Alexander Piper @bigsnpenergy Twitter profile | Pikagi

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Alexander Piper

@bigsnpenergy

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1,266

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Biologist. Using genes 🧬 and computers 💻 to study the evolution and global spread of invasive Insect pests. Research Scientist @VicGovAg .

Naarm / Melbourne, Victoria

Joined October 2017

Don't wanna be here? Send us removal request.

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@bigsnpenergy

Alexander Piper

5 months

Stoked to have my first 'inventorship' on a patent app for fruit fly attractants! This partly came from my pre-doctoral work on microbes associated w/ pest flies, but mostly through years of extensive chemical ecology and field-trials by my co-inventors.

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@istkaorgtr

@azelfk

@VmaniakJ

@Jayne4Susan

@collin_spencer_

@bigsnpenergy

Alexander Piper

6 years

This is extremely cool - Open source protocols to make your own SPRI beads & use them for nucleic acid extraction, purification & size selection. #bioRxiv

@teamBOMBbio

BOMB.bio

6 years

Making a batch of magnetic beads for your lab is easier and faster than you'd think (and incredibly inexpensive, too). Give it a try and head over to #bioRxiv or our community platform #BOMBbio

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@bigsnpenergy

Alexander Piper

4 years

Would the taxonomy funding situation be fixed if we simply called it TaxonOmics?

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@bigsnpenergy

Alexander Piper

3 years

After a v challenging final year I've finally submitted my PhD thesis "Genomic Biosurveillance for Insect Pests", which uses metabarcoding and population genetics to improve detection, outbreak tracing, and population monitoring of horticultural pests in Aus. Papers coming soon!

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@bigsnpenergy

Alexander Piper

5 years

Excited to announce the first paper of my PhD is online now with @GigaScience ! - Prospects and challenges of implementing DNA #Metabarcoding for high-throughput insect surveillance. Thanks to my coauthors @mozztacular & others at @VicGovAg

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

Abstract. Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well

academic.oup.com

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@bigsnpenergy

Alexander Piper

4 years

Today's #RStats challenge is attempting to use image segmentation to count these drosophila communities, because I haven't been allowed in the lab for 6 months to do it manually🙃

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@bigsnpenergy

Alexander Piper

3 years

Put up my first ever preprint👀"Computational Evaluation of DNA Metabarcoding for Universal Diagnostics of Invasive Insect Pests". Comments and suggestions welcome as it goes through peer review.

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Computational Evaluation of DNA Metabarcoding for Universal Diagnostics of Invasive Insect Pests

Appropriate design and selection of PCR primers plays a critical role in determining the sensitivity and specificity of a metabarcoding assay. Despite several studies applying metabarcoding to insect...

www.biorxiv.org

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@bigsnpenergy

Alexander Piper

5 years

Oops i accidentally some album art #rstats @accidental__aRt

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@bigsnpenergy

Alexander Piper

4 years

Whopping Arthropod Phylogeny (WAP)

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@bigsnpenergy

Alexander Piper

10 months

🎉Thrilled to announce I've secured 8 years of funding to develop genomic tracing methods for invasive Fruit Flies & other pests through this massive new initiative. Looking forward to analysing lots of FASTA files in the FASTA (Fresh and Secure Trade Alliance) project! 💻🍊

@Hort_Au

Hort Innovation

10 months

#Horticulture makes #history with $130 million #trade deal. @Hort_Au , @DAFQld and many others are partnering to deliver eight-year project Fresh and Secure Trade Alliance #FASTA . Read more:

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@bigsnpenergy

Alexander Piper

4 years

Not the way i thought I’d be presenting my PhD pre-submission seminar, but very happy to be this close to completion. Beer time now.

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@bigsnpenergy

Alexander Piper

4 years

Predicting sample origins from genomic data using deep learning with @cj_battey new Locator tool. Still lots of cleaning to be done with my training data which should improve the confidence intervals, but a fun start!

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@bigsnpenergy

Alexander Piper

2 years

Stoked to announce ive accepted a new 3 year Research Scientist position @VicGovAg to continue developing genomic and bioinformatic methods for identification and tracing incursions of agricultural insect pests. Glad to have some job security after the tumultuous last few years.

