Base by Base - Music

This release contains only the music track from Base by Base Episode 294.

Song title: The Splice of Life
Original Base by Base episode: 294: Alternative splicing, exonization and lineage-specific isoforms: PTBP1, MAPT and TE-derived exons in mammalian evolution
Original episode link: https://basebybase.com/episodes/alternative-splicing-exonization-evolution

Article metadata:
Article title: The splice of life: how alternative splicing shapes regulatory and phenotypic evolution
Journal: The EMBO Journal, doi:10.1038/s44318-025-00666-z
DOI: 10.1038/s44318-025-00666-z
Reference: Hunter CE, Xing Y. The splice of life: how alternative splicing shapes regulatory and phenotypic evolution. The EMBO Journal. 2026. https://doi.org/10.1038/s44318-025-00666-z

Lyrics:
Verse 1
Late labs and looping screens where letters shift and slide,
We cut and sew the code, revealing doors we used to hide,
Tiny exons pop like stars, new shapes that redefine,
Isoforms hum their different tunes along the spine.

Pre-Chorus
Across the tree of life the patterns cluster by their kind,
Some changes live in the sequence; some wander from mobile lines,
Alu's small notes can find a voice, a fragment redefined.

Chorus
We call it the splice of life, where choices make a song,
A decoy that calms the storm, a beat that mends a wrong,
A skipped exon tunes the heart, a tau ratio re-sings strong.

Verse 2
Long-read lights and single cells peel isoforms into view,
Mass spec finds the bodies where those coded fragments do come true,
Many edits keep the frame, some outcomes still unknown,
But each revealed possibility becomes a clue, a tone.

Bridge
Cis changes open doors; trans factors rewire the halls,
Old jumps from transposons become new scripts that call,
Evolution drafts in whispers, then the phenotype enthralls.

Final Chorus
This splice, a small conviction that rewrites how we feel,
From immune decoy to faster pulse, the hidden parts reveal,
We stitch the threads of life, and for a moment, it is real.

This release contains only the music track from Base by Base Episode 293.

Song title: Singing the Gaps
Original Base by Base episode: 293: IndeLLM (ESM2) zero-shot scoring and Siamese transfer learning for in-frame indel prediction (MCC 0.77)
Original episode link: https://basebybase.com/episodes/indellm-indel-siamese-model

Article metadata:
Article title: Leveraging protein language models and a scoring function for indel characterization and transfer learning
Journal: Patterns, 7 (2026) 101425. doi:10.1016/j.patter.2025.101425
DOI: 10.1016/j.patter.2025.101425
Reference: Gracia Carmona O, Leipart V, Amdam GV, Orengo C, Fraternali F. Leveraging protein language models and a scoring function for indel characterization and transfer learning. Patterns. 7 (2026) 101425. https://doi.org/10.1016/j.patter.2025.101425

Lyrics:
Verse 1
Late-night screens unfold the long code, quiet like tide lines
Tiny edits—insertions and deletions—tilt a protein's folded face
We watch how subtle shifts carve shadows and open new rooms

Pre-Chorus
Overlapping windows listen to the breath of sequence
A soft scoring current gathers small probabilities into a compass
Points of resonance light where the shape gives way and signs appear

Chorus
We trace the ripple, read the maps of what a single note removes
From whispered odds the outline clears and a new form finds a voice
Not weighed by length but by the places that wake, the places that move

Verse 2
Separate the new thread from its context, let each fragment speak
Embedding threads untangle, the signal loses its fear and sings
Per-residue lights reveal the rooms where edges fray and mend

Bridge
Probabilities fold like tides, their sums a patient rising swell
A paired listening weave learns from labeled nights to point and choose
Small labeled echoes sharpen the compass, turning doubt to edge

Final Chorus
We trace the ripple, read the maps of what a single note removes
From probability light the outline reappears — clear, whole, awake
Small edits become maps of meaning, guiding hands to where to heal
We rise on that bright proof: quiet tension blooming into hope

This release contains only the music track from Base by Base Episode 293.

