CV

Education

• B.S Biochemestry, University of Granada, 2005.
• M.S. in Bioinformatics for health science, University of Pompeu Fabra, 2008.
• Ph.D. in Biomedicine, Center for Genomic Regulation, 2011.

GitHub contribution

Community supported project I actively participate:

• bcbio-nextgen
• cloudbiolinux
• bcbio.rnaseq
• bioconda
• multiqc

Open projects I lead:

• seqcluster 20008100
• seqclusterViz 26530722 and 21976421
• isomiRs
• DEGreport
• mirTOP
• mirGFF3

Work experience

• Research Scientist at Harvard Chan School Bioinformatic Core, 2017-to date.
  • Development of tools for NGS data analysis
  • Analyst of high-throughput data
  • Leading Bioinformatic analysis in the fibrosis project collaboration between Harvard and Boehringer Ingelheim

• Msc project supervisor at UOC, 2018 - to date.

• Research Associate at Harvard Chan School Bioinformatic Core, 2014–2017.
  • Development of tools for NGS data analysis
  • Analyst of high-throughput data
  • Leading Bioinformatic analysis in the fibrosis project collaboration between Harvard and Boehringer Ingelheim
• Post-doct fellow at IBB, 2013–2014.
  • Analyzing de-novo transcripts due to inversion
  • Differential expression due to inversion in HapMap population
  • Involve in inversion database development
• Founder and CTO at ASCIDEA (http://ascidea.com), 2011-2014
  • Leading a group of 3 bioinformaticians
  • Cloud computing architect
  • Development of computational pipelines
• Post-doctoral fellow at Institut de Medicina Predictiva i Personalitzada del Cancer, 2011–2013.
  • small RNA characterization in human sperm samples
• PhD student at Center for Genomic Regulation, 2006–2011.
  • small RNA characterization in human mental diseases
  • Development of tools for miRNA and small RNA analysis
• Msc student at Granada University, 2004–2006.

Talks

small RNAseq data in bcbio-nexgen

December 03, 2015

Talk at MIT, Cambridge, MA

Characterization of the small RNA transcriptome using the bcbio-nextgen python framework

July 09, 2016

Talk at Walt Disney World Yacht, Orlando, Florida

miRNA and isomiR annotation

December 15, 2016

Talk at MIT, Cambridge, MA

miRTop: An open source community project for the development of a unified format file for miRNA data

June 27, 2018

Talk at Reed College, Portland, OR

Teaching

Small RNAseq analysis

Differential Expression analysis

Service and leadership

• Founder of women in bioinformatics meet up at cambridge, 2014 – to date.
• Co-founder of RSG Spain, the spanish student group of ISCB student council, 2010.

• Former member of ISCB student council, 2010–2014.

• Peer review, NAR journal, 2017
• Programme committee, BOSC, 2014-to date
• Chari, Mind the Gap Barcelona, 2013

• Master Thesis Supervisor, 2014, Universidad Autonoma de Barcelona

• Programme committee, Student Council Symposium
• ISCB Student Council Symposium Long Beach, 2012 - Travel Fellowship chair
• Spain, Portugal and North Africa Student Symposium Barcelona, 2012 - Program committee chair
• ISCB Student Council Symposium Vienna, 2012 - Chair
• Spain, Portugal and North Africa Student Symposium Malaga, 2011 - Chair
• ISCB Student Council Symposium Boston, 2010 - Volunteer

Skills

• LINUX SO
• Cloud computing: Amazon EC2, S3, SQS, IAM
• Control version system: svn and git
• High Performance Computing systems: lsf, slurm, sge
• Basic web Server Development: HTML, DHTML, javascript, ccs3, php and cgi

• Advance database management: mysql, sqlite3 and google datastore

• Programming knowledge:
  • Basic C,C++ environment
  • Intermediate Java environment
  • Advance Perl and Python environment
  • Expert in R and Bioconductor for statistics and visualisation
• Analysis of large-scale data:
  • Analysis of microarrays with R/Rstudio
  • SNPs data mining: samtools, BayesSeq, GATK, freebayes, verdict, mutect.
  • RNA-Seq: tuxedo kit, STAR, salmon, sailfish, kallisto, sleuth, DESeq2 and edgeR/limma.
  • Chip-Seq for histone modifications and transcription factor: macs2, diffbind.
  • Small RNA-Seq: mirdeep2, seqbuster, seqcluster, targetscan custom
• Biostatistics:
  • Machine learning applications for phenotype classification of case/control studies
  • Regression model application to data integration

Courses

• Fundamentals and Applications of Microfluidics @ Harvard Extension School 2018
• Tissue Engineering for Clinical Applications @ Harvard Extension School 2017
• Principles of fMRI 1 @ Coursera 2016
• Practical Machine Learning @ Coursera 2016
• Calculus One @ Coursera 2015
• Regression Model @ Coursera 2014
• HPC programming (not finished) @ Coursera 2013
• Analysis of hight-throughput sequencing data @ EMBL-EBI 2012
• Web applications @ Udacity (CS253) 2012
• Machine learning @ Coursera 2012
• Introduction to Artificial Intelligence (www.ai-class.org) 2011
• Advance R (CRG) 2008

Publications

Google Scholar

Genome assembly comparison identifies structural variants in the human genome.