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@bigsnpenergy

Alexander Piper

5 years

When the robots rebel... #phdlife

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@bigsnpenergy

Alexander Piper

5 years

Cryptic diversity in the Piper genus. Ran into an apparantly unrelated individual with the same last name and origin location presenting at the same conference #JointAusBio19

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@bigsnpenergy

Alexander Piper

11 months

Molecular wizard @dnawhisperer revealing a smorgasbord of novel RNA isoforms and methylation identified with #nanopore direct RNA sequencing but missed by other tech. #ICG2023 #genomics #genetics

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@bigsnpenergy

Alexander Piper

2 years

While cleaning out my great-grandmas farmhouse, i discovered this 1951 NSW Department of Agriculture insect pest leaflet on Queensland fruit fly (Bactrocera tryoni), a species that was a major focus of my PhD thesis 70 years later. 1/6

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@bigsnpenergy

Alexander Piper

6 years

Here comes the future of #metabarcoding , folks

@nanopore

Oxford Nanopore

6 years

CB: Linear consensus sequencing (LCS): new method to achieve *very* high single molecule accuracy: target >Q30. Multiple copies of long reads joined by adding adapters to both ends, then sequenced in 1 read. LCS preserves original template strand & base mods #nanoporeconf

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@bigsnpenergy

Alexander Piper

8 months

Reminder that our group is recruiting a Postdoc (Computational biology) and PhD Student (Insect Metabarcoding) to work on a new Grains industry Biosecurity / Surveillance project! See details below 👇

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@bigsnpenergy

Alexander Piper

5 years

Hostile Architecture - Vector Image on digital pixels, 2019. Aka forgetting to set columns as numeric. @accidental__aRt

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@bigsnpenergy

Alexander Piper

2 years

Great to have been involved in this important work developing internationally relevant guidelines for adopting HTS approaches in plant pest diagnostics. Give it a read!

@Be_Phytopath

Sebastien Massart

2 years

Published today: Guidelines for using HTS technologies in plant pest diagnostic (part 1): (open access soon) All you need to know to start using HTS With >50 scientist from 40 countries & 35 labs From @ValitestProject #sequencing #planthealth

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@bigsnpenergy

Alexander Piper

5 years

Putting finishing touches on figures for a Hemiptera #Metabarcoding collaboration with @mozztacular . Look at these little cuties i just drew!

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@bigsnpenergy

Alexander Piper

5 years

My fav robot Mike making equimolar pooling of 478 sequencing libraries an absolute breeze

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@bigsnpenergy

Alexander Piper

11 months

If you’re at #icg2023 drop by former masters and soon-to-be PhD student Stephen Penrose’s poster on chemoreceptor gene evolution in Queensland fruit fly #genetics #genomics

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@bigsnpenergy

Alexander Piper

4 years

Looking back through old files from pre-PhD days when i was working on insect associated yeasts. Check out this bubbly boi @ContamClub

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@bigsnpenergy

Alexander Piper

6 months

What a great conference and opportunity to present my recent population genomics work with fruit fly pests. Lots of cool entomological (and genomics) research happening in Aus!

@Aust_Ent_Soc

Australian Entomological Society

6 months

Thank you to all attendees, presenters, sponsors and everyone who contributed to making #AusEnto2023 such as success. We hope to see you to do it all again next year!

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@bigsnpenergy

Alexander Piper

2 years

New paper out in Environmental DNA with Conrad Trollip, a brilliant PhD student here at @VicGovAg . This study establishes a #metabarcoding pipeline for diagnostics of Ophiostomatales, a group of fungal phytopathogens vectored by bark and ambrosia beetles.

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Modular, multi‐barcode amplicon sequencing for improved species‐level detection of fungal phytopa...

Environmental DNA is an open access eDNA journal that provides an international forum for basic & applied research on all areas of eDNA analysis.

onlinelibrary.wiley.com

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@bigsnpenergy

Alexander Piper

11 months

Lots of very impressive pangenome, structural variant, and long-read based population #genomics in non model organisms on display at day 1 of #ICG2023

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@bigsnpenergy

Alexander Piper

4 years

Signaling to my colleagues that I am 100% not doing any more lab experiments.

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@bigsnpenergy

Alexander Piper

11 months

When you walk into the wrong symposium room #ICG2023

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@bigsnpenergy

Alexander Piper

2 years

First work travel in 3 years! Heading to @BiosecurityRDE Symposium in Adelaide to chat all things #biosecurity

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@bigsnpenergy

Alexander Piper

4 years

Anyone in #entomology twitter know any references to ants or other predators entering insect traps and feeding on or removing other trapped insects? Curious if theres anything published to back up some observation/speculation of mine.

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@bigsnpenergy

Alexander Piper

2 years

Very stoked to have my new paper "DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) Within Unsorted Trap Catches" published in the Fronteirs in E&E Special issue on SWD! 1/7

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DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii)...