Song title: Singing the Gaps
Original Base by Base episode: 293: IndeLLM (ESM2) zero-shot scoring and Siamese transfer learning for in-frame indel prediction (MCC 0.77)
Original episode link: https://basebybase.com/episodes/indellm-indel-siamese-model

Article metadata:
Article title: Leveraging protein language models and a scoring function for indel characterization and transfer learning
Journal: Patterns, 7 (2026) 101425. doi:10.1016/j.patter.2025.101425
DOI: 10.1016/j.patter.2025.101425
Reference: Gracia Carmona O, Leipart V, Amdam GV, Orengo C, Fraternali F. Leveraging protein language models and a scoring function for indel characterization and transfer learning. Patterns. 7 (2026) 101425. https://doi.org/10.1016/j.patter.2025.101425

Lyrics:
Verse 1
Late-night screens unfold the long code, quiet like tide lines
Tiny edits—insertions and deletions—tilt a protein's folded face
We watch how subtle shifts carve shadows and open new rooms

Pre-Chorus
Overlapping windows listen to the breath of sequence
A soft scoring current gathers small probabilities into a compass
Points of resonance light where the shape gives way and signs appear

Chorus
We trace the ripple, read the maps of what a single note removes
From whispered odds the outline clears and a new form finds a voice
Not weighed by length but by the places that wake, the places that move

Verse 2
Separate the new thread from its context, let each fragment speak
Embedding threads untangle, the signal loses its fear and sings
Per-residue lights reveal the rooms where edges fray and mend

Bridge
Probabilities fold like tides, their sums a patient rising swell
A paired listening weave learns from labeled nights to point and choose
Small labeled echoes sharpen the compass, turning doubt to edge

Final Chorus
We trace the ripple, read the maps of what a single note removes
From probability light the outline reappears — clear, whole, awake
Small edits become maps of meaning, guiding hands to where to heal
We rise on that bright proof: quiet tension blooming into hope

This release contains only the music track from Base by Base Episode 292.

Song title: Two Copies, One Truth
Original Base by Base episode: 292: INS R6C signal-peptide defect reduces preproinsulin ER translocation in iPSC-derived βcells
Original episode link: https://basebybase.com/?episode=292-ins-r6c-signal-peptide-defect-reduces-preproinsulin-er-t-vf8bv9

Article metadata:
Article title: A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data
Journal: EMBO Molecular Medicine, doi:10.1038/s44321-025-00362-9
DOI: 10.1038/s44321-025-00362-9
Reference: Tong Y, Becker M, Schierloh U, Natividade da Silva F, Haataja L, Cai Y, Patel KA, Kobaisi F, Mirshahi UL, Colclough K, Javed MS, Wakeling MN, Fantuzzi F, Lytrivi M, Sawatani T, Arroyo MN, Yi X, Vinci C, Montaser H, Pachera N, Otonkoski T, Igoillo-Esteve M, Scharfmann R, Hattersley AT, Arvan P, De Beaufort C, Cnop M. A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data. EMBO Molecular Medicine. 2026;18:620–645. https://doi.org/10.1038/s44321-025-00362-9

Lyrics:
New track inspired by a genetic breakthrough: when two tiny copies tip cellular doors closed, we turned that discovery into a hopeful piano anthem — a closing song that listens to science and people. Hear it now: {spotify_link}

```text
Two Copies, One Truth
```

```text
Verse 1
Small change in the language, a whisper in the code,
A single light still shines and keeps the hours slow,
But when the mirror doubles what was hidden at the gate,
The factory stalls and the day begins to wait.

Pre-Chorus
Hands at the doorway, signals out of line,
A crowded hallway where the bright things lose their time,
We traced the pattern, followed where the shadows sign.

Chorus
Two copies brought the silence, two copies broke the chain,
We read the map and learned to call the name,
Now we hold the pieces — light the work, relight the flame.

Verse 2
Cells keep their secrets, shelves of gifts held tight,
One voice can steady through a long and quiet night,
But burden doubled, promise thins into the fight.

Bridge
We watched in patient gardens where small seeds were grown,
Found how doors were closing, how the rhythm was overthrown,
Population maps and lab-born echoes showed what was sown.

Final Chorus
Two copies brought the silence, two copies broke the chain,
We read the map and called the name, and changed the frame,
From lab to life we carry this truth, to guide the healing rain.
```

```text
Title: Two Copies, One Truth
Genre/Subgenre: Piano-driven pop (style #20)
Vocal Style: neutral
Tempo & Key: around 105 BPM, key around A major
Mood: thoughtful, clarifying, hopeful — a scientific revelation turned human story
Arrangement: intimate piano intro, soft ambient pad bed, upright bass and light brushed drums enter in pre-chorus; full band (warm strings, subtle electric piano, rhythmic acoustic guitar) for chorus; bridge strips back then swells into final chorus with layered vocal harmonies.
Dynamics: build steadily; final chorus is the climatic release with a brief luminous outro.
Production notes: keep piano bright and forward, vocals clear and close-mic’d, tasteful reverb for space, add gentle synth pad under verses for modern sheen. Emphasize a strong, singable chorus tag and a gradual crescendo into the final chorus; avoid heavy distortions or aggressive electronics.
```

This release contains only the music track from Base by Base Episode 292.

Song title: Two Copies, One Truth
Original Base by Base episode: 292: INS R6C signal-peptide defect reduces preproinsulin ER translocation in iPSC-derived βcells
Original episode link: https://basebybase.com/?episode=292-ins-r6c-signal-peptide-defect-reduces-preproinsulin-er-t-vf8bv9

Article metadata:
Article title: A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data
Journal: EMBO Molecular Medicine, doi:10.1038/s44321-025-00362-9
DOI: 10.1038/s44321-025-00362-9
Reference: Tong Y, Becker M, Schierloh U, Natividade da Silva F, Haataja L, Cai Y, Patel KA, Kobaisi F, Mirshahi UL, Colclough K, Javed MS, Wakeling MN, Fantuzzi F, Lytrivi M, Sawatani T, Arroyo MN, Yi X, Vinci C, Montaser H, Pachera N, Otonkoski T, Igoillo-Esteve M, Scharfmann R, Hattersley AT, Arvan P, De Beaufort C, Cnop M. A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data. EMBO Molecular Medicine. 2026;18:620–645. https://doi.org/10.1038/s44321-025-00362-9

Lyrics:
New track inspired by a genetic breakthrough: when two tiny copies tip cellular doors closed, we turned that discovery into a hopeful piano anthem — a closing song that listens to science and people. Hear it now: {spotify_link}

```text
Two Copies, One Truth
```

```text
Verse 1
Small change in the language, a whisper in the code,
A single light still shines and keeps the hours slow,
But when the mirror doubles what was hidden at the gate,
The factory stalls and the day begins to wait.

Pre-Chorus
Hands at the doorway, signals out of line,
A crowded hallway where the bright things lose their time,
We traced the pattern, followed where the shadows sign.

Chorus
Two copies brought the silence, two copies broke the chain,
We read the map and learned to call the name,
Now we hold the pieces — light the work, relight the flame.

Verse 2
Cells keep their secrets, shelves of gifts held tight,
One voice can steady through a long and quiet night,
But burden doubled, promise thins into the fight.

Bridge
We watched in patient gardens where small seeds were grown,
Found how doors were closing, how the rhythm was overthrown,
Population maps and lab-born echoes showed what was sown.

Final Chorus
Two copies brought the silence, two copies broke the chain,
We read the map and called the name, and changed the frame,
From lab to life we carry this truth, to guide the healing rain.
```

```text
Title: Two Copies, One Truth
Genre/Subgenre: Piano-driven pop (style #20)
Vocal Style: neutral
Tempo & Key: around 105 BPM, key around A major
Mood: thoughtful, clarifying, hopeful — a scientific revelation turned human story
Arrangement: intimate piano intro, soft ambient pad bed, upright bass and light brushed drums enter in pre-chorus; full band (warm strings, subtle electric piano, rhythmic acoustic guitar) for chorus; bridge strips back then swells into final chorus with layered vocal harmonies.
Dynamics: build steadily; final chorus is the climatic release with a brief luminous outro.
Production notes: keep piano bright and forward, vocals clear and close-mic’d, tasteful reverb for space, add gentle synth pad under verses for modern sheen. Emphasize a strong, singable chorus tag and a gradual crescendo into the final chorus; avoid heavy distortions or aggressive electronics.
```

This release contains only the music track from Base by Base Episode 290.

Song title: The Quiet Rescue
Original Base by Base episode: 290: SMN1 p.Arg288AlafsTer5 exon 7 deletions evade PCR newborn screening yet yield functional SMN isoform
Original episode link: https://basebybase.com/?episode=290-smn1-p-arg288alafster5-exon-7-deletions-evade-pcr-newbor-z64oqq

Article metadata:
Article title: SMN1 variants identified by false-positive SMA newborn screening tests: Therapeutic hurdles and functional and epidemiological solutions
Journal: The American Journal of Human Genetics, Corrected proof. doi:10.1016/j.ajhg.2026.01.012
DOI: 10.1016/j.ajhg.2026.01.012
Reference: Wirth B., Das J., Kölbel H., Goh S., Farrar M.A., Piano V., Zetzsche S., Fuhrmann N., Becker J., Karakaya M., Zhang Y., Cao Y., Taghipour-Sheshdeh A., Stringer B.W., Giacomotto J., et al. SMN1 variants identified by false-positive SMA newborn screening tests: Therapeutic hurdles and functional and epidemiological solutions. The American Journal of Human Genetics. 2026 Mar 5;113:1–9. https://doi.org/10.1016/j.ajhg.2026.01.012

Lyrics:
Verse 1
In the hum of midnight labs we read the signs,
A light that flickered on a drying line.
They said the code was missing, the result was stark,
A small, strange silence in a newborn's mark.

Pre-Chorus
We followed traces where the primers failed,
Found a four-letter gap where fear prevailed.
Low the signal, lower than the rest,
But something in the shadow held a quiet test.

Chorus
There's a quiet rescue in a broken line,
A little shape that learned to keep the light.
Not whole, not loud, but steady through the night,
A fragile spark that kept the motor right.

Verse 2
We sent that whisper out to tiny fins,
Watched a borrowed heartbeat teach us how it wins.
Population maps said they should be gone,
Yet hundreds live on, and the children hold on.

Bridge
We were taught to fix the absent and replace,
To race to fill the silence, to hurry every case.
But some small changes bend and do not break,
A softer answer in the space they make.

Final Chorus
There's a quiet rescue in a broken line,
A little shape that learned to keep the light.
Not whole, not loud, but steady through the night,
We learned to wait, to guard the fragile sight.

This release contains only the music track from Base by Base Episode 290.

Song title: The Quiet Rescue
Original Base by Base episode: 290: SMN1 p.Arg288AlafsTer5 exon 7 deletions evade PCR newborn screening yet yield functional SMN isoform
Original episode link: https://basebybase.com/?episode=290-smn1-p-arg288alafster5-exon-7-deletions-evade-pcr-newbor-z64oqq

Article metadata:
Article title: SMN1 variants identified by false-positive SMA newborn screening tests: Therapeutic hurdles and functional and epidemiological solutions
Journal: The American Journal of Human Genetics, Corrected proof. doi:10.1016/j.ajhg.2026.01.012
DOI: 10.1016/j.ajhg.2026.01.012
Reference: Wirth B., Das J., Kölbel H., Goh S., Farrar M.A., Piano V., Zetzsche S., Fuhrmann N., Becker J., Karakaya M., Zhang Y., Cao Y., Taghipour-Sheshdeh A., Stringer B.W., Giacomotto J., et al. SMN1 variants identified by false-positive SMA newborn screening tests: Therapeutic hurdles and functional and epidemiological solutions. The American Journal of Human Genetics. 2026 Mar 5;113:1–9. https://doi.org/10.1016/j.ajhg.2026.01.012

Lyrics:
Verse 1
In the hum of midnight labs we read the signs,
A light that flickered on a drying line.
They said the code was missing, the result was stark,
A small, strange silence in a newborn's mark.

Pre-Chorus
We followed traces where the primers failed,
Found a four-letter gap where fear prevailed.
Low the signal, lower than the rest,
But something in the shadow held a quiet test.

Chorus
There's a quiet rescue in a broken line,
A little shape that learned to keep the light.
Not whole, not loud, but steady through the night,
A fragile spark that kept the motor right.

Verse 2
We sent that whisper out to tiny fins,
Watched a borrowed heartbeat teach us how it wins.
Population maps said they should be gone,
Yet hundreds live on, and the children hold on.

Bridge
We were taught to fix the absent and replace,
To race to fill the silence, to hurry every case.
But some small changes bend and do not break,
A softer answer in the space they make.

Final Chorus
There's a quiet rescue in a broken line,
A little shape that learned to keep the light.
Not whole, not loud, but steady through the night,
We learned to wait, to guard the fragile sight.

This release contains only the music track from Base by Base Episode 222.

Song title: Sand in the Gears
Original Base by Base episode: 222: snaR-A disrupts mRNA splicing in cancer
Original episode link: https://basebybase.castos.com/episodes/snar-a-splicing-disruption

Article metadata:
Article title: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations
Journal: Nature Communications
DOI: 10.1038/s41467-025-65448-x
Reference: Zhou S. et al., Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. Nature Communications (2025). DOI: 10.1038/s41467-025-65448-x

Lyrics:
Verse 1:
Nuclear bodies hum with silent codes,
Small RNAs drift where shadows flow,
Inside the heart of every growing cell,
Unseen hands shape what stories tell.

