then clustered into 62 quantity motifs (51 positive, 11 negative) and 100 profile motifs (60 positive and 40 negative).…”

Section: Motif Discovery and Frequency Analysismentioning

confidence: 99%

Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation

He,

Danko

2024

Preprint

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Our understanding of how the DNA sequences of cis-regulatory elements encode transcription initiation patterns remains limited. Here we introduce CLIPNET, a deep learning model trained on population-scale PRO-cap data that accurately predicts the position and quantity of transcription initiation with single nucleotide resolution from DNA sequence. Interpretation of CLIPNET revealed a complex regulatory syntax consisting of DNA-protein interactions in five major positions between -200 and +50 bp relative to the transcription start site, as well as more subtle positional preferences among different transcriptional activators. Transcriptional activator and core promoter motifs occupy different positions and play distinct roles in regulating initiation, with the former driving initiation quantity and the latter initiation position. We identified core promoter motifs that explain initiation patterns in the majority of promoters and enhancers, including DPR motifs and AT-rich TBP binding sequences in TATA-less promoters. Our results provide insights into the sequence architecture governing transcription initiation.

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PYOMPA version 0.3: Technical Note

Cited by 8 publications

References 7 publications

Characterizing Subsurface Oxygen Variability in the California Current System (CCS) and Its Links to Water Mass Distribution

Characterizing Subsurface Oxygen Variability in the California Current System (CCS) and Its Links to Water Mass Distribution

Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging

Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation

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