Thomas Lux
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Articles by Thomas Lux
Sex without crossovers mimics clonal reproduction in Rhynchospora tenuis
Abstract Meiotic recombination ensures accurate chromosome segregation and promotes genetic diversity by generating crossovers between homologous chromosomes1. Although essential in most sexually reproducing organisms, recombination is variably regulated and can be absent in some lineages, a condition known as achiasmy2. However, obligate achiasmy in both sexes of a sexual species has not been documented.
Best time on this Pauma Valley dairy is the early morning
Best time on this Pauma Valley dairy is the early morning Pete Verboom mostly births his calves In a year, nearly 2000 calves are born on this farm. Pete (Pieter Johannes) Verboom, owner of Pauma Valley Dairy, a family operation milking a thousand cows in the town of Pala, was only a few months old when Nazis invaded and occupied his homeland, Holland, in the spring of 1940. The first five years of his life contained jackboots, oppression, shortages, ration cards.
I study the Coronado bridge close up
I study the Coronado bridge close up Always open, 24 hours a day, 365 days a year. A bridge walker. It’s very dangerous to break down or run out of gas on the bridge. It’s a slash of light blue against the bay’s darker blue.
Artificial intelligence assisted colorectal lesion detection in private practices a randomized controlled study
Abstract Computer-aided colonoscopy (CAC) may improve polyp detection and characterization compared to traditional colonoscopy (TC). However, recent studies also reported no relevant effect on adenoma detection rate (ADR). This study evaluates the real-time polyp detection system EndoMind during screening and surveillance colonoscopy in a multicenter randomized controlled trial.
The Coronado bridge up close
The Coronado bridge up close Not the Golden Gate or the Brooklyn Bridge All sorts of things fall out of cars or off trucks. Bob Morbeu told me he saw a huge sheet of plywood fly off a truck and over the railing. The Reader has started this series of its best stories from the past 52 years — 2600 cover stories and some remarkable interior features — to help make up for the loss of its physical edition, which was once large enough to hold whole oceans of print.
Author Correction: A pangenome and pantranscriptome of hexaploid oat - Nature
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Correction to: Nature https://doi.org/10.1038/s41586-025-09676-7 Published online 29 October 2025 In the version of the article initially published, the wrong caption was included for Extended Data Fig. 10. The correct caption is now available in the HTML and PDF versions of the article, and the original, incorrect caption is available for comparison in the Supplementary information accompanying this notice. Supplementary information is available in the online version of this amendment.
By Raz Avni, Nadia Issabella Kamal, Eric Jellen, Wubishet A. Bekele, Petri Auvinen, Brian Boyle Verified, Francisco Canales, Craig Carlson, Brett Chapman, Yutang Chen, Viet A. Dang, Steven R Eichten, Amit Fenn, Anne Fiebig, Yong-Bi Fu, Heidrun Gundlach, Rajeev Gupta Verified, Georg Haberer, Matthias Herrmann, Axel Himmelbach, Catherine Howarth, Haifei Hu, Asuka Itaya, Jean-Luc Jannink, Yong Jia, Thomas Lux, Sofia Marmon, Raja Sekhar Nandety, Asher Pasha, Nicholas Provart, Jaswinder Singh, Mehtab Karan Singh, Nick Sirijovski, Nils Stein, Sean Walkowiak, Penghao Wang, Charlene P. Wight, Nicholas A. Tinker, Jason Fiedler, Peter Maughan, Manuel Spannagl
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Nature
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A pangenome and pantranscriptome of hexaploid oat - Nature
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Abstract Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4.
By Raz Avni, Nadia Issabella Kamal, Eric Jellen, Wubishet A. Bekele, Petri Auvinen, Brian Boyle Verified, Francisco Canales, Craig Carlson, Brett Chapman, Yutang Chen, Viet A. Dang, Steven R Eichten, Amit Fenn, Anne Fiebig, Yong-Bi Fu, Heidrun Gundlach, Rajeev Gupta Verified, Georg Haberer, Matthias Herrmann, Axel Himmelbach, Catherine Howarth, Haifei Hu, Asuka Itaya, Jean-Luc Jannink, Yong Jia, Thomas Lux, Raja Sekhar Nandety, Asher Pasha, Nicholas Provart, Jaswinder Singh, Mehtab Karan Singh, Nick Sirijovski, Nils Stein, Sean Walkowiak, Penghao Wang, Charlene P. Wight, Nicholas A. Tinker, Jason Fiedler, Peter Maughan, Manuel Spannagl, Sofia Marmon
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Nature
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De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome - Nature Communications
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Abstract Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues.