The spotted wing drosophila (Drosophila suzukii, Matsumara) is a rapidly spreading global pest of soft and stone fruit production. Due to the similarity of many of its life stages to other cosmopol...

www.frontiersin.org

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@bigsnpenergy

Alexander Piper

11 months

Very exciting session this morning at #ICG2023 around genetic biocontrol for population suppression and replacement of pests and disease vectors. Lots of lab and computation validation of gene drives. #Genomics

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@bigsnpenergy

Alexander Piper

3 years

Great to have this paper with @mozztacular finally published! The non-destructive approach allowed us to detect exotic spp. in large unsorted trap catches with metabarcoding, then confirm the detections with gold-standard microscopic examination and conventional DNA barcoding.

@mozztacular

Jana Batovska

3 years

1000s of aphids and psyllids, 3 loci, 2 PhDs and 1 department name change later, our paper on non‑destructive metabarcoding for pest insect detection is finally published in @SciReports ! Big shout out to my co-first author @bigsnpenergy - we did it! 💪

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@bigsnpenergy

Alexander Piper

5 years

Kulczynski distance between #Metabarcoding samples from of a dilution series of insect communties, each replicated 3 times #rstats @accidental__aRt

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@bigsnpenergy

Alexander Piper

5 years

Procrastination for the day, remade my CV in R using @mitchoharawild 's vitae package #rstats

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@bigsnpenergy

Alexander Piper

3 years

510 days since ive used a pipette🥴

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@bigsnpenergy

Alexander Piper

4 years

Hope everyone's having an auspicious festive period!

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@bigsnpenergy

Alexander Piper

5 years

Finally got data from my first NovaSeq S2 lane, 2.35 billion reads to play with...

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@bigsnpenergy

Alexander Piper

5 years

Kicking off the long weekend with an assertion of dominance over the compute cluster queue.

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@bigsnpenergy

Alexander Piper

5 years

Naturally selected from the Liqourland bargain bin

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@bigsnpenergy

Alexander Piper

2 years

First time back in the field since thesis submission! Sampling for Phylloxera in the picturesque vineyards of the Yarra Valley, with impromptu Christmas party.

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@bigsnpenergy

Alexander Piper

5 years

Do I publicly embrace the nerd within and put these on my laptop? #rstats

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@bigsnpenergy

Alexander Piper

10 months

Delighted to see the @arc_gov_au Training Centre in Plant Biosecurity funded! Very excited to be representing @VicGovAg on this program. Prospective PhD students keep your eyes peeled for some scholarships aligned with this initiative coming soon!

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@bigsnpenergy

Alexander Piper

3 months

Great to see this paper getting some attention! A simple but crucial method that underpins some of our recent metabarcoding studies

@theBentoLab

Bento Lab 🧬

3 months

Here’s a DNA extraction method called “HotSOAK” designed for extracting DNA from whole fruit flies and other tiny invertebrates while preserving the morphology for later identification purposes. The method is gentle on specimens, rapid, cost-effective, and suitable for bulk or

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@bigsnpenergy

Alexander Piper

3 years

My 63yo non-scientist mother who lives rurally attended a Fungus discovery workshop recently and is now barraging me with mushroom pics and requests for pdf's of fungi textbooks. Absolutely here for it.

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@bigsnpenergy

Alexander Piper

4 years

Reached the stage of PhD where I’ve now got a prewritten a email template to say No to anything asked of me.

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@bigsnpenergy

Alexander Piper

4 years

Great to see Australia finally raising the unemployment benefits payment in response to mass job losses. Interestingly it’s now higher than my PhD scholarship 🤔

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@bigsnpenergy

Alexander Piper

2 years

Great to have this work with @CescoMartons published!

@CescoMartons

Francesco Martoni

2 years

Our article on disentangling bias for non-destructive #metabarcoding of #insects is out on @PeerJLife ! Another collaboration with @bigsnpenergy and my first real work on metabarcoding despite playing with it for more than 7 years!! You can read it here:

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@bigsnpenergy

Alexander Piper

4 years

Pretending I live in the tropics rather than plague city.

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@bigsnpenergy

Alexander Piper

4 years

This feels like a very long time ago 👶

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@bigsnpenergy

Alexander Piper

4 years

With Melbourne in Stage 4 lockdown and much less traffic on the streets I'm hearing birdcalls i've never heard before in the city. Just wish they would start a little later in the morning...

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@bigsnpenergy

Alexander Piper

5 years

Whenever someone asks how my PhD is going...