R Khaja,J Zhang,J MacDonald,Y He,A Joseph-George,J Wei,M Rafiq,C Qian,M Shago,**L Pantano**,H Aburatani,K Jones,R Redon,M Hurles,L Armengol,X Estivill,R Mural,C Lee,S Scherer,L Feuk (2006) Genome assembly comparison identifies structural variants in the human genome. Nature Genetics

Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology

P Grynberg,T Abeel,P Lopes,G Macintyre,**L Pantano** (2007) Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology BMC Bioinformatics

ProSeeK A web server for MLPA probe design

**L Pantano**,L Armengol,S Villatoro,X Estivill (2008) ProSeeK A web server for MLPA probe design BMC Genomics

Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups

L Armengol,S Villatoro,J Gonzalez,**L Pantano**,M Garcia-Aragones,R Rabionet,M Caceres,X Estivill (2009) Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups PLoS ONE

Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.

F Varas,M Stadtfeld,A De,N Maherali,T di,**L Pantano**,C Notredame,K Hochedlinger,T Graf (2009) Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions. Stem cells (Dayton Ohio)

A myriad of miRNA variants in control and Huntingtons disease brain regions detected by massively parallel sequencing

E Marti,**L Pantano**,M Banez-Coronel,F Llorens,E Minones-Moyano,S Porta,L Sumoy,I Ferrer,X Estivill (2010) A myriad of miRNA variants in control and Huntingtons disease brain regions detected by massively parallel sequencing Nucleic Acids Research

SeqBuster a bioinformatic tool for the processing and analysis of small RNAs datasets reveals ubiquitous miRNA modifications in human embryonic cells

**L Pantano**,X Estivill,E Marti (2010) SeqBuster a bioinformatic tool for the processing and analysis of small RNAs datasets reveals ubiquitous miRNA modifications in human embryonic cells Nucleic Acids Research

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.

**L Pantano**,X Estivill,E Marti (2011) A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. Bioinformatics (Oxford England)

A Pathogenic Mechanism in Huntingtons Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity.

M Banez-Coronel,S Porta,B Kagerbauer,E Mateu-Huertas,**L Pantano**,I Ferrer,M Guzman,X Estivill,E Marti (2012) A Pathogenic Mechanism in Huntingtons Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity. PLoS genetics

A highly expressed miR-101 isomiR is a functional silencing small RNA.

F Llorens,M Banez-Coronel,**L Pantano**,R del,I Ferrer,X Estivill,E Marti (2013) A highly expressed miR-101 isomiR is a functional silencing small RNA. BMC genomics

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor.

F Llorens,M Hummel,**L Pantano**,X Pastor,A Vivancos,E Castillo,H Mattlin,A Ferrer,M Ingham,M Noguera,R Kofler,J Dohm,R Pluvinet,M Bayes,H Himmelbauer,R del,E Marti,L Sumoy (2013) Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor. BMC genomics

Regulation of miRNA strand selection follow the leader?

H Meijer,E Smith,M Bushell,A Kozomara,S Griffiths-Jones,V Kim,J Han,M Siomi,Y Wang,S Juranek,H Li,G Sheng,G Wardle,T Tuschl,D Patel,S Chi,J Zang,A Mele,R Darnell,M Hafner,M Landthaler,L Burger,M Khorshid,J Hausser,P Berninger,A Rothballer,M Ascano,A Jungkamp,M Munschauer,S Djuranovic,A Nahvi,R Green,E Huntzinger,D Kuzuoglu-Ozturk,J Braun,A Eulalio,L Wohbold,E Izaurralde,Q Liu,P Halvey,Y Shyr,R Slebos,D Liebler,B Zhang,H Meijer,Y Kong,W Lu,A Wilczynska,R Spriggs,S Robinson,J Godfrey,A Willis,M Bushell,J Krol,I Loedige,W Filipowicz,M Biasiolo,G Sales,M Lionetti,L Agnelli,K Todoerti,A Bisognin,A Coppe,C Romualdi,A Neri,S Bortoluzzi,M He,Y Liu,X Wang,M Zhang,G Hannon,Z Huang,A Mathelier,A Carbone,F Rivas,N Tolia,J Song,J Aragon,J Liu,G Hannon,L Joshua-Tor,N Tahbaz,F Kolb,H Zhang,K Jaronczyk,W Filipowicz,T Hobman,J Pare,N Tahbaz,J Lopez-Orozco,P LaPointe,P Lasko,T Hobman,C Noland,J Doudna,S Gu,L Jin,F Zhang,Y Huang,D Grimm,J Rossi,M Kay,S Iwasaki,M Kobayashi,M Yoda,Y Sakaguchi,S Katsuma,T Suzuki,Y Tomari,E Elkayam,C Kuhn,A Tocilj,A Haase,E Greene,G Hannon,L Joshua-Tor,M Yoda,T Kawamata,Z Paroo,X Ye,S Iwasaki,Q Liu,Y Tomari,P Kwak,Y Tomari,C Matranga,Y Tomari,C Shin,D Bartel,P Zamore,D Schwarz,G Hutvagner,T Du,Z Xu,N Aronin,P Zamore,J Krol,K Sobczak,U Wilczynska,M Drath,A Jasinska,D Kaczynska,W Krzyzosiak,A OToole,S Miller,N Haines,M Zink,M Serra,S Miller,L Jones,K Giovannitti,D Piper,M Serra,H Hu,Y Zheng,Y Xu,H Hu,C Menzel,Y Zhou,W Chen,P Khaitovich,M Ohanian,D Humphreys,E Anderson,T Preiss,D Fatkin,E Marti,**L Pantano**,M Banez-Coronel,F Llorens,E Minones-Moyano,S Porta,L Sumoy,I Ferrer,X Estivill,C Neilsen,G Goodall,C Bracken,D Humphreys,C Hynes,H Patel,G Wei,L Cannon,D Fatkin,C Suter,J Clancy,T Preiss,H Zhou,M Arcila,Z Li,E Lee,C Henzler,J Liu,T Rana,K Kosik,M Xie,M Li,A Vilborg,N Lee,M Shu,V Yartseva,N Sestan,J Steitz,H Lee,K Zhou,A Smith,C Noland,J Doudna,J Winter,S Diederichs,J Yang,M Philips,D Betel,P Mu,A Ventura,A Siepel,K Chen,E Lai,L Guo,Z Lu,S Ro,C Park,D Young,K Sanders,W Yan,H Chiang,L Schoenfeld,J Ruby,V Auyeung,N Spies,D Baek,W Johnston,C Russ,S Luo,J Babiarz,S Bortoluzzi,A Bisognin,M Biasiolo,P Guglielmelli,F Biamonte,R Norfo,R Manfredini,A Vannucchi,S Griffiths-Jones,J Hui,A Marco,M Ronshaugen,A Packer,Y Xing,S Harper,L Jones,B Davidson,L Jiang,C Lin,L Song,J Wu,B Chen,Z Ying,L Fang,X Yan,M He,J Li,M Li,M Rubio,R Montanez,L Perez,M Milan,X Belles,S Shan,L Fang,T Shatseva,Z Rutnam,X Yang,W Du,W Lu,J Xuan,Z Deng,B Yang,X Yang,W Du,H Li,F Liu,A Khorshidi,Z Rutnam,B Yang,H Zhou,X Huang,H Cui,X Luo,Y Tang,S Chen,L Wu,N Shen,L Tarassishin,O Loudig,A Bauman,B Shafit-Zagardo,H Suh,S Lee,C Giles,R Girija-Devi,M Dozmorov,J Wren,S Chatterjee,M Fasier,I Bussing,H Gro$\beta$hans,M Gantier,C McCoy,I Rusinova,D Saulep,D Wang,D Xu,A Irving,M Behlke,P Hertzog,F Mackay,B Williams,J Krol,V Busskamp,I Markiewicz,M Stadler,S Ribi,J Richter,J Duebel,S Bicker,H Fehling,D Schrubeler,T Miki,H Grosshans,S Balaraman,E Lunde,O Sawant,T Cudd,S Washburn,R Miranda (2014) Regulation of miRNA strand selection follow the leader? Biochemical Society transactions

Paternal Diet Defines Offspring Chromatin State and Intergenerational Obesity

A Ost,A Lempradl,E Casas,M Weigert,T Tiko,M Deniz,**L Pantano**,U Boenisch,P Itskov,M Stoeckius,M Ruf,N Rajewsky,G Reuter,N Iovino,C Ribeiro,M Alenius,S Heyne,T Vavouri,J Pospisilik (2014) Paternal Diet Defines Offspring Chromatin State and Intergenerational Obesity Cell

InvFEST a database integrating information of polymorphic inversions in the human genome

A Martinez-Fundichely,S Casillas,R Egea,M Ramia,A Barbadilla,**L Pantano**,M Puig,M Caceres (2014) InvFEST a database integrating information of polymorphic inversions in the human genome Nucleic Acids Research

Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinsons disease revealed by deep sequencing analysis.

**L Pantano**,M Friedlander,G Escaramis,E Lizano,J Pallares-Albanell,I Ferrer,X Estivill,E Marti (2015) Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinsons disease revealed by deep sequencing analysis. Bioinformatics (Oxford England)

Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript

M Puig,D Castellano,**L Pantano**,C Giner-Delgado,D Izquierdo,M Gaya-Vidal,J Lucas-Lledo,T Esko,C Terao,F Matsuda,M Caceres (2015) Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript PLoS Genetics

The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes.

**L Pantano**,M Jodar,M Bak,J Ballesca,N Tommerup,R Oliva,T Vavouri (2015) The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes. RNA (New York N.Y.)

Genomic analyses identify molecular subtypes of pancreatic cancer

P Bailey,D Chang,K Nones,A Johns,A Patch,M Gingras,D Miller,A Christ,T Bruxner,M Quinn,C Nourse,L Murtaugh,I Harliwong,S Idrisoglu,S Manning,E Nourbakhsh,S Wani,L Fink,O Holmes,V Chin,M Anderson,S Kazakoff,C Leonard,F Newell,N Waddell,S Wood,Q Xu,P Wilson,N Cloonan,K Kassahn,D Taylor,K Quek,A Robertson,**L Pantano**,L Mincarelli,L Sanchez,L Evers,J Wu,M Pinese,M Cowley,M Jones,E Colvin,A Nagrial,E Humphrey,L Chantrill,A Mawson,J Humphris,A Chou,M Pajic,C Scarlett,A Pinho,M Giry-Laterriere,I Rooman,J Samra,J Kench,J Lovell,N Merrett,C Toon,K Epari,N Nguyen,A Barbour,N Zeps,K Moran-Jones,N Jamieson,J Graham,F Duthie,K Oien,J Hair,R Grutzmann,A Maitra,C Iacobuzio-Donahue,C Wolfgang,R Morgan,R Lawlor,V Corbo,C Bassi,B Rusev,P Capelli,R Salvia,G Tortora,D Mukhopadhyay,G Petersen,P Australian,D Munzy,W Fisher,S Karim,J Eshleman,R Hruban,C Pilarsky,J Morton,O Sansom,A Scarpa,E Musgrove,U Bailey,O Hofmann,R Sutherland,D Wheeler,A Gill,R Gibbs,J Pearson,N Waddell,A Biankin,S Grimmond (2016) Genomic analyses identify molecular subtypes of pancreatic cancer Nature

bcbioRNASeq R package for bcbio RNA-seq analysis

M Steinbaugh,**L Pantano**,R Kirchner,V Barrera,B Chapman,M Piper,M Mistry,R Khetani,K Rutherford,O Hofmann,J Hutchinson,S Ho (2017) bcbioRNASeq R package for bcbio RNA-seq analysis F1000Research

Viewing RNA-seq data on the entire human genome

B Busby,E Weitz,**L Pantano**,J Zhu,B Upton (2017) Viewing RNA-seq data on the entire human genome F1000Research

Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution

E Ransey,A Bjorkbom,V Lelyveld,P Biecek,**L Pantano**,J Szostak,P Sliz (2017) Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution RNA Biology

Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140

S Mehta,D Cronkite,M Basavappa,T Saunders,F Adiliaghdam,H Amatullah,S Morrison,J Pagan,R Anthony,P Tonnerre,G Lauer,J Lee,S Digumarthi,**L Pantano**,S Ho,F Ji,R Sadreyev,C Zhou,A Mullen,V Kumar,Y Li,C Wijmenga,R Xavier,T Means,K Jeffrey (2017) Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140 Science Immunology

Molecular phenotypic and sample-associated data to describe pluripotent stem cell lines and derivatives

K Daily,S Ho,L Schriml,P Dexheimer,N Salomonis,R Schroll,S Bush,M Keddache,C Mayhew,S Lotia,T Perumal,K Dang,**L Pantano**,A Pico,E Grassman,D Nordling,W Hide,A Hatzopoulos,P Malik,J Cancelas,C Lutzko,B Aronow,L Omberg (2017) Molecular phenotypic and sample-associated data to describe pluripotent stem cell lines and derivatives Scientific Data

Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

J Carmona,W Accomando,A Binder,J Hutchinson,**L Pantano**,B Izzi,A Just,X Lin,J Schwartz,P Vokonas,S Amr,A Baccarelli,K Michels (2017) Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans npj Genomic Medicine

Circulating miRNAs isomiRs and small RNA clusters in human plasma and breast milk

M Rubio,M Bustamante,C Hernandez-Ferrer,D Fernandez-Orth,**L Pantano**,Y Sarria,M Pique-Borras,K Vellve,S Agramunt,R Carreras,X Estivill,J Gonzalez,A Mayor (2018) Circulating miRNAs isomiRs and small RNA clusters in human plasma and breast milk PLoS ONE