Computational Biology & Scientific Communication

Turning complex biological data into results you can stand behind.

Cortessa helps researchers, labs, and early-stage biotech teams analyze data, communicate findings clearly, and present their work credibly online — backed by published research and open-source tools with real usage.

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We don't sell templates or generic execution. We sell judgment — the difference between an analysis that looks right and one that is right.

Data doesn't need more tools. It needs judgment.

Most researchers aren't short on software — they're short on someone who can look at a result and tell them whether to trust it.

That's the actual job. Every Cortessa deliverable is built to survive that question — from raw file to a figure and a written interpretation you could defend to a reviewer.
01

Data arrives messy, not analysis-ready

Raw FASTQs, half-labeled sample sheets, no documented QC — cleanup eats the timeline before the real question even gets asked.

02

Generic output can look confident, not correct

A plot with no judgment behind it can't tell you whether a result reflects real biology or noise in the dataset.

03

A number isn't a finding

Without a plain-language interpretation you can stand behind, results sit in a folder instead of a manuscript, a committee meeting, or a pitch.

Three services. One standard of scientific rigor.

Each module can stand alone — but most clients start with analysis, and grow into the rest once trust is established.

Module 01 — Core

Data Analysis & Interpretation

RNA-seq and NGS analysis, statistics, and publication-ready figures — with a written interpretation, not just a script output. Delivered as a report or a reproducible notebook, your choice.

  • QC & preprocessing
  • Differential expression
  • Figures built for publication
  • Plain-language interpretation
  • Report or reproducible notebook
Start here
Module 02 — Upsell

Scientific Communication

Replaces vague claims with precise scientific language that a reviewer or investor can actually evaluate — the same standard of precision as the analysis itself, applied to how it's written.

  • Abstracts & summaries
  • Manuscript sections
  • Technical explanations
  • Investor-facing copy
Module 03 — Parallel

Scientific Digital Presence

A website that reads the way a real lab page should: publications pulled in automatically and correctly, research interests described the way a scientist would say them — not boilerplate agency copy.

  • Auto-synced publications
  • Research-interest framing
  • Fixed, templated scope
  • Fast turnaround

The pipeline, before you commit to anything.

Every analysis follows a defined, defensible workflow — not a black box. Pick an assay type below and watch each stage run.

nf-core / workflows
Public Workflows Documentation Community
Nextflow ecosystemValidated workflows
public
nf-core/rnaseqnextflow

RNA sequencing analysis using STAR, RSEM, HISAT2 and extensive QC.

rna-seqv3.18.0
nf-core/sareknextflow

Variant calling and annotation from WGS and targeted sequencing.

genomicsvariant-calling
nf-core/scrnaseqnextflow

Single-cell RNA-seq pipelines for barcode-based protocols and modern aligners.

single-cellrna-seq
nf-core/magnextflow

Assembly and binning workflows for metagenomic datasets.

metagenomicsassembly
nf-core/chipseqnextflow

ChIP-seq peak calling, QC and downstream analysis.

chip-seqpeak-calling
nf-core/ampliconseqnextflow

Amplicon sequencing analysis with validated QC and reporting.

ampliconmicrobiome
nf-core/nanoseqnextflow

Nanopore demultiplexing, QC and alignment workflows.

nanoporeqc
nf-core/atacseqnextflow

ATAC-seq peak-calling and chromatin accessibility analysis.

atac-seqchromatin
nf-core/eagernextflow

Reproducible ancient DNA analysis from raw reads to results.

ancient-dnagenomics
Move over the registry to inspect it
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Nextflow ecosystem

Use established nf-core workflows where they fit the biological question — versioned, community-maintained infrastructure rather than a one-off script stack.

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Reproducible execution

Pipeline versions, parameters and outputs stay tied to the same analysis so another run can be understood and reproduced.

✓

Custom where necessary

When no existing workflow fits, custom notebooks and analysis code extend the stack without pretending every problem is the same.

→

From pipeline to finding

Computation is only the middle of the process. QC, figures and biological interpretation are what make the output useful.

nf-core / pipeline.run

The capabilities behind the difference.

The point is not to build another platform. It is to combine proven scientific infrastructure with careful interpretation and a deliverable a researcher can actually use.

Use established workflows where they fit. Build custom analysis where they don't. Always connect the computation back to the biological question.

Reproducible by default

Pipeline versions, parameters, notebooks, figures, and interpretation stay tied to the same analysis rather than becoming disconnected files.

Judgment at the handoff

QC is not the finish line. Results are checked for whether they support the biological question before they become a finding.

Analysis into explanation

Publication-ready figures and a plain-language interpretation turn a technically correct output into something usable in a manuscript, meeting, or pitch.

Custom analysis when needed

When an existing workflow does not fit the question, custom notebooks and analysis code extend the analysis without forcing every problem into the same pipeline.

Science-correct digital presence

For the separate website offer, publications, research interests, and workflow explanations are structured for scientific credibility rather than generic agency polish.

Track record before the pitch.

00
Independent research preprints
00
Published open-source packages
0
Combined package downloads
0
Typical analysis turnaround

A track record you can check.

Every entry here is independently verifiable — not portfolio copy.

Three open-source packages, 7,000+ combined downloads — three sole-author preprints — one live example of the website module.

Open-source

gene-id-resolver

A Python package that resolves gene identifiers across naming conventions and databases, cutting out one of the most common friction points in cross-dataset analysis.

View on PyPI →
Open-source

Phredator

A tool for working with Phred quality scores in sequencing data, built to speed up a routine but essential step of NGS quality control.

View on PyPI →
Open-source

EvoMotif

A package for evolutionary motif analysis, used to identify and compare conserved sequence patterns across genomic datasets.

View on PyPI →
Preprint

TCGA-BRCA Multi-Omics

Sole-author analysis integrating multiple omics layers within the TCGA breast cancer cohort to characterize patterns across the dataset.

Read preprint →
Preprint

MEF2C Haploinsufficiency

A multi-omics investigation into MEF2C haploinsufficiency, examining its molecular signatures independently, sole-author, start to finish.

Read preprint →
Preprint

HCC1395 Somatic WGS

Whole-genome sequencing analysis of the HCC1395 reference cell line, characterizing somatic variation with a fully reproducible pipeline.

Read preprint →

One person, doing the actual work.

No account managers, no subcontracted analysts. When you work with Cortessa, you work directly with the person who runs the analysis.

Taha Ahmad
→ B.Sc. Biology, METU
→ Research experience, Biomedical Engineering, Ankara University
→ BIOMATEN, METU — Biotechnology
→ M.Sc. TUM School of Life Sciences

Hi, my name is Taha Ahmad.

I graduated in Biology from METU and am currently pursuing an M.Sc. at TUM School of Life Sciences. Along the way, I've gained experience across both academia and industry, working on projects in computational biology, bioinformatics, biotechnology, and scientific software development, including R&D at Ankara University Biomedical Engineering and industry experience at BIOMATEN, METU's biomaterials research center.

I started Cortessa because I genuinely enjoy using computation to solve biological problems. Whether it's analyzing sequencing data, building reproducible workflows, developing scientific software, or creating research-focused digital platforms, my goal is always the same: to deliver work that is technically sound, practical, and genuinely useful.

Cortessa is an independent consultancy, and every project is handled personally—from the initial discussion to the final deliverables. I intentionally take on a limited number of projects so that each client receives the time, attention, and quality their work deserves.

Fixed scope, fixed price. No surprises.

A clear starting price for a defined analysis scope. Larger or more complex projects are quoted separately.

Custom / Larger-Scope Project
Let's talk
Multiple datasets · Extended analysis · Timeline scoped to the work
  • Multi-dataset or multi-omics integration
  • Extended statistics or a custom pipeline
  • Manuscript-length written interpretation
  • Timeline set to match the scope

Price and timeline are worked out together after a short conversation about what you need — same fixed-scope principle, just sized to a bigger project.

A fixed, predictable process.

No open-ended hours. You know the scope and the price before we start.

01

Share your data

Send the dataset and the question you're trying to answer — no need to pre-clean it.

02

Fixed-scope quote

A flat price for a defined deliverable, confirmed before any work begins.

03

Analysis & figures

QC, analysis, and publication-ready visuals delivered within about a week.

04

Plain-language summary

A written interpretation so the result is usable, not just technically correct.

Early feedback from real projects.

"

Handed over a messy RNA-seq dataset with almost no documentation and got back clean figures and a summary I could actually put in front of my committee. Faster than I expected for the price.

M.K.
M.K.
PhD Candidate, Molecular Biology
"

What stood out was the fixed scope. I knew exactly what I'd get and what it would cost before anything started. No scope creep, no vague hourly invoice at the end.

A.R.
A.R.
Postdoctoral Researcher
"

We needed our lab's site to actually reflect our publications correctly, not just look nice. It was the first time a website felt like it understood what a research page needs to say.

H.K
H.K
Principal Investigator
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Not sure if we're a fit?

Cortessa is deliberately narrow. That's not a limitation — it's the point.

We're a good fit if

  • You're a researcher, PhD/MSc student, or PI with a dataset that needs proper analysis and interpretation
  • You're a lab or early-stage biotech team that needs your research presented credibly online
  • You need scientific writing that survives a reviewer's or investor's scrutiny
  • You'd rather have one accountable person than a rotating agency team

We won't take on

  • Generic web design, marketing sites, or e-commerce builds
  • Social media management or SEO campaigns
  • Open-ended hourly work with no defined scope
  • Bespoke custom design work outside the science-site template
  • Clinical or diagnostic variant classification — analysis here is for research use

Your data stays within the scope of the project.

Cortessa is a research-use service, not a data-hosting platform. Handling, access, retention, and deletion are agreed before analysis begins.

01

Project-specific access

Client datasets are accessed only for the agreed analysis and are kept separate from unrelated projects.

02

No unrelated reuse

Client data is not reused for unrelated projects or purposes.

03

Retention is explicit

Storage and deletion expectations are agreed at project start rather than leaving files indefinitely by default.

04

Research use only

Clients remain responsible for the permissions and authorizations required for the data they provide. Clinical or diagnostic use is outside scope.

Things people usually ask before starting.

Just tell us upfront — most academic clients pay via a lab purchase order or invoice rather than a personal card. We'll confirm your institution's process before quoting, and issue a formal invoice that fits it. If your university's PO process takes a few weeks, we'll plan the timeline around that rather than assuming a same-week start.

Yes. QC and preprocessing are part of the Analysis Starter Package, not a prerequisite for it. Send the data as it exists — raw, messy, partially labeled — and the cleanup happens as step one, not something you need to solve before reaching out.

Yes, happily, especially for unpublished data or pre-patent work. It's normal to ask, and we'll sign before any dataset changes hands if you'd like one in place.

Most commonly RNA-seq and other NGS data (FASTQ, BAM, count matrices), along with standard tabular formats (CSV, TSV, Excel) for other omics or experimental data. If you're not sure your format is supported, ask — it's a five-minute answer either way.

Yes. Every project can be delivered as a written report, a reproducible notebook containing the actual code, outputs, and Explanatory notes, or both — whichever is more useful for how you plan to use the results. Just mention your preference when we scope the project.

No — Cortessa is a personal service, not a hosted product. Tools are used internally to deliver analysis and writing faster and more clearly, but there's no software you log into and no data sitting on a shared platform. Your files stay with you and with the person actually doing the work.

That happens, and it's not a failure — it's often the actual finding. The written summary will say so plainly, and one round of clarifying revisions is included if you need the analysis extended or re-framed around a follow-up question.

No — this is a paid service, not a collaboration seeking authorship. If your contribution standards call for acknowledgment given the scope of analytical work involved, that's entirely your call to make.

Yes — all work is remote, and most communication happens over email or a short call. Time zones are rarely an issue given the project turnaround is measured in days, not hours.

Then you'll be told that directly, ideally before any money changes hands. Generic web design, marketing work, and open-ended consulting are explicitly outside scope — see the section above — and it's more useful to say so early than to take on a project outside real expertise.

Have a dataset that needs a clear answer?

Tell us what you're working with — we'll tell you honestly whether we're the right fit.

Please don't submit confidential, identifiable, or sensitive research data here. If the project is a fit, we'll arrange secure data transfer separately.

Tell me what you have, what you are trying to answer, and where you are stuck. I will tell you directly whether Cortessa is the right fit.