@ChadBourgeoisie

Norman French Bates

@ChadBourgeoisie

5 years

Avoiding the jaws of depression and not really thriving but doing alright

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Alexander Piper

5 years

Ya boy is going Bayesian

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@bigsnpenergy

Alexander Piper

5 years

Saying 'ok boomer' to my supervisor when he asks for that one more experiment

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@bigsnpenergy

Alexander Piper

4 years

Hey look it’s my thesis

@tunguz

Bojan Tunguz

4 years

Product development

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Alexander Piper

5 years

MiSeq, HiSeq and NovaSeq flow cells. Eppy for scale. #Need4Speed

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@bigsnpenergy

Alexander Piper

5 years

Got a new washing machine for the lab #novaseq

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@bigsnpenergy

Alexander Piper

4 years

@accidental__aRt Oops, candy mountain is now a sharps disposal bin

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@bigsnpenergy

Alexander Piper

5 years

It's only a true replicate if it's from the replication region of France, otherwise it's a pseudo replicate

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@bigsnpenergy

Alexander Piper

2 years

Had a pleasant time in the Yarra Valley talking to Berry growers and agronomists about Biosecurity, Spotted Wing Drosophila, and our recent surveillance program where we used #metabarcoding to screen >18k specimens collected from around Victoria

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@bigsnpenergy

Alexander Piper

1 year

Another paper with soon-to-be-Dr Trollip, applying multi-locus metabarcoding to survey bark-beetle vectored Ophiostomatales fungi within Australian forestry plantations, and evaluate compatibility with existing forestry surveillance programs.

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High throughput screening of fungal phytopathogens caught in Australian forestry insect surveilla...

Post-border surveillance for forestry’s high priority pests and pathogens is conducted routinely through established programs focused on the main points-of-entry and across the major plantation...

www.frontiersin.org

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@bigsnpenergy

Alexander Piper

4 years

I've always been intrigued by the militarisation of language around invasive species, this is definitely one of the more striking examples of the genre.

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@bigsnpenergy

Alexander Piper

5 years

This face-completion example in the scikit-learn documentation is going to keep me awake at night #MachineLearning

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@bigsnpenergy

Alexander Piper

4 years

For any other sequencing folks fighting the constant battle with file sizes, this neat tool clumpify (part of BBMap) sorts fastqs in order to losslessly maximize gzip compression. Reduced 754GB of fastq.gz files to 594GB (27% reduced). Heres how i used it:

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Clumpify fastq.gz files

Clumpify fastq.gz files. GitHub Gist: instantly share code, notes, and snippets.

gist.github.com

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@bigsnpenergy

Alexander Piper

4 years

For anyone wondering why theres no chicken breasts in the supermarket. Its not just panic buyers!

@VicGovAg

Agriculture Victoria

4 years

The Golden Plains Shire is under movement controls in response to avian influenza. No birds, bird products, or equipment related to bird keeping can move into, out of, or within the shire without a permit. If you need a permit, call (03) 4334 2715.

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Alexander Piper

4 years

Thinking of adopting "Genomic bio-surveillance" as my research buzzword for 2020

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@bigsnpenergy

Alexander Piper

5 years

Putting things in perspective with this slide for an upcoming talk (Modified from Hug et al 2016 -)

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@bigsnpenergy

Alexander Piper

5 years

Today's go at pretending i went to art school. Moving average of sequence entropy within COI barcoding gene for ~98k sequences, split into 79 families of interest. Higher peaks = more conserved.

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Alexander Piper

5 years

After 3 years in an entomology department I've finally replaced my morning cereal with a bowl of crickets

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@bigsnpenergy

Alexander Piper

4 years

Thanks, I hate it. #dataviz

@lizardbill

Bill the Lizard

6 years

Stacked Pie Charts! (current year on the bottom is a nice touch)

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Alexander Piper

4 years

It seems strange for an online only journal like @MethodsEcolEvol to count reference lists within the article word limit. Doesn't help the cause of scientific reproducibility if an author must trade off comprehensive methods & software citations with fitting under a word-count.

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@bigsnpenergy

Alexander Piper

9 months

🌾Exciting PhD opportunity! Help shape the future of pest surveillance in the grains industry using #metabarcoding ! 🧬HTS, genomics, machine learning & more 📈 Optimize pest quantification 🌦️ Integrate environmental data 🤝 Collaborate with experts & industry Details below:

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@bigsnpenergy

Alexander Piper

4 years

Me seeing all the US election content on the timeline

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@bigsnpenergy

Alexander Piper

5 years

All journals that count references towards word limits in 2019 need to get in the bin

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Alexander Piper

5 years

We believe #Metabarcoding may overcome this by allowing entire communities of diverse organisms containing target pests, endemic species, and unexpected invaders to be simultaneously identified, but first need to overcome technical and regulatory challenges.

