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PHATE specifications

Information


Unique identifier OMICS_25599
Name PHATE
Alternative names Potential of Heat-diffusion for Affinity-based Transition Embedding, phater
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB, Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Krishnan Srinivasan <>
  • person_outline Kevin Moon <>
  • person_outline David van Dijk <>
  • person_outline Zheng Wang <>
  • person_outline Guy Wolf <>

Additional information


https://github.com/SmitaKrishnaswamy/PHATE https://github.com/KrishnaswamyLab/phater

Publication for Potential of Heat-diffusion for Affinity-based Transition Embedding

PHATE in publications

 (84)
PMCID: 5947705
PMID: 29497023
DOI: 10.1107/S2053230X18002819

[…] structure was elucidated to 3.5 å resolution., pyruvate decarboxylase (pdc; ec 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. pdcs are thiamine pyrophos­phate- and mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. as this enzyme class is rare in bacteria, current knowledge […]

PMCID: 5872033
PMID: 29315240
DOI: 10.3390/biology7010007

[…] of pyrophosphate. the proteinaceous enzymes use a two-mg2+-ion mechanism: one mg2+ lowers the pka of the 3′-hydroxyl for the in-line nucleophilic attack, while the other mg2+ assists in the pyrophos­phate release by stabilizing the negative charge []. kissing-loop interaction typically involves complete base pairing and continuous stacking of helices [,]. the base pairing through the loop […]

PMCID: 5786004
PMID: 29372894
DOI: 10.1107/S2059798317017132

[…] been solved., here, we describe the crystal structure of the activated form of rubisco from a. thaliana at 1.5 å resolution with a bound transition-state analogue, 2-carboxy-d-arabinitol 1,5-bisphos­phate (2-cabp). these data provide a structural context for interactions between the lsu and ssus of a. thaliana rubisco., arabidopsis (a. thaliana col-0) seeds were sterilized in 20%(v/v) […]

PMCID: 5801538
PMID: 29435434
DOI: 10.15171/bi.2017.31

[…] sah, s-adenosylhomocysteine; dump, deoxyuridine monophosphate; dtmp, deoxythymidine monophosphate. , overview of folate transporter (rfc (reduced folate carrier/slc19a1), organic phos- phate [op -])., this study was executed to determine whether the rfc1 (rs1051266, a80g) polymorphism has a relationship with increased risk of nscl/p in iranian infants consisting 122 cases and 164 […]

PMCID: 5752180
PMID: 29207009
DOI: 10.3892/ijmm.2017.3260

[…] protein extracts were isolated from skov3/ddp cells using cell lysis buffer [50 mm tris-hcl, ph 7.5; 150 mm nacl; 1 mm sodium-edta, 1 mm edta; 1% (v/v) triton x-100; 2.5 mm sodium pyrophos-phate; 1 mm β-glycerophosphate; 1 mm na3vo4; 1 mm naf; 1 μg/ml leupeptin and 1 mm phenylmethylsulfonyl fluoride] for western blotting. protein concentration was quantified using the quick start […]


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PHATE institution(s)
Department of Genetics, Yale University, New Haven, CT, USA; Applied Mathematics Program, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Department of Genetics, Yale University, New Haven, CT, USA; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Mathematics, Michigan State University, East Lansing, MI, USA

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