Publications by Sahand Jamal Rahi

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BackgroundHigh-throughput and selective detection of organelles in immunofluorescence images is an important but demanding task in cell biology. The centriole organelle is critical for fundamental cellular processes, and its accurate detection is key for a ...

Rationale: Given the expanding number of COVID-19 cases and the potential for new waves of infection, there is an urgent need for early prediction of the severity of the disease in intensive care unit (ICU) patients to optimize treatment strategies.Objecti ...

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimen ...

Sophisticated genetic engineering tasks such as protein domain grafting and multi-gene fusions are hampered by the lack of suitable vector backbones. In particular, many restriction sites are in the backbone outside the polylinker region (multiple cloning ...

We present a novel optical nanomotion-based rapid antibiotic and antifungal susceptibility test. The technique consisted of studying the effects of antibiotics or antifungals on the nanometric scale displacements of bacteria or yeasts to assess their sensi ...

The identification of cell borders ('segmentation') in microscopy images constitutes a bottleneck for large-scale experiments. For the model organism Saccharomyces cerevisiae, current segmentation methods face challenges when cells bud, crowd, or exhibit i ...

Scarless genome editing in budding yeast with elimination of the selection marker has many advantages. Some markers such as URA3 and TRP1 can be recycled through counterselection. This permits seamless genome modification with pop-in/pop-out, in which a DN ...

Tracking cells is a time-consuming part of biological image analysis, and traditional manual annotation methods are prohibitively laborious for tracking neurons in the deforming and moving Caenorhabditis elegans brain. By leveraging machine learning to dev ...

Cells have built-in mechanisms for checking for errors during replication, but these checkpoints can slow down reproduction. A theory accounting for optimal checkpoint strategies is presented and tested against observations in budding yeast. Checkpoints ar ...

The ability to independently control the expression of different genes is important for quantitative biology. Using budding yeast, we characterize GAL1pr, GALL, MET3pr, CUP1pr, PHO5pr, tetOpr, terminator-tetOpr, Z(3)EV, blue-light inducible optogenetic sys ...

Sahand Jamal Rahi

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CenFind: a deep-learning pipeline for efficient centriole detection in microscopy datasets

Using Machine Learning to Predict Mortality for COVID-19 Patients on Day 0 in the ICU

The multimodality cell segmentation challenge: toward universal solutions

Minimal shuttle vectors for Saccharomyces cerevisiae

A simplified version of rapid susceptibility testing of bacteria and yeasts using optical nanomotion detection

A convolutional neural network segments yeast microscopy images with high accuracy

Automated plasmid design for marker-free genome editing in budding yeast

Inferring how animals deform improves cell tracking

The optimal strategy balancing risk and speed predicts DNA damage checkpoint override times

Using optogenetics to dissect the signals maintaining the DNA damage checkpoint

Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor