Presentation

Blaise Li

IGH, Systemic impact of small regulatory RNAs

Department retreat, April 2nd 2014

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogeny

Example: swordfish is closer to flatfishes than to tunaMethods: comparing trees made using different genes toidentify the most reliable groupings

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic treesToo new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplastsMethods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogenyExample: swordfish is closer to flatfishes than to tuna

Methods: comparing trees made using different genes toidentify the most reliable groupings

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic treesToo new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplastsMethods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogenyExample: swordfish is closer to flatfishes than to tunaMethods: comparing trees made using different genes toidentify the most reliable groupings

Aacbde

Bcdabe

Cabced

αA ∪ B ∪ C

abcde

α

→

↓A ∪ B

abdec

α data number ofsets occurrences for α

A,B,C 1A ∪ B ∪ C 1A ∪ B,C 2

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic treesToo new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplastsMethods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogenyExample: swordfish is closer to flatfishes than to tunaMethods: comparing trees made using different genes toidentify the most reliable groupings

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic trees

Too new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplastsMethods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogenyExample: swordfish is closer to flatfishes than to tuna

Hindi

VaishMarathi

Lodi

Satnami

Sahariya

Telugu/Kannada

Velama

Vysya

Naidu

Hallaki

Kurumba

Madiga

Mala

Chenchu

Santhal

Kharia

Great Andamanese

Onge

Alorese

Lembata

Manggarai

Mamanwa

Ayta

Agta

Ati

Iraya

Minanubu Manobo

Mentawai

Toraja

Batak Karo

Batak TobaMalay

Malay Singapore

Bidayuh Jagoi

Javanese

Temuan

Negrito Kensiu

Negrito Jehai

Htin Mal

Wa

Lawa

Paluang

Mon

Ami

Atayal

Zhuang N

Hmong

Hmong Miao

Han BJ

Okinawan

Uyghur

Methods: comparing trees made using different genes toidentify the most reliable groupings

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic treesToo new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplastsMethods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogenyExample: swordfish is closer to flatfishes than to tunaMethods: comparing trees made using different genes toidentify the most reliable groupings

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic treesToo new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplasts

Methods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

Where I come from

I PhD in MNHN (Paris) on fish phylogenyExample: swordfish is closer to flatfishes than to tunaMethods: comparing trees made using different genes toidentify the most reliable groupings

I Post-doc in the Politecnico di Torino (Italy)Testing new algorithms for making phylogenetic treesToo new to work. . .→ Studied computer sciences and did some amateur workwith human population genetics data

I Postdoc in the University of Algarve (Portugal)Phylogeny of Cyanobacteria: searching the origins ofchloroplastsMethods: how to avoid errors due to convergence innucleotide composition

Blaise Li Presentation

What I’m here for

I Research engineer in bioinformaticsArrived in NovemberJointly hired by 2 teams

I Learning specific techniques with Hervé Seitz(RNA-Seq reads mapping, . . . )

I Teaching general techniques to Séverine Chambeyron(Linux command-line work)

I Applying the new skills in both teams

Blaise Li Presentation

What I’m here for

I Research engineer in bioinformaticsArrived in NovemberJointly hired by 2 teams

I Learning specific techniques with Hervé Seitz(RNA-Seq reads mapping, . . . )

I Teaching general techniques to Séverine Chambeyron(Linux command-line work)

I Applying the new skills in both teams

Blaise Li Presentation

What I’m here for

I Research engineer in bioinformaticsArrived in NovemberJointly hired by 2 teams

I Learning specific techniques with Hervé Seitz(RNA-Seq reads mapping, . . . )

I Teaching general techniques to Séverine Chambeyron(Linux command-line work)

I Applying the new skills in both teams

Blaise Li Presentation

What I’m here for

I Research engineer in bioinformaticsArrived in NovemberJointly hired by 2 teams

I Learning specific techniques with Hervé Seitz(RNA-Seq reads mapping, . . . )

I Teaching general techniques to Séverine Chambeyron(Linux command-line work)

I Applying the new skills in both teams

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualizationI System administration:

program installationdata transfer and backupressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualization

10 15 20 25 30read size

1000

800

600

400

200

0

200

read

s pe

r mill

ion

42AB

str

ict m

appe

rs

I System administration:program installationdata transfer and backupressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualizationI System administration:

program installationdata transfer and backupressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualizationI System administration:

program installation

data transfer and backupressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualizationI System administration:

program installationdata transfer and backup

ressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualizationI System administration:

program installationdata transfer and backupressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

What my activities are

I Debugging / updating / setting up pipelines for sequencedreads mapping and annotation

I Results visualizationI System administration:

program installationdata transfer and backupressource management (disk space, memory usage,input-output constraints)

I Tutoring / help

Blaise Li Presentation

Last slide

Thanks for your attention.

Blaise Li Presentation