Search

Your search keyword '"Leila Safari"' showing total 3 results
Start Over Author "Leila Safari" Publisher elsevier
3 results on '"Leila Safari"'

1. DTMP-prime: A deep transformer-based model for predicting prime editing efficiency and PegRNA activity

Author

Roghayyeh Alipanahi, Leila Safari, and Alireza Khanteymoori

Subjects
MT: Bioinformatics, CRISPR, prime editing, PegRNA, off-target, deep learning, Therapeutics. Pharmacology, RM1-950
Abstract

Prime editors are CRISPR-based genome engineering tools with significant potential for rectifying patient mutations. However, their usage requires experimental optimization of the prime editing guide RNA (PegRNA) to achieve high editing efficiency. This paper introduces the deep transformer-based model for predicting prime editing efficiency (DTMP-Prime), a tool specifically designed to predict PegRNA activity and prime editing (PE) efficiency. DTMP-Prime facilitates the design of appropriate PegRNA and ngRNA. A transformer-based model was constructed to scrutinize a wide-ranging set of PE data, enabling the extraction of effective features of PegRNAs and target DNA sequences. The integration of these features with the proposed encoding strategy and DNABERT-based embedding has notably improved the predictive capabilities of DTMP-Prime for off-target sites. Moreover, DTMP-Prime is a promising tool for precisely predicting off-target sites in CRISPR experiments. The integration of a multi-head attention framework has additionally improved the precision and generalizability of DTMP-Prime across various PE models and cell lines. Evaluation results based on the Pearson and Spearman correlation coefficient demonstrate that DTMP-Prime outperforms other state-of-the-art models in predicting the efficiency and outcomes of PE experiments.

Published
2024
Full Text
View/download PDF

2. A novel COA-based electronically adjustable current-mode instrumentation amplifier topology

Author

Leila Safari, Shahram Minaei, Doğuş Üniversitesi, Mühendislik Fakültesi, Elektronik ve Haberleşme Mühendisliği Bölümü, TR1566, and Minaei, Shahram

Subjects
Current Operational Amplifier, Engineering, CMRR, COA, Topology (electrical circuits), 02 engineering and technology, Topology, law.invention, law, 0202 electrical engineering, electronic engineering, information engineering, Electronic engineering, Hardware_INTEGRATEDCIRCUITS, Current-Mode, Electrical and Electronic Engineering, Total harmonic distortion, business.industry, Amplifier, 020208 electrical & electronic engineering, Transistor, Electrical engineering, 020206 networking & telecommunications, CMOS, Operational amplifier, Instrumentation amplifier, Instrumentation Amplifier, CMIA, Resistor, business
Abstract

Minaei, Shahram (Dogus Author) In this paper a new topology for implementing Current-Mode Instrumentation Amplifiers (CMIA) is presented. The proposed CMIA is based on two single input-multiple output (SI-MO) current operational amplifiers (COAs) as basic building blocks and 2 resistors. To electronically control the differential mode gain, a transistor operating in triode region is used which acts as a variable resistor. The significant feature of the proposed CMIA is that the active building blocks operate in closed loop configuration. Therefore it exhibits numerous remarkable features such as improved frequency performance, low THD and very low input impedance. In addition, it has fully differential output which reduces the output noise and increases its application. The proposed CMIA is analyzed and simulated with SPICE program using parameters of 0.18 mu m CMOS technology and supply voltage of +/- 0.9 V.

Published
2017

3. A low power current controllable single - input three - output current - mode filter using MOS transistors only

Author

Leila Safari, Shahram Minaei, Bilgin Metin, Doğuş Üniversitesi, Mühendislik Fakültesi, Elektronik ve Haberleşme Mühendisliği Bölümü, TR1566, TR146118, and Minaei, Shahram

Subjects
Engineering, Passive integrator circuit, business.industry, Low-pass filter, Transistor, Electrical engineering, Hardware_PERFORMANCEANDRELIABILITY, Current mode filter, law.invention, High impedance, Capacitor, MOS only filter, Multi-function filter, Filter (video), law, Fully integrated filter, Electronic engineering, Hardware_INTEGRATEDCIRCUITS, Electrical and Electronic Engineering, Resistor, business, Active filter
Abstract

A novel circuit configuration for the realization of low power single-input three-output (SITO) current mode (CM) filters employing only MOS transistors are presented. The proposed circuit can realize low-pass (LP), band-pass (BP) and high-pass (HP) filter functions simultaneously at three high impedance outputs without changing configuration. Despite the other previously reported works, the proposed circuit is free from resistors and passive capacitors. Instead of passive capacitors; the gate-source capacitor of MOS transistor is used making the proposed circuit ideally suitable for integration. Compared to other works, the proposed filter has also the lowest number of transistors and lowest power consumption. The proposed circuit exhibits low-input and high-output impedances, which is highly desirable for cascading in CM signal processing. Moreover, it is center frequency can be electronically adjusted using a control current without a significant effect on quality factor (Q) granting it the highly desirable capability of electronic tunability. Transfer functions of the LP, BP and HP outputs are derived and the performance of the proposed circuit is proved through pre layout and post layout simulations at supply voltage of 1.8 V and using 0.18 μm CMOS process parameters. The power consumption and the required chip area are only 0.5 mW and 77.4 μm × 70.2 μm, respectively.

Published
2014

Catalog

Books, media, physical & digital resources
See catalog results