PYOMPA Technical Note

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

doi:10.1002/essoar.10507053.4

Cited by 7 publications

(14 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The predicted and observed enhancer-activity profiles were highly similar for both developmental (Pearson correlation coefficient (PCC)=0. In order to understand the features and rules learned by DeepSTARR, we quantified how each individual nucleotide in every sequence contributes to the predicted developmental and housekeeping enhancer activities 47,55,63,64 56 . This uncovered distinct TF motifs that are known to occur in developmental and housekeeping enhancers 26,40 , thus validating the approach and reinforcing the mutual incompatibility of the two transcriptional programs (Fig 2A ,B, S2).…”

Section: Deepstarr Quantitatively Predicts Enhancer Activity From Dna...mentioning

confidence: 99%

“…In contrast, deep learning, in particular convolutional neural networks, do not require prior knowledge and can learn accurate models directly from raw data [44][45][46][47][48][49][50][51][52][53] . Once trained on raw data, these models allow the extraction and interpretation of the learned rules by novel types of tools 44,45,47,48,[54][55][56][57][58][59][60] . For example, when applied to ChIP-nexus data that measures TF-binding genome-wide at high resolution, a convolutional neural network was able to learn motifs and syntax rules for cooperative TF binding 47 .…”

mentioning

confidence: 99%

See 1 more Smart Citation

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

et al. 2022

View full text Add to dashboard Cite

Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally non-equivalent instances of the same TF motif that are determined by motif-flanking sequence and inter-motif distances. We validated these rules experimentally and demonstrated their conservation in human by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo..

show abstract

Section: Deepstarr Quantitatively Predicts Enhancer Activity From Dna...mentioning

confidence: 99%

mentioning

confidence: 99%

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

et al. 2022

View full text Add to dashboard Cite

show abstract

“…analysis was employed to determine water mass fractions in GP15 samples (Shrikumar et al, 2022). The work presented here provides water mass and circulation context for GP15, a foundation needed to align to GEOTRACES's objectives at the basin-scale and beyond.…”

Section: Introductionmentioning

confidence: 99%

Water mass analysis of the 2018 US GEOTRACES Pacific Meridional Transect (GP15)

Lawrence

Shrikumar

Roy

et al. 2022

Preprint

View full text Add to dashboard Cite

A water mass analysis is a tool for interpreting the effect of ocean mixing on the distributions of trace elements and isotopes (TEI's) along an oceanographic transect. The GEOTRACES GP15 transect along 152°W covers a wide range in latitude from Alaska to Tahiti. Our objective is to present the nutrients and hydrography of GP15 and quantify the distributions of water masses to support our understanding of TEI distributions along GP15. We used a modified Optimum Multiparameter (OMP) analysis to determine the distributions of water masses with high importance to nutrient and hydrographic features in the region. In the thermocline, our results indicated the dominance of Pacific Subarctic Upper Water (PSUW) in the subpolar gyre, Eastern North Pacific Central Water (ENPCW) in the northern subpolar gyre, and Equatorial Subsurface Water (ESSW) in the equatorial region. South Pacific Subtropical Water (SPSTW) dominated the top of the thermocline in the southern subtropical gyre, while South Pacific Central Water (SPCW) dominated the lower thermocline. Antarctic Intermediate Water (AAIW), Equatorial Intermediate Water (EqIW), and North Pacific Intermediate Water (NPIW) in the southern hemisphere, equatorial region, and northern hemisphere, respectively, occupied waters just below the thermocline. Dominant water masses in the deep waters of the southern hemisphere include Upper Circumpolar Deep Water (UCDW) and Lower Circumpolar Deep Water (LCDW) with minimal contributions from Antarctic Bottom Water (AABW). Pacific Deep Water (PDW) dominated the deep water in the northern hemisphere. Our results align well with literature descriptions of these water masses and related circulation patterns.

show abstract

“…Unfortunately, the omp2 package used in these analyses only included one remineralization term and is thus not appropriate for analysis within an ODZ. Fortunately, the pyompa water mass analysis software package can calculate multiple different remineralization terms, each with a flexible remineralization stoichiometry (Shrikumar et al 2022). This flexible stoichiometry feature can calculate the anaerobic remineralization stoichiometry for every measured sample independently, whereas our regression analysis needed to bin this data.…”

Section: Teos-10mentioning

confidence: 99%

Prolific nitrite reoxidation across the Eastern Tropical North Pacific Ocean

Evans

Tichota

Moffett

et al. 2023

Limnology & Oceanography

View full text Add to dashboard Cite

Nitrite is a key intermediate during fixed nitrogen loss in the ocean, and it accumulates within marine Oxygen Deficient Zones (ODZ). ODZs are vast subsurface regions where nitrate is the dominant electron acceptor, and these regions host approximately 50% of the fixed nitrogen loss in the world's oceans. Nitrite accumulates in these waters, and recent research has discovered substantial reoxidation of nitrite back to nitrate, a significant process in the global nitrogen cycle. Partitioning between reduction and oxidation determines if marine fixed nitrogen is lost or recycled. Investigations into nitrite oxidation typically rely on results from incubations, which limits the spatiotemporal sampling coverage. Using basin‐scale data, we analyzed the ratios of nutrient regeneration within the three water masses that feed the Eastern Tropical North Pacific (ETNP) ODZ. Deviations in the ratios of nutrient regeneration from Redfield stoichiometry indicated prolific nitrite reoxidation across this region. We estimate that 79 ± 7% of the nitrite produced in the ODZ between the 26.2 and 26.4 kg m−3 isopycnals is reoxidized, whereas 54 ± 2% of the nitrite produced between the 26.7 and 26.9 kg m−3 isopycnals is reoxidized. Our analysis also illustrates discrete “metabolic switching points” from primarily aerobic to primary anaerobic processes, which occur in each water mass. We applied water mass analysis to repeat cruises on the WOCE P18 line from Baja California to 10°N, which revealed high spatiotemporal variability in nitrite reoxidation. These results confirm previous measurements of significant fixed nitrogen recycling across the ETNP; however, our analysis enables high‐resolution estimates of this process.

show abstract

PYOMPA Technical Note

Abstract: This a preprint and has not been peer reviewed. Data may be preliminary.

Cited by 7 publications

References 12 publications

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

Water mass analysis of the 2018 US GEOTRACES Pacific Meridional Transect (GP15)

Prolific nitrite reoxidation across the Eastern Tropical North Pacific Ocean

Contact Info

Product

Resources

About