By Thomas Lux, Rachel Rusholme-Pilcher, Angéla Juhász, Gemy Kaithakottil, Susan Duncan, James Simmonds, Jonathan Wright, Benedict Coombes, Karim Gharbi, Moeko Okada, Hirokazu Handa, Kentaro Shimizu, Heidrun Gundlach, Daniel Lang, Michelle L. Colgrave, Wilfried Haerty, Cristobal Uauy, David Swarbreck, Philippa Borrill, Jesse Poland, Simon G. Krattinger, Nils Stein, Curtis Pozniak, Benjamen White
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Nature
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A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum - Nature
Abstract Wild plants can contribute valuable genes to their domesticated relatives1. Fertility barriers and a lack of genomic resources have hindered the effective use of crop–wild introgressions. Decades of research into barley’s closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes2.
Multilayer interdependencies in the banking system of Japan: correlation dynamics and determinants
Abstract In this paper, we analyse the multilayer architecture of the correlation dynamics among Japanese banks over the period from 1982 to 2011. This period encompasses nearly all significant events in the Japanese economy over the past few decades. The two layers we consider represent the loan portfolio correlations stemming from the credit market and the stock return correlations arising from the equity market, respectively.
Genomic and transcriptomic insights into legume-rhizobia symbiosis in the nitrogen‐fixing tree Robinia pseudoacacia
Supporting Information Filename Description nph70101-sup-0001-Supinfo.docxWord 2007 document , 9.4 MB Fig. S1 Schematic graph of rhizobia strain inoculation and noninoculation control treatments on the roots of Robinia pseudoacacia seedlings. Fig. S2 Phenotypic schemes of roots (a) and seedlings (b) of Robinia pseudoacacia with rhizobia inoculation and noninoculation treatments. Fig. S3 Genome scope analysis of the Robinia pseudoacacia assembly. Fig.
Usability Evaluation of a Digital Teleradiology Case Study Using the System Usability Scale in the WFDT Project
Abstract Background: The global pandemic has significantly increased the use of e-learning. In the project “Knowledge modules and case studies in the digital transformation” (Wissensbausteine und Fallstudien in der digitalen Transformation – WFDT), digital learning content is created in H5P and integrated into the Learning Management System (LMS) to be made available as Open Source Material. The teleradiology content is presented through case studies oriented towards case-based learning.
Date palm acclimates to aridity by diverting organic osmolytes for root osmotic adjustment in parallel with leaf membrane remodeling and ROS scavenging
Abstract Date palm (Phoenix dactylifera L.) is an important crop in arid regions that is well-adapted to desert ecosystems. To understand the remarkable ability to grow and yield in water-limited environments, experiments were conducted in a simulated desert environment with water-withholding for up to four weeks. In response to drought, root, rather than leaf, osmotic strength increased, with sugars contributing more to the osmolyte increase than minerals.
Ode to the Electric Fish that Eat Only the Tails of…
which regenerate their tails and also eat only the tails of other electric eels, presumably smaller, who, in turn, eat ... Without consulting an ichthyologist — eels are fish — I defer to biology’s genius. I know little of their numbers and habitat, other than they are river dwellers. Guess which river. I have only a note, a note taken in reading or fever — I can’t tell, from my handwriting, which.
Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning - Nature Plants
Abstract Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics, influencing the overall distribution and frequency of crossovers. Here we show how recombination is regulated and distributed in the holocentric plant Rhynchospora breviuscula, a species with diffused centromeres.
De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome
Abstract Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled the genomes of 15 wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat.
San Diego's rocks move all the time
Opossums came around 1890, San Diego pigeon fanciers favor females, taxidermist knows ducks, the hated roof rats, panthers – only tigers and lions are larger Looking at the first of many instances of San Diego hydroseeding, across from Costco and Ikea along Friars Road, Deméré declared, "I don't mean to dis botany completely. I can appreciate plants." But more often along our trip he would indicate that roadside landscaping was, to a geologist, a kind of proliferating evil. By Geoff Bouvier, Jan.
Reducing scope 3 carbon emissions in gastrointestinal endoscopy: results of the prospective study of the ‘Green Endoscopy Project Würzburg’
Discussion To the best of our knowledge, this is the first study that prospectively assessed the efficacy of certain measures to reduce scope 3-related carbon emissions of a gastrointestinal endoscopy unit. We were able to show that a general environmental consciousness and switching to alternative accessories reduce carbon emissions without impairing the endoscopic workflow or harming patients.
