AnaConesa
@anaconesa
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Computational biologist and developer of bioinfo tools for the people. Commuting between 2 continents. Runner and mom of 2.
Valencia and Florida
Joined June 2010
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My dear Biologist colleague, solely stating that “Statistical analysis were done in R” is NOT a sufficient description of the bioinformatics Methods of your paper, as just saying “experiments were performed in a lab” would not be of the experimental Material and Methods
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2K
A few days ago someone wrote to me telling me that I was a role model for female bioinformaticians. I replied thanks and that I hoped I could be a role model for male bioinformaticians too...
@Bioinfo4women
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Reading the reviews of a rejected proposal makes my blood boil. R3 states that the project doesn't develop a new methodology but "only" novel bioinformatics methods. How long will this disregard for computational research continue? Try to do your sequencing data analysis by hand!
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Today our
@NatureComms
paper on multi-omics harmonization and experimental design is out. Hope you enjoy the reading and the software!
@UFGenetics
@UF_MCS
@STATegra
@ConesaLab
3
107
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Our paper in Multi-Omics experimental design just accepted in
@NatureComms
! The MultiPower and MultiML methods are available as R packages and scripts from
@STATegra
@ConesaLab
8
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268
I´m thrilled to see our
#LRGASP
paper published in
@naturemethods
today. This is the work of many to benchmark long-read methods for transcriptomics, and a must-read paper for those using lrRNA-seq. Special thnks to
@FJPardoPalacios
and
@TheBrooksLab
(1/6)
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I just got notified that our
@MSCActions
ETN LongTREC proposal has been selected for funding. We will be recruiting 10 excellent early-stage researchers to develop bioinformatics tools to move the long-reads transcriptomics field forward!
@nanopore
@PacBio
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Honored to become a member of the Spanish Royal Academy of Engineering. Thank you to the
@RAI_Ingenieria
for this recognition and to the
@CasaReal
for the support of the Queen. The best, sharing this unique moment with family and friends
@CSIC
@i2sysbio
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Excited about joining
@i2sysbio
in Valencia, Spain, as
@CSIC
research professor. Sad for leaving the amazing
@UFExplore
environment, but pleased to continue collaborations as UF courtesy faculty. Watch out for upcoming science positions at the new
@ConesaLab
location!
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Going to
#ECCB2022
and
#ESCS22
by bike!!! 3 days , >300 km to promote
#sustainableConferenceTravel
and
#bioinformatics
! Vamooosssss
@ISMBinfo
@iscbsc
@bio_bam
@i2sysbio
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I am SO happy to see our paper published in Bioinformatics!. MultiBac can help you to create multi-omics experiments by joining data across labs and removing batch effects. Cool!
MultiBaC: An R package to remove batch effects in multi-omic experiments
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Super proud of my team for seeing the
#SQANTI3
paper published today in
@naturemethods
. Thanks to all who contributed to this milestone of the
@Conesa_Lab
@FJPardoPalacios
@aarzalluz_
@Tian_Yuan_Liu
@berbe_ld
@Magdoll
@LaurenMMcIntyr1
@LongtrecEU
@CSIC
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We arrived in Lyon after 3 days and 305 kms
#Cycling4GreenSciene
to raise awareness about sustainable conference travel . We have now one day to rest and get ready. Looking forward to the science and the people at
#ISMBECCB2023
!!!
@iscb
@i2sysbio
@CSICval
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I am thrilled and honored to join the editorial board of
@GenomeBiology
and be part of such an amazing team of scientists. Looking forward to contributing to this exciting journal, now with a special call for papers on long reads sequencing!!!!
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Acquiring NGS data and complaining you cannot analyze them because you do not know how to run a script is like buying a Mercedes and complaining you cannot drive it because you do not have a driving permit.
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The Spanish National Research Council
@CSIC
is offering positions to displaced Ukrainian scientists to continue their reserach in Spanish labs. At the
@ConesaLab
we are happy to offer a hosting lab to researchers in Bioinformatics, Biostatistics, and Genomics.
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Looking for datasets to develop your cool multi-omics integrative analysis method? Check out the
@ScientificData
Multi-omics Data Collection where six fully linked multi-omics datasets are made accessible.
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Yesterday, a PhD student in my lab pointed out that our Best Practises in RNA-seq manuscript is listed as the most accessed paper ever in
@GenomeBiology
, followed by the Kardashian index paper... Not sure if I am bushing more about the first position or who follows us as second.