Pre-Chorus:
Threads of life are woven tight,
But something’s slipping out of sight.

Chorus:
Sand in the gears, slowing the song,
Signals misfiring, where did we go wrong?
Hidden messengers shift the line—
A fault in our time, multiplying signs.

Verse 2:
Simple spirals twist the fate within,
Splicing dreams with secret kin,
Tangled messages caught on the breeze,
Unraveling futures with delicate ease.

Pre-Chorus:
What once was seamless, whole and pure,
Now echoes cracks we can’t ignore.

Chorus:
Sand in the gears, slowing the song,
Signals misfiring, where did we go wrong?
Hidden messengers shift the line—
A fault in our time, multiplying signs.

Bridge:
Beneath the rush of every storm,
Some silent force reworks the form,
Growth unchecked runs ever deep—
But at its core, the errors creep.

Final Chorus:
Sand in the gears, slowing the song,
Signals misfiring, where did we go wrong?
Lost in the static, patterns distort—
New stories emerge, old battles are fought.

This release contains only the music track from Base by Base Episode 213.

Song title: BRAIN-MAGNET Atlas
Original Base by Base episode: 213: BRAIN-MAGNET: a functional atlas for non-coding variants
Original episode link: https://basebybase.castos.com/episodes/brain-magnet-ncre-atlas

Article metadata:
Article title: BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
Journal: Cell
DOI: 10.1016/j.cell.2025.10.029
Reference: Deng R., Perenthaler E., Nikoncuk A., et al., BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants, Cell 189, 1–20 (2026). https://doi.org/10.1016/j.cell.2025.10.029

Lyrics:
[Verse]
BRAIN-MAGNET, a convolutional neural network trained on 148,198 functionally tested non-coding regulatory elements
A functional genomics atlas for interpretation of non-coding variants
A functional genomics atlas of 148,198 regulatory regions in neural stem cells
Comparative-ChIP-STARR-seq identifies primed non-coding regulatory elements

[Chorus]
Predicts enhancer activity directly from DNA sequence and identifies nucleotides essential for function
Prioritize disease-relevant non-coding variants, advancing functional interpretation of the regulatory genome
In neurodevelopment and neurological disease
Fine-mapping of GWAS loci and prioritizing candidate disease-causing rare non-coding variants

[Bridge]
BRAIN-MAGNET predicts NCRE activity from DNA sequence and identifies nucleotides required for NCRE function
Provides gene regulatory insights into neural stem cells and evidence of NCRE priming already in embryonic stem cells for later neural activity
Together, this NCRE atlas and BRAIN-MAGNET represent a powerful resource, possibly aiding the identification of previously unrecognized enhanceropathies

This release contains only the music track from Base by Base Episode 187.

Song title: Leave a Gap for the Light
Original Base by Base episode: 187: Gapped scheduling: CRLX101 + olaparib Phase I trial

Article metadata:
Article title: Tumor-targeted top1 inhibitor delivery with optimized parp inhibition in advanced solid tumors: a phase i trial of gapped scheduling
Journal: Nature Communications
DOI: 10.1038/s41467-025-64509-5
Reference: Nature Communications (2025) 16:9457; https://doi.org/10.1038/s41467-025-64509-5

Lyrics:
Verse 1
Late-night monitors, steady fluorescent glow
A small white pill and a slow-release flow
Two ways to break what a tumor will hide
But we learned not to hit it all at once—
We learned to time the tide

Pre-Chorus
Hold back, then press in
Let the marrow breathe, let the next round begin
Damage shows up like a signal flare
In the roots of hair, in the blood we carry there

Chorus
Leave a gap for the light, leave a gap for the fight
Step, then strike—make the timing right
Thread the needle through a dangerous tune
Break the chain, trap the repair too soon
Leave a gap for the light, and we rise through the night

Verse 2
Nanoparticles drifting, patient and precise
A quiet kind of power at a measured price
No clash in the bloodstream, no crossing of lanes
Just a longer run and controlled release—
And a plan that reins in pain

Bridge
We don’t call it a cure, but we saw it move
A couple steps forward when there wasn’t much room
Some held their ground, some turned the page
And the warning signs stayed mostly manageable—
So we keep the courage, keep the gauge

Final Chorus
Leave a gap for the light, leave a gap for the fight
Step, then strike—make the timing right
Let the damage mark bloom, then close the door
Push the dose up near the edge, still asking for more
Leave a gap for the light, and we rise through the night