Trotz großem Konfliktpotenzial: Die Gesellschaft ist nicht gespalten
Konfliktmanagement Populist:innen kennen die „Triggerpunkte“ der aktuellen Gesellschaft und nutzen sie für ihre Zwecke: Ob Heizungshammer oder Sozialtourismus – die Debatten werden hitzig geführt. Warum der Schein einer Spaltung der Gesellschaft trügt Exklusiv für Abonnent:innen | Ausgabe 41/2023 Illustration: der Freitag Heizungshammer! Genderverbot! Sozialtourismus! Fast täglich schießt ein neuer Aufreger durch die Republik und sorgt für hitzige Debatten, Kopfschütteln und Wut.
Introgressions lead to reference bias in wheat RNA-Seq analysis
Abstract RNA-Seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-Seq quantification and thus the conclusions made downstream. Reference bias in RNA-Seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes.
To Help the Monkey Cross the River
which he must cross, by swimming, for fruits and nuts, to help him I sit with my rifle on a platform high in a tree, same side of the river as the hungry monkey. How does this assist him? When he swims for it I look first upriver: predators move faster with the current than against it.
Repeat-based holocentromeres influence genome architecture and karyotype evolution
Chromosome fusions explain karyotype evolution in beak-sedges To explore the genome duplications seen in R. pubera, we compared its genome with its close relative R. breviuscula, which has the same chromosome number but a genome that is one-quarter the size (415 Mb) (Figure S2A). Assessment of the R. breviuscula genome revealed a high level of completeness, with a BUSCO score of 98.3%, and little gene duplication (2.1%) (Figures S2B and S2C), confirmed by the absence of self-synteny (Figure S1D).
The mosaic oat genome gives insights into a uniquely healthy cereal crop - Nature
Abstract Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics.
Advances in the Agent-Based Modeling of Economic and Social Behavior
References: Aberg, Y., Hedstrom, P., 2011. Youth unemployment: a self-reinforcing pro-cess? In: Demeulenaere, P. (Ed.), Analytical sociology and social mecha-nisms. Cambridge University Press. 26 Acemoglu, D., Carvalho, V., Ozdaglar, A., Tahbaz-Salehi, A., 2012. The network origins of aggregate uctuations. Econometrica 80 (5), 1977{2016. Albert, R., Jeong, H., Barabasi, A.-L., 1999. Diameter of the world-wide web. Nature 401, 130{131. Alfarano, S., Milakovic, M., 2009.
Redux: Sightseer in Oblivion
Every week, the editors of The Paris Review lift the paywall on a selection of interviews, stories, poems, and more from the magazine’s archive. You can have these unlocked pieces delivered straight to your inbox every Sunday by signing up for the Redux newsletter. Truman Capote, 1957. Sketch: Rosalie Seidler. This week at The Paris Review, no one wants to get out of bed.
Requiem Shark with Lilies
Sailor boy in pantaloons guides his jacaranda caravel through a labyrinth of skulls, lichens bleeding in fontanels, Easter winds spraying heliotropes with ammonia. Another makes a halo stirring sand in brine that has preserved a martyr’s spleen 1,000 years. St. Agnes sweeps the beach with coco fronds collecting crossfish, aureole urchins, angels’ quills. Jumps over a small requiem shark half buried in wet sand: its transparent body barbed with diamonds, ten lilies suspended inside a glass womb.
Ode to the Unbroken World, Which Is Coming by Thomas Lux
It must be coming, mustn’t it? Churches and saloons are filled with decent humans. A mother wants to feed her daughter, fathers to buy their children things that break. People laugh, all over the world, people laugh. We were born to laugh, and we know how to be sad; we dislike injustice and cancer, and are not unaware of our terrible errors. A man wants to love his wife. His wife wants him to carry something. We’re capable of empathy, and intense moments of joy. Sure, some of us are venal, but not most.
Southeast Locals - a well-educated, violent San Diego gang
Psychiatrist goes bad, Chula Vista crime lab, San Diegans on death row, computer hacker's thinking, darkness in Sabre Springs Author Jeanne Schinto, Jill Underwood, Justin Wolff, Leslie Ryland, Matt Potter, Thomas Lux Publish Date June 27, 2020 1193 Thalia Street in Nestor. Vega and Vasquez were in “grim” condition, the detective said. They had both been shot in the head. Vasquez’s brain stem was perforated; Vega had a bullet hole near his right ear. Trigger Happy or Just Plain Happy?