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19
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I woke up with the news I've been elected to join the
@iscb
Board of Directors as COSI representative for the new term. Thank you so much to ISCB and my COSI chair peers for the trust! It will be my honor and privilege to serve our Society
@HiTSeq
@ISMBinfo
@SEBiBC_es
@i2sysbio
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SOO excited to see the final LRGASP preprint out! The largest benchmark of
#longreads
for transcriptomics. A must-read if you plan on doing lrRNA-seq. Thanks to so many for the huge work
@FJPardoPalacios
@TheBrooksLab
@MarkDiekhans
@GSheynkman
@calizavi
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For those who think that bioinformatics is about to press the button....
@AliciaOshlack
shows the steps in sc-RNA-seq, each one requires s human decision. This is how the same data can produce very different results.
#FGS19
@UFGenetics
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Our latest multi-omics paper is out. We present MultiBac, an across-omics batch correction algorithm that will allow you to create multi-omics datasets by combining studies from different laboratories.
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New postdoc positons at the
@ConesaLab
to model multi-omics short, long and single-cell sequencing data!!! Come work with us in a multidisciplinar, multicultural, world-class and fun research team in
#computationalbiology
and
#bioinformatics
.
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Menudo día... Nuestra propuesta de Red
@CSIC
en Biología Computacional y Bioinformática seleccionada para financiación! Red abierta con 60 grupos de investigación, 24 unidades y 12 acciones que incluyen cooperación, formación, oferta de valor, sostenibilidad. Vamos a por ello!
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Me roban mi portátil un viernes noche. Tengo que entregar el Plan Nacional al martes siguiente me compro otro a toda prisa el sábado y trabajo todo el fin de semana. El
@CSIC
dice no me reembolsa el equipo porque tendría que haber avisado por los cauces de compra. ¿Estamos locos?
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You can now apply for a PhD position at the
@ConesaLab
to develop methods for multi-omics and single-cell and long reads data integration for disease modeling.
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Yesterday I received a phone call telling saying I had been elected to become a member of the Spanish Royal Academy of Engineers . I am overwhelmed by this incredible recognition and I’d like to thank the
@RAI_Ingenieria
for their trust. But also others.
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It’s time! Today we start our sustainable journey to
#ISMBECCB2023
. First train to Avignon, then bike to Lyon!
#Cycling4GreenScience
#Bioinformatics
@bio_bam
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I love this slide by
@RodericGuigo
showing the carbon footprint of two gene prediction methods. Maybe we should be start thinking of including this information when publishing algorithms?
@iscb
#GreenScience
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I am humbled to have been elected as a Fellow of the 2023 Class of the
@iscb
. Thank you the Society for this recognition.
Ana Conesa Cegarra (
@anaconesa
), profesora de investigación del
@CSIC
en el
@i2sysbio
, nueva
#Fellow
de la
@iscb
, una sociedad académica que agrupa a personal investigador de todo el mundo reconocido por sus aportaciones a la
#bioinform
ática.
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Today a collaborator PI ask me to exclude him (not his students) from our paper cause national evaluation committees penalize non-last-author papers...Really? Do we want to kill scientific collaboration? I thought the motto was interdisciplinarity! So sick of this author stuff...
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I am super excited to announce the launch of the official site of the
@LongtrecEU
@MSCActions
for bioinformatics methods in
#LongreadsTranscriptomics
. WE ARE HIRING 12 international PhD students to join us in this amazing project.
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I am so happy to finally see our
#tappAS
paper out in
@GenomeBiology
! tappAS is a comprehensive framework for functional iso-transcriptomics analysis. Hard work by
@manueltard
@dlfuente_lorena
,
@aarzalluz_
and many others! . Now presented at
#SMRTLeiden
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I am thrilled to see this paper by magnificent
@aarzalluz_
published today in
@NatureComms
. Acorde overcomes data sparsity to unravel and interpret isoform co-expression networks from single-cell and long-reads transcriptomics data.
#sqanti
#tappAS
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About to give a talk on long reads transcriptomics benchmark at
#LRUA
under this magnificent ceiling at Uppsala University…
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Rewiews from our last paper are in.R2: “This is a useful tool from a group known to deliver robust software”. On behalf of my hard-working students, I want to thank the reviewer for these encouraging remarks.
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Felizmente nuestro proyecto ha sido propuesto para financiación, incluido becario FPI. Nuevas posibilidades para unirte al
@ConesaLab
para hacer tesis, postdoc o simple% trabajar en
#bioinformatics
de multiomics, single-cell y long-reads. Buscamos candidatos!