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@bigsnpenergy

Alexander Piper

9 months

Hiring a postdoc-level Research Scientist in CompBio / Bioinformatics! Developing #metabarcoding and #metagenomics pipelines for surveillance of Grains pests and pathogens. 3 year position with opportunities for independent research and further employment

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Alexander Piper

3 years

Metabarcoding of Airborne insect DNA, incredible stuff from @Latrunculia ! 🤯Also nice to see a shoutout to @iMapPESTS in there, a project i am currently involved in.

@Latrunculia

Fabian Roger

3 years

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Alexander Piper

5 years

@hitRECordJoe @Mozziebites

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Alexander Piper

3 years

Very cool and normal times for Australian Universities

@CUPUWorkers

Casualised, Unemployed & Precarious Uni Workers AU

3 years

Today at a USyd staff meeting, FASS Dean Anna-Marie Jagose said that rather than paying casuals for the time spent marking essays, that she would rather do away with essays altogether. The pedagogical consequences of this should be obvious.

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Alexander Piper

4 years

Gettting manuscript comments back from all my coauthors 😬

@janerichsen

Jan Hakon Erichsen

4 years

Lasagna slapping machine

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Alexander Piper

4 years

Back on the HPC cluster after a couple of months of solid writing... #Bioinformatics #nichetweet

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Alexander Piper

5 years

Me attempting to non destructively extract DNA from on-loan insect specimens

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Alexander Piper

5 years

fish tube has completely broke me

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Alexander Piper

4 years

Sounds like a cool study but I absolutely cannot handle the sketches in this figure🤣

@tvatanen

Tommi Vatanen

4 years

Data from PASTURE study: Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma by M Depner, MJ Ege and colleagues in @NatureMedicine

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Alexander Piper

6 years

1 step closer to doing genomics from the comfort of a pub

@Amandatron89

Dr. Amanda Warr 🧬

6 years

MinION mk1c!

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Alexander Piper

5 years

Once again preparing for my biannual PhD progress meeting by opening up my progress plan and pushing back every single item by 3 months

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Alexander Piper

4 years

Funny choice of header image here. How to support our grad researchers during COVID, give them a modular synthesizer? (Ill take one).

@LTUresearchers

La Trobe Researchers

@LTUresearchers

4 years

This RED Alert post for supervisors shares reflections and strategies to help support our grad researchers during #COVIDlife :

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Alexander Piper

5 years

@mozztacular @M_Hajibabaei Interesting result, id love to see a further comparison of index switching between the two.

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Alexander Piper

6 months

So long to Sanger sequencing! 👋

@AaronPomerantz

Aaron Pomerantz, PhD

@AaronPomerantz

6 months

🔥 🔥 🔥 Kudos to Paul Hebert & team demonstrating that you can sequence 100,000 DNA barcodes in a single @nanopore run at incredibly high accuracy and low cost “ONT has effectively solved the challenge for sequencing” to barcode all the things

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Alexander Piper

3 years

Please no more "10 simple rules" papers🙃🔫

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Alexander Piper

5 years

I was never very good at collage 😵

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@bigsnpenergy

Alexander Piper

4 years

I’ll be sure to tell the police checkpoint that reviewer #2 wanting a larger sample size is the essential reason I’m outside my home!

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@bigsnpenergy

Alexander Piper

4 years

See the paper describing the tool here:

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Predicting geographic location from genetic variation with deep neural networks

Neural networks allow fast and accurate prediction of individual spatial locations from genotypes or sequencing data.

elifesciences.org

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@bigsnpenergy

Alexander Piper

5 years

Me returning to COI barcoding after analysing genome wide SNPs all week

@ladbible

LADbible

5 years

Man opens can of Heinz beans and finds only one inside.

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Alexander Piper

4 years

If you're a university administrator thinking of sending out a happy clappy email to grad students about how to make the most out of being locked inside for 23 hours a day, just don't.

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@bigsnpenergy

Alexander Piper

4 years

Evolution did not prepare humanity for bumping into colleagues in long workplace corridors.

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Alexander Piper

3 years

All i want for christmas is some job security 🙃

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@bigsnpenergy

Alexander Piper

5 years

Spring has arrived in Melbourne

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