San Diego's mosquitos, ferrets, sea lions
Classifieds News & Politics Stories Events Music Movies Food Drinks Cannabis Deals News & Politics City Lights Neighborhood News News Ticker Under the Radar Food & Drink Beverage News Booze News Feast! Here's the Deal Pour Over San Diego Beer News Set 'Em Up Joe Tin Fork Movies Big Screen Movie Archives Movie Reviews [email protected] Happenings Fashion Out & About Reader Travel Roam-O-Rama Sports Theater reviews Theater antireviews Your Week Waterfront Music Blurt Classical Music Live Five...
Opposums, rats, pigeons, plus San Diego's geologist who hates roadside landscaping
Close look at San Diego's natural world Author Don McCullough, Geoff Bouvier, Jeannette DeWyze, Thomas Lux "The highest-priced bird sold here in the United States was a couple of years ago, sold for $32,000. The bird’s name was Senna.” Our Panther Our fair city does have one black jaguar resident, downtown, in Cat Canyon, near Sun Bear Forest, across from the Hunte Amphitheater, in the San Diego Zoo. He was born October 1992 at Wildlife World Zoo, in Litchfield, Arizona.
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Cécile Monat1, Sudharsan Padmarasu1, Thomas Lux2, Thomas Wicker3, Heidrun Gundlach2, Axel Himmelbach1, Jennifer Ens4, Chengdao Li5,6, Gary J. Muehlbauer7, Alan H. Schulman8, Robbie Waugh9,10, Ilka Braumann11, Curtis Pozniak4, Uwe Scholz1, Klaus F. X.
Details (Wanting a Child)
A boy stumbles forward in the bus each morning as his father, young and bearded, with a long body, holds the door. Slowed by a snowsuit and questions which must get asked, he allows people to catch and help him, their smiles lasting several stops down the road. In my lap, my neice speaks to me painfully, half with words and half drumming in what she must make known, and I surprise myself scolding her like a wise, unhappy man when she has said or done or eaten something wrong.
Ode to the Unbroken World, Which Is Coming by Thomas Lux - Poems | Academy of American Poets
Boil it down: feet, skin, gristle, bones, vertebrae, heart muscle, boil it down, skim, and boil again, dreams, history, add them and boil again, boil and skim in closed cauldrons, boil your horse, his hooves, the runned-over dog you loved, the girl by the pencil sharpener who looked at you, looked away, boil that for hours, render it down, take more from the top as more settles to the bottom, the heavier, the denser, throw in ache and sperm, and a bead of sweat that slid from your armpit to...
The People of the Other Village
hate the people of this village and would nail our hats to our heads for refusing in their presence to remove them or staple our hands to our foreheads for refusing to salute them if we did not hurt them first: mail them packages of rats, mix their flour at night with broken glass. We do this, they do that. They peel the larynx from one of our brothers’ throats. We devein one of their sisters. The quicksand pits they built were good. Our amputation teams were better.
A Little Tooth
Thomas Lux was born in Northampton, Massachusetts, on December 10, 1946, and attended Emerson College and the University of Iowa.
What San Diegans do with spare time
It is possible one or two other “lone nuts” might also have been jogging somewhere in the county back then. But he knew of none, and the common wisdom in 1948, he points out, was that exercise harmed adults. The molten bronze is poured from the furnace into the crucible and then from the crucible into molds. The crucibles are made of graphite and clay and can hold molten metal with a temperature of 2600 degrees.
Refrigerator, 1957 - Song of America
The composer's note and the audio clip for "Refrigerator, 1957" are made possible through a collaboration between the Hampsong Foundation and SongFest. The performers are Jean Bernard Cerin, baritone, and Andrew Rosenblum, piano, and this performance took place at Pepperdine University at SongFest 2010.
Poetry Friday: The State Champ, The Teacher and 'Tarantulas on the Lifebuoy'
A high school junior from Flagstaff is this year's Poetry Out Loud state champion. Sophie Weinzinger won the prestigious poetry recitation competition, advancing to the national championships in Washington, D.C. Though she didn't place in the top 3, Sophie still won, according to her poetry teacher. We hear from both of them in this week's installment of Poetry Friday. Tarantulas on the LIfebuoy, by Thomas Lux into swimming pools, these otherwise a little, but not for long.
Tarantulas on the Lifebuoy
For some semitropical reason when the rains fall relentlessly they fall into swimming pools, these otherwise bright and scary arachnids. They can swim a little, but not for long and they can’t climb the ladder out. They usually drown—but if you want their favor, if you believe there is justice, a reward for not loving the death of ugly and even dangerous (the eel, hog snake, rats) creatures, if you believe these things, then you would leave a lifebuoy or two in your swimming pool at night.
Identifying patterns in the bank-sector credit network of Spain
Abstract We study the topological and structural properties of the bank–sector credit network of Spain over the period 1997–2007. In particular, we start by analyzing assortativity, different types of motifs and the nestedness phenomenon, both in the bipartite structure of the binary version of the network and in its weighted version.
The Writer's Almanac with Garrison Keillor
Your baby grows a tooth, then two, and four, and five, then she wants some meat directly from the bone. It’s all over: she’ll learn some words, she’ll fall in love with cretins, dolts, a sweet talker on his way to jail. And you, your wife, get old, flyblown, and rue nothing. You did, you loved, your feet are sore. It’s dusk. Your daughter’s tall. “A Little Tooth” by Thomas Lux from The Drowned River. © Houghton Mifflin, 1997. Reprinted with permission.
The Writer's Almanac with Garrison Keillor
That they walk, even stumble, among us is reason to praise them, or protect them—even the sound of a lead slug dropped on a lead plate, even that, for them, is music. Because they bring laughter’s brief amnesia. Because they stand, talking, taking pleasure in others, with their hands on the shoulders of strangers and the shoulders of each other. Because you don’t have to tell them to walk toward the light. Because if there are two pork chops they will serve you the better one.
The Strange History of Internment Camp Print Shops
The cover of the Amache Camp brochure, made by the silkscreen shop. Photo: Amache Preservation Society, via Atlas Obscura Colorado’s Camp Amache was one of many hastily constructed internment camps that opened in the early forties, built by American armed forces to house thousands of Japanese Americans. Its detainees were dragooned into all kinds of labor—including, in an unlikely turn, printmaking and silk-screening.
In Which George du Maurier Feels Neglected By His Mom
George du Maurier A letter from George du Maurier to his mother, March 1862. My dear Mamma, I have just received your letter which is disgustingly short and disappointing after I’ve been waiting day after day—as if you didn’t owe me a letter—fact is, you don’t care half so much for your firstborn as you used, and I’m not going to stand it Madam.
Alexia Arthurs Wins 2017 Plimpton Prize; Vanessa Davis Wins Terry Southern Prize
The Paris Review’s Spring Revel is coming up—tickets are available here—and our board has chosen the winners of two annual prizes for outstanding contributions to the magazine. It’s with great pleasure that we announce our 2017 honorees, Alexia Arthurs and Vanessa Davis. Alexia Arthurs. The Plimpton Prize for Fiction is a $10,000 award given to a new voice from our last four issues. Named after our longtime editor George Plimpton, it commemorates his zeal for discovering new writers.
Three Essays Celebrating Paula Fox (1923-2017)
Paula Fox at The Paris Review’s 2013 Spring Revel. In memory of Paula Fox, who died last week at age ninety-three, we’re looking back at a series of essays published on the Daily in 2013, when Fox received The Paris Review’s Hadada Prize for Lifetime Achievement. First, Tom Bissell has the story of how, as a twenty-four-year-old editorial assistant, he brought Fox’s masterpiece, Desperate Characters, back into print: W.?W.
At “Naked Boys Reading,” Boys Read…Nakedly
Illustration: Anthony Gross, 1940. Let’s cut to the chase: I’m talking exposed peen. I’m talking gender-queering the Victorian classics. I’m talking nude men, reciting Jane Eyre, on stage, for you. It happens. Lara Williams, who attended a in London performance of Naked Boys Reading, writes, “Watching Naked Boys Reading is an experience akin to a hen do hijacked by a spoken word event: a unexpectedly cerebral night of nude performance art.
Tuesday: Norman Ohler in Conversation with Dan Piepenbring
New York: This Tuesday night (March 7) at NeueHouse, I’m talking to Norman Ohler about his new book Blitzed: Drugs in the Third Reich, which reveals how drugs pervaded Nazi society from the front lines of the World War II all the way to the Führerbunker. Kirkus calls the book “a vivid, highly readable account of drug use run amok.” Our talk begins at 7 P.M.; entry is free, but space is limited, so please RSVP by e-mailing RSVPNY@NeueHouse.com. See you there.
Staff Picks: Raymond Pettibon, Jaume Plensa, Carlos Fonseca
Raymond Pettibon I roamed around the New Museum last weekend in awe of the eight hundred or so works on display as part of Raymond Pettibon’s retrospective, “A Pen of All Work”—a name lifted from Byron’s poem “The Vision of Judgment.” The exhibition is stellar: vibrant colors drench the walls; morsels of enigmatic, sometimes illegible prose are, in typical Pettibon fashion, tucked into nearly every work.
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