213: Chapter 213 Two Days! I only need two days!

Zhao Yang didn't give an immediate answer. He looked at the gene expression regulatory network diagram on the screen with a serious expression, his mind racing at high speed.

Under the deduction of his 179 IQ, combined with his Level 5 Mathematics and Informatics levels, several mathematical models for processing this kind of high-dimensional biological data quickly formed in his mind.

"Using a conventional negative binomial distribution model to process data with such a large number of repetitive sequences will inevitably lead to inaccurate variance estimation."

After a moment of silence, Zhao Yang looked at Professor Professor Gu Ming and the others around him, slowly voicing his analysis.

"The genome of this crop itself is too massive. The underlying statistical algorithms of most ready-made commercial bioinformatics analysis software on the market are based on ordinary binomial or Poisson distributions. When facing massive repetitive sequences and uneven sequencing depth, it's extremely easy to amplify background noise. This is the root cause of why you ended up with tens of thousands of false-positive differential genes."

Everyone in the conference room listened quietly. Two second-year graduate seniors nodded repeatedly; they had been tormented to the point of misery by these false-positive data over the past few days.

"Let me do it, Professor. Copy all the raw sequencing data files to me."

Zhao Yang looked at Professor Professor Gu Ming and directly provided the final solution.

"I'll go back and rewrite an alignment and quantification algorithm. I won't use existing software; I'll directly use a combination of Hidden Markov Models (HMM) and Multidimensional Principal Component Analysis (PCA) at the base level to re-cluster your expression matrix."

Zhao Yang's tone carried absolute confidence.

"Hidden Markov Models can infer the hidden true gene expression states through the observed sequencing states, filtering out physical noise generated by the sequencer to the greatest extent. Then, PCA will be used for dimensionality reduction to strip away secondary factors."

"I will compress the range of false positives to within a hundred genes as much as possible. Then, combined with Weighted Gene Co-expression Network Analysis, I'll find the Hub genes with the highest connectivity. In two days at most, I'll give you a list of candidate genes in the single digits. You can then just go straight to antibody production or qPCR verification."

The conference room fell silent.

The people around looked at Zhao Yang with expressions of disbelief.

Two days?

The two seniors looked at each other, both seeing shock in the other's eyes.

The raw sequencing data here was measured in Terabytes! Just to decompress and read these several TBs of FASTQ files on a computer would take an ordinary server over a dozen hours.

Writing his own underlying algorithm? And running all the data to output a final single-digit target list within two days?

Two days was simply too short. In a traditional bioinformatics analysis pipeline, this was an absolutely impossible task.

"Is two days enough?"

Professor Professor Gu Ming also looked at Zhao Yang with some hesitation. He knew Zhao Yang was extremely strong in mathematics and computer science, but this was, after all, a massive amount of data.

"Our experiment isn't that urgent; there's still some time before the project deadline. You can take a bit more time to handle it steadily..."

"It's enough."

Zhao Yang smiled and waved his hand, interrupting Professor Professor Gu Ming.

"It's just a matter of cleaning data and modifying algorithms. I've already constructed the underlying mathematical logic in my head just now. What's left is just the physical time for typing code and letting the CPU run calculations. Two days is plenty."

"Truly a mathematical genius! A computer genius! Truly impressive!"

Professor Professor Gu Ming said excitedly, rubbing his hands together vigorously.

"If our lab can pin down this core drought-resistance gene, we can definitely publish another high-level paper in 'Nature Communications' or a sub-journal. This would be a major achievement for our School of Life Sciences as well!"

The two seniors also looked at Zhao Yang with faces full of admiration. TB-level data that made others' scalps tingle with numbness seemed as easy as a common middle school math word problem to God Zhao. This was an absolute crushing of IQ.

"Alright, then this afternoon you guys organize the data and copy it onto a mobile hard drive. Later, if there's a need for Wet Lab operations like Gel Electrophoresis, PCR, or Plasmid Extraction, I'll participate as well."

Zhao Yang said. He hadn't forgotten his fundamental purpose for coming to the lab. Doing real biochemical experiments could earn him Biology experience, and Zhao Yang would definitely not pass up these opportunities to grind experience.

"No problem. For the Wet Lab part, let Gu Qing lead you through the process. She has the steadiest technique among this batch of people in our lab. You'll learn the fastest by following her."

Professor Professor Gu Ming arranged immediately.

The group meeting was very short and efficient. Once the direction and division of labor were determined, everyone adjourned.

Zhao Yang followed Gu Qing out of the conference room and back to the workstation outside the laboratory.

"Those few TBs of sequencing data are on the hard drive of that data server. The files are too large; it'll take about two hours to copy them out."

Gu Qing pointed to a host machine in the corner.

"While the data is copying, I'll first walk you through the current experimental process and the most recent batch of samples."

"Okay."

Zhao Yang nodded, casually took a brand-new white lab coat from the nearby hanger, put it on, and buttoned it up.

Gu Qing looked at Zhao Yang in the white coat. Usually consistently cold and aloof, her lips couldn't help but curve up in an extremely tiny arc at this moment.

Since Zhao Yang arrived, she seemed much happier overall. With Zhao Yang in the lab, she felt that the originally dull experiments now seemed exceptionally interesting.

"These are plant leaves we just took from the greenhouse yesterday, which have undergone forty-eight hours of severe drought stress treatment. They were plunged into liquid nitrogen immediately after sampling and have been kept there to prevent RNA degradation."

Gu Qing put on heavy anti-freeze gloves and walked to the liquid nitrogen tank in the corner.

Opening the lid, a thick cloud of white smoke instantly billowed out, and the surrounding temperature plummeted.

Using a pair of long-handled tweezers, Gu Qing skillfully fished a labeled cryovial from the cryo-rack at the bottom and placed it on the ice box on the lab bench.

"We need to grind these leaves into an extremely fine powder under the low temperature of liquid nitrogen, and then add Trizol Reagent to extract total RNA. This process is very prone to exogenous RNase contamination and self-degradation, so we must act fast, and the mortar and pestle must maintain an extremely low temperature throughout."

While skillfully pouring liquid nitrogen into a white ceramic mortar for pre-cooling, Gu Qing extremely patiently explained the precautions for each step, the reagent ratios, and the underlying biochemical principles to Zhao Yang.

Zhao Yang stood beside her, watching seriously.

Although he had spent some time in the lab before and followed along with some basic PCR amplification, he hadn't personally done the subject of RNA extraction yet. The experimental process and reagent characteristics of every subject would have subtle differences.

The liquid nitrogen boiled violently in the mortar. Gu Qing quickly poured the leaves from the cryovial into the mortar and picked up the pestle to begin grinding vigorously.

"Here, you try the feel of it. Be careful not to let the powder splash out."

After grinding a few times, Gu Qing handed the pestle to Zhao Yang.