@i2sysbio
@AgEInves
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Today I was determined to do my weekly grocery shopping avoiding plastic consumption. Took tupperware, cotton bags and shopping cart, and went to the local bulk shop, greengrocer, fisherman and butcher. Got legums, pasta, fish, meat, vegetables and bread with ZERO plastic waste!!
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El próximo día 20/2 presentaremos en
@CSICval
la Conexión de Biología Computacional y Bioinformática del
@CSIC
, aglutinando a cerca de 100 grupos de investigación. Síguelo en streaming y en RRSS
@BCBHubCSIC
@INB_Official
@SEBiBC_es
@i2sysbio
@RSGSpain
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Excited to see
#longreadssequencing
as the Method of the Year. We have been working on their application to the transcriptome since 2014 and our tools
#SQANTI
and
#tappAS
are widely used. Want to do your PhD on this exciting technology? Apply here !!!
It's finally here!! Our Method of the Year 2022 is....long-read sequencing! 🎉
Read our (free!) Editorial to learn why we felt the time was right to select this class of powerful technologies as the Method of the Year.
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I just reached the 20,000 citations milestone a couple of days before my birthday. Happy birthday to me!
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Do you know that scientific conferences create a significant carbon footprint? The
@Conesa_Lab
together with
@bio_bam
wants to create awareness about this by biking 3days, 300kms, from Avignon to Lyon to attend
#ISMBECCB2023
. Today Viviers-Tournon-sur-Rhône étape.
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Nuestra propuesta de Conexión
@CSIC
en Biologia Computacional y Bioinformática seleccionada para la segunda fase de preparación de propuestas! Invitamos a la comunidad
#bioinfo
dentro y fuera del CSIC a sumarse a esta iniciativa!!
@INB_Official
@i2sysbio
@iata_csic
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Today we have to celebrate the thesis defense of Teresa Rubio from the
@ConesaLab
. I am so proud!!! I am blessed to work with such an amazing team. Thanks Teresa and good luck in the future!
@victorgreiff
@trubi0
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If you liked
#SQANTI
, you're gonna love our latest
#SQANTI
-reads to support raw-long-read QC in multi-sample experiments. Detect outliers, find biases, and assess discovery power in your LRS dataset. Great collaboration with
@LaurenMMcIntyr1
team. Preprint
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Today I run the Gainesville half marathon under 2h and found out I got a fundable score in my last R21 proposal. These two 21’s are so much related!!!! Long run & long reads!!!! Yeah!!!
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The
@ConesaLab
at
@i2sysbio
continues growing!! Two new positions,
#postdoc
and
#projectManager
within two recently awarded
@NIH
and
@MSCActions
Doctoral Network projects on long reads transcriptome sequencing. See more info at
@PacBio
@nanopore
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See the latest work from the
@Conesa_Lab
published in
@GenomeBiology
. SQANTI-SIM simulates long-read transcriptomics data with realistic novel isoforms and orthogonal datasets, to evaluate novel transcript discovery using long-reads.
@PacBio
@nanopore
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I am very excited to share our latest preprint, SQANTI3, for improved curation and annotation of long-read transcriptomes. Amazing work by
@FJPardoPalacios
@aarzalluz_
and
@Magdoll
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Un honor entrar a formar parte del directorio de Mujeres Científicas e Innovadoras del
@UMyC_Ciencia
en el
#DiaDeLaMujerYLaNinaEnLaCiencia
. En el
@ConesaLab
desarrollamos software para estudiar genomas y transcriptomas.
#YosoyCientificaInnovadora
@RAI_Ingenieria
@i2sysbio
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If you are a PhD for < 8 years and willing to move to Spain for a postdoc on
#bioinformatics
#longreadsequencing
#multiomics
#singlecell
, contact us to submit an MSCA-PF application to join the
@ConesaLab
!
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#ISMB2022
just started for me! Excited about my first in-persons meeting of the ISCB Board of Director and so proud of my
#GreenISCB
ribbon!!
@iscb
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Delighted to see our Perspective “Undisclosed, unmet and neglected challenges in multi-omics studies” published in
@NatComputSci
. Happy to see my first publication including my new
@i2sysbio
affiliation
@CSIC
.
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The last manuscript from the lab is out! scMaSigPro to identify genes responsible for cell type fate decisions in
#single
-cell trajectory analyses. In collaboration with
@bio_bam
and under the
@MSCActions
@intercept_mds
project.
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What is harder, to explain the Central Dogma of Biology to a Computer Science student or the concept of function arguments to a Biology Major? I had to do both today. I am drained....
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Today my daughter (19 yo, STEM student) taught me how to program a recursive function in R. So proud! So excited! So old..
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Next time you complain about the time teaching takes you from writing grants and papers, remember a reviewer would never leave you a note like this. Found by my desk, reminds me the value of mentoring.
#WomeninScience
#WomenInSTEM
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Working in AI in Biology and longing for a research career in a growing and vibrant Systems Biology Institute in sunny Valencia? Check out new positions as
@CSIC
staff researcher (Cientifico Titular) at (
#106
) and contact us at
@i2sysbio
@ELIXIREurope
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One of the great things of in-person conferences is that you finally meet your close remote collaborators to discover they are amazing people. Here with Bambu, TALON, IsoTools and Isoseq3 developers of
#longreads
RNA-seq tools
#LRGASP
@GencodeGenes
#ISMB2022
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It´s official! The
@Conesa_Lab
now a member of
@INB_Official
@ELIXIREurope
in Spain. Honored to contribute to a sustainable & useful computational infrastructure in the EU. Proud that now 5
@CSIC
groups are part of INB/ELIXIR_ES
@jhcepas
@jdelasrivas
@BrunoContrerasM
@JM_Carazo
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Bike trip to
#ECCB2022
. km 80 We missed the road and ended up climbing a “little” mountain. The views were fabulous, though.
#SustainableConferenceTravel
#bioinformatics
@ISMBinfo
@iscbsc
@i2sysbio
@bio_bam
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Our first keynote
#hitseq2021
is Angela Brooks, delivering a very exciting talk about long reads, isoform expression and cancer!!!
#ismbeccb21
@TheBrooksLab
. Now presenting their FLAIR software for
@nanopore
lrRNA-seq analysis.
@ISMBinfo
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I just found out that both my brother Jose Carlos and I are in the recently published Stanford list of top 2% most cited scientists in the world. Olé, Olé pappa & mamma.....
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The decision is made! we will travel to
#ISMBECCB2023
combining train and bike to promote sustainable conference travel. The plan: Valencia-Avignon by train (28 KgC02) + Avignon-Lyon by rental bike (3 days, ~300 km, 7500 Kcal). Back by train. Sponsor
@bio_bam
. Wanna join?
@iscb
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We arrived in Viviers after 92 km biking. Zero carbon footprint but 9400 Kcal total for the team. We crossed all kind of fields in the french campagne: sunflowers, vineyards, peer trees, corn… Now resting in an amazing monastery in a carcassonne village.
#Cycling4GreenScience
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For my R class, I asked my students to run an anonymised script from other student and report their experience. Several used "he" or "his code" when describing the other student's code. One (girl) used his/her. My class has 60% females and 40% males.
#genderbias
#womenintech
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Today I am presenting at the
#JAXLongReads
workshop the
@ConesaLab
software tools for the analysis of lr-RNA-seq from reads to function
#LRGASP
#LongReads
#transcriptomics
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2
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New publication from the
@Conesalab
with collaborations with
@LaurenMMcIntyr1
from
@UFGenetics
and
@GrudenKristina
from
@NIB_FITO_SI
. PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases
0
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Have you heard of
#SQANTi
, tappAS, Paintomics, NOISeq??? Meet their developers all dressed up for another awesome
@ConesaLab
wedding
@Sarvaorin
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Excited to see so much interest by the long-reads RNA-seq community in the
#LRGASP
challenge. In this second community call, we presented our strategies for quantification and experimental evaluations. Stay tuned @
@TheBrooksLab
@calizavi
@PacBio
@nanopore
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10
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Today we are teaching again a fully booked Iso-seq tutorial with
@Magdoll
@aarzalluz_
&
@FJPardoPalacios
, this time at the New Trends in Bioinformatics section of
#ECCB2020
: Full-Length RNA-Seq Analysis using PacBio long reads: from reads to functional interpretation
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We are delighted to have
@nanopore
as associated partner of the
@LongtrecEU
@MSCActions
network. Aino Jarvelin is presenting the technology and applications
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What I am finding so awesome of the
#AdvCompBio
conference is the number of AMAZING talks by strong young female scientists. Look at that! PI gender balance in computational biology is just around the corner! Onward and upward, girls!
#womeninSTEM
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9
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📢 New positions
@Conesa_Lab
. Seeking enthusiastic graduates/postdocs in
#ComputationalBiology
to join our new
@oscars_eu
funded project for long-reads driven annotation of
#biodiversity
genomes. Also incorporating a postdoc to set up our new wet lab. See
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The
@ConesaLab
at full gas at the
#ECCB2022
poster session
@aarzalluz_
@FJPardoPalacios
@Tian_Yuan_Liu
@CarolMonzo
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1
45
Happy with my new group of latin
#bioinformatics
girls in the lab! 🇲🇽 🇺🇾 🇪🇨 🇪🇸
#WomenInSTEM
#womeninscience
#bioinfosabros
ón
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Working on
#multiomics
methods and need to simulate data? Check out MOSim, our new package for multiomics data simulation. Available at the
@biorxivpreprint
.
0
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PaintOmics3, the new paper from our group on the analysis of multi-omics data, published in
@NAR_Open
.
@CIPFciencia
@STATegra
@UFGenetics
@UF_MCS
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Very happy with our recent INFRA2024 award to foster the participation of
@CSIC
in
@ELIXIREurope
@INB_Official
, with the support of the
@BCBHubCSIC
, the CSIC Conexion in Bioinformatics and Computational Biology
@jhcepas
@jdelasrivas
@BrunoContrerasM
@JM_Carazo
@MChagoyen
1
13
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#FilSostenibilitatUVInici
@UV_EG
@Sostenible_UV
En el I2SysBio hemos constituido recientemente la Comision de Sostenibilidad con el fin de promover una práctica de la investigación sostenible en nuestro instituto y mas allá.
(abro hilo 1/12)
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13
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Our Genome Biology paper on scRNA-seq and isoforms is finally out!!!
Single-cell RNAseq for the study of isoforms—how is that possible?
@aarzalluz_
@conesagroup
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Excited to be part of this initiative!!! Hope this will be useful for the community using Long Reads to characterize transcriptomes!
@PacBio
@nanopore
@UF_ICBR
The Long-read RNAseq Genome Annotation Assessment Project Consortium is organizing a systematic evaluation of methods for transcript identification & quantification using long-read data. Those interested in participating can join the mailing list here:
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11
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Gracias! un honor pertenecer a la Academia!
Tenemos nueva académica en la
#RAING
. La Dra. Ana Conesa
@anaconesa
, del Instituto de Biología Integrativa de Sistemas (I2SysBio) bióloga computacional y desarrolladora de herramientas de
#bioinformaci
ón para las personas. ¡Bienvenida!
#MujereIngenier
ía
#RealAcademiadeIngenier
ía
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Esta semana celebraremos el primer retiro científico del
@I2SysBio
en la hermosa villa El Molinar, joya arquitectónica del s. XIX, sita en el Campo de Cartagena. Inmejorable entorno e inspiración para diseñar entre todos el futuro de nuestro instituto.
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7
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Happy with my brand new grant from Florida Space to discover extreme genes that may help to adapt terrestrial life to survive outside Earth. My son reminded me that as I child I dreamt to travel to Mars. I will not, maybe my science will?
#keepondreaming
@astro_duque
4
3
37
Enjoying
@jsb_ucla
keynote at
#ISMBECCB2023
about false positives and distribution concepts in genomics, frequently overlooked! Surprised to see our NOISeq method does well in controlling false positives compared to popular solutions (we knew!!!)
0
10
41
Last training ride before our biking tour to Lyon for
#ISMBECCB2023
to promote sustainable conference travel. We are ready!
#Biking4GreenSciene
@bio_bam
1
5
40
Finally, our tappAS preprint is out. Be ready to discover the functional potential of alternative splicing and UTRs! Better if you use long reads!
@PacBio
@GencodeGenes
@UF_MCS
@UFGenetics
0
15
40
Honored to present our keynote speakers Mark Blaxter
@darwintreelife
,
@JulioSaezRod
and
@YolsanzSanz
of the X Genomics and Bioinformatics Symposium, Valencia Dec. 15th and 16th. You can still your abstract and join!!
@SEBiBC_es
@iscbsc
@RSGSpain
0
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First intercontinental flight after 8 months. Aircraft is at 5% occupancy and everybody wears a mask. One thing has not changed. It is still chicken or pasta.
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A new Doctora is born! congratulations Lorena you did an amazing job!!! Look up for
#SQANTI
and
#tappAS
to leran about Lorena’s work.
@ConesaLab
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5
37
Thank you SO MUCH to the Spanish Society for Bioinformatics and Computational Biology
@SEBiBC_es
() for my election as an Honorary Member of the society. It is a great great honor. I look forward to continuing to collaborate in